Starting phenix.real_space_refine on Fri Aug 7 13:58:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10dk_75090/08_2026/10dk_75090.cif Found real_map, /net/cci-nas-00/data/ceres_data/10dk_75090/08_2026/10dk_75090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/10dk_75090/08_2026/10dk_75090.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10dk_75090/08_2026/10dk_75090.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/10dk_75090/08_2026/10dk_75090.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10dk_75090/08_2026/10dk_75090.map" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 112 5.16 5 C 13909 2.51 5 N 3729 2.21 5 O 4213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21963 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7318 Classifications: {'peptide': 921} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 868} Chain breaks: 2 Chain: "B" Number of atoms: 7327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7327 Classifications: {'peptide': 922} Link IDs: {'PCIS': 4, 'PTRANS': 49, 'TRANS': 868} Chain breaks: 2 Chain: "C" Number of atoms: 7318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 921, 7318 Classifications: {'peptide': 921} Link IDs: {'PCIS': 4, 'PTRANS': 48, 'TRANS': 868} Chain breaks: 2 Time building chain proxies: 4.40, per 1000 atoms: 0.20 Number of scatterers: 21963 At special positions: 0 Unit cell: (116.864, 115.456, 137.984, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 112 16.00 O 4213 8.00 N 3729 7.00 C 13909 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.39 Conformation dependent library (CDL) restraints added in 891.1 milliseconds 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5134 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 53 sheets defined 17.3% alpha, 28.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.59 Creating SS restraints... Processing helix chain 'A' and resid 6 through 13 Processing helix chain 'A' and resid 19 through 24 Processing helix chain 'A' and resid 25 through 35 Processing helix chain 'A' and resid 97 through 99 No H-bonds generated for 'chain 'A' and resid 97 through 99' Processing helix chain 'A' and resid 378 through 384 removed outlier: 3.628A pdb=" N GLY A 383 " --> pdb=" O ALA A 380 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN A 384 " --> pdb=" O MET A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 398 through 401 Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 462 through 467 removed outlier: 3.546A pdb=" N ARG A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 462 through 467' Processing helix chain 'A' and resid 531 through 545 Processing helix chain 'A' and resid 546 through 549 removed outlier: 3.862A pdb=" N LEU A 549 " --> pdb=" O ALA A 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 546 through 549' Processing helix chain 'A' and resid 550 through 554 removed outlier: 3.589A pdb=" N LYS A 554 " --> pdb=" O ASP A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 575 removed outlier: 3.658A pdb=" N ARG A 575 " --> pdb=" O TYR A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 582 removed outlier: 3.758A pdb=" N VAL A 582 " --> pdb=" O PRO A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 617 Processing helix chain 'A' and resid 668 through 673 Processing helix chain 'A' and resid 691 through 702 Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.690A pdb=" N ASP A 708 " --> pdb=" O ASP A 705 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 778 Processing helix chain 'A' and resid 782 through 784 No H-bonds generated for 'chain 'A' and resid 782 through 784' Processing helix chain 'A' and resid 831 through 843 Processing helix chain 'A' and resid 853 through 857 Processing helix chain 'B' and resid 2 through 13 removed outlier: 4.084A pdb=" N MET B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N MET B 7 " --> pdb=" O THR B 3 " (cutoff:3.500A) Proline residue: B 8 - end of helix Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.604A pdb=" N LEU B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 35 Processing helix chain 'B' and resid 97 through 99 No H-bonds generated for 'chain 'B' and resid 97 through 99' Processing helix chain 'B' and resid 191 through 195 Processing helix chain 'B' and resid 378 through 384 removed outlier: 3.523A pdb=" N GLY B 383 " --> pdb=" O ALA B 380 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 384 " --> pdb=" O MET B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 401 Processing helix chain 'B' and resid 408 through 412 removed outlier: 4.044A pdb=" N MET B 412 " --> pdb=" O THR B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 444 Processing helix chain 'B' and resid 462 through 467 removed outlier: 3.782A pdb=" N ILE B 467 " --> pdb=" O PRO B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 531 through 545 Processing helix chain 'B' and resid 546 through 549 Processing helix chain 'B' and resid 550 through 554 removed outlier: 3.701A pdb=" N LYS B 554 " --> pdb=" O ASP B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 575 removed outlier: 3.594A pdb=" N ARG B 575 " --> pdb=" O TYR B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 578 through 582 removed outlier: 3.773A pdb=" N LEU B 581 " --> pdb=" O ALA B 578 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VAL B 582 " --> pdb=" O PRO B 579 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 578 through 582' Processing helix chain 'B' and resid 608 through 619 removed outlier: 4.018A pdb=" N LEU B 618 " --> pdb=" O ARG B 614 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY B 619 " --> pdb=" O SER B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 660 Processing helix chain 'B' and resid 691 through 702 Processing helix chain 'B' and resid 773 through 778 Processing helix chain 'B' and resid 782 through 784 No H-bonds generated for 'chain 'B' and resid 782 through 784' Processing helix chain 'B' and resid 831 through 843 Processing helix chain 'B' and resid 861 through 866 removed outlier: 4.015A pdb=" N ASN B 865 " --> pdb=" O SER B 861 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 13 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 25 through 35 Processing helix chain 'C' and resid 378 through 384 removed outlier: 3.818A pdb=" N GLN C 384 " --> pdb=" O MET C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 398 through 401 Processing helix chain 'C' and resid 433 through 444 Processing helix chain 'C' and resid 462 through 467 removed outlier: 3.530A pdb=" N ILE C 467 " --> pdb=" O PRO C 463 " (cutoff:3.500A) Processing helix chain 'C' and resid 531 through 545 Processing helix chain 'C' and resid 546 through 549 removed outlier: 3.958A pdb=" N LEU C 549 " --> pdb=" O ALA C 546 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 546 through 549' Processing helix chain 'C' and resid 550 through 554 removed outlier: 3.593A pdb=" N LYS C 554 " --> pdb=" O ASP C 551 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 575 removed outlier: 3.671A pdb=" N ARG C 575 " --> pdb=" O TYR C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 582 removed outlier: 3.604A pdb=" N VAL C 582 " --> pdb=" O PRO C 579 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 619 removed outlier: 4.035A pdb=" N LEU C 618 " --> pdb=" O ARG C 614 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLY C 619 " --> pdb=" O SER C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 660 Processing helix chain 'C' and resid 668 through 673 Processing helix chain 'C' and resid 691 through 703 Processing helix chain 'C' and resid 773 through 778 Processing helix chain 'C' and resid 782 through 784 No H-bonds generated for 'chain 'C' and resid 782 through 784' Processing helix chain 'C' and resid 831 through 843 Processing helix chain 'C' and resid 853 through 857 Processing helix chain 'C' and resid 861 through 866 removed outlier: 3.967A pdb=" N ASN C 865 " --> pdb=" O SER C 861 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 68 removed outlier: 3.575A pdb=" N LEU A 683 " --> pdb=" O PHE A 68 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG A 104 " --> pdb=" O ASP A 679 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE A 681 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N ASP A 102 " --> pdb=" O ILE A 681 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LEU A 683 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 100 " --> pdb=" O LEU A 683 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 105 " --> pdb=" O PHE A 626 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.737A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 75 removed outlier: 3.737A pdb=" N ASP A 72 " --> pdb=" O ARG A 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 94 through 95 Processing sheet with id=AA5, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.632A pdb=" N GLU C 519 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 172 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N PHE A 272 " --> pdb=" O ILE C 496 " (cutoff:3.500A) removed outlier: 8.489A pdb=" N ALA C 498 " --> pdb=" O MET A 270 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N MET A 270 " --> pdb=" O ALA C 498 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N PHE A 273 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 230 " --> pdb=" O TYR A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 133 through 137 removed outlier: 3.632A pdb=" N GLU C 519 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA A 172 " --> pdb=" O GLU C 519 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR C 507 " --> pdb=" O THR C 499 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 180 through 182 removed outlier: 4.140A pdb=" N ALA A 180 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ILE A 201 " --> pdb=" O ILE A 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 257 through 260 Processing sheet with id=AA9, first strand: chain 'A' and resid 365 through 369 removed outlier: 6.410A pdb=" N GLN A 385 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 396 Processing sheet with id=AB2, first strand: chain 'A' and resid 479 through 480 removed outlier: 3.857A pdb=" N ASN A 479 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 482 through 483 removed outlier: 3.870A pdb=" N ASN C 479 " --> pdb=" O ILE C 530 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 508 through 510 removed outlier: 3.535A pdb=" N ASP A 491 " --> pdb=" O ILE A 520 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N GLU A 519 " --> pdb=" O ALA B 172 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ALA B 174 " --> pdb=" O GLU A 519 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY A 521 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N CYS B 133 " --> pdb=" O TYR B 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 508 through 510 removed outlier: 4.239A pdb=" N PHE B 272 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA A 498 " --> pdb=" O MET B 270 " (cutoff:3.500A) removed outlier: 12.692A pdb=" N MET B 270 " --> pdb=" O ALA A 498 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ALA B 226 " --> pdb=" O VAL B 352 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N TYR B 354 " --> pdb=" O ALA B 226 " (cutoff:3.500A) removed outlier: 7.066A pdb=" N GLY B 228 " --> pdb=" O TYR B 354 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLU B 356 " --> pdb=" O GLY B 228 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 230 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 709 through 712 removed outlier: 3.542A pdb=" N GLN A 709 " --> pdb=" O VAL A 996 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU A1009 " --> pdb=" O VAL A 993 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 717 through 724 removed outlier: 3.524A pdb=" N PHE A 988 " --> pdb=" O ALA A 718 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 745 " --> pdb=" O GLU A 989 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 730 through 738 removed outlier: 4.700A pdb=" N SER A 737 " --> pdb=" O HIS A 967 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS A 967 " --> pdb=" O SER A 737 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 968 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE A 793 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 970 " --> pdb=" O ILE A 791 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A 791 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 972 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A 789 " --> pdb=" O THR A 972 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU A 974 " --> pdb=" O LYS A 787 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ILE A 791 " --> pdb=" O TRP A 799 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 730 through 738 removed outlier: 4.700A pdb=" N SER A 737 " --> pdb=" O HIS A 967 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N HIS A 967 " --> pdb=" O SER A 737 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA A 968 " --> pdb=" O PHE A 793 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N PHE A 793 " --> pdb=" O ALA A 968 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N ASP A 970 " --> pdb=" O ILE A 791 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE A 791 " --> pdb=" O ASP A 970 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR A 972 " --> pdb=" O VAL A 789 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N VAL A 789 " --> pdb=" O THR A 972 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU A 974 " --> pdb=" O LYS A 787 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 823 through 824 removed outlier: 4.423A pdb=" N MET A 829 " --> pdb=" O VAL A 824 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 867 through 874 Processing sheet with id=AC3, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.914A pdb=" N ARG B 104 " --> pdb=" O ASP B 679 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE B 681 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 102 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 683 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 100 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 65 through 68 removed outlier: 6.914A pdb=" N ARG B 104 " --> pdb=" O ASP B 679 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N ILE B 681 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 102 " --> pdb=" O ILE B 681 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU B 683 " --> pdb=" O TYR B 100 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N TYR B 100 " --> pdb=" O LEU B 683 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.629A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 82 " --> pdb=" O TRP B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 72 through 75 removed outlier: 3.629A pdb=" N ASP B 72 " --> pdb=" O ARG B 83 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA B 82 " --> pdb=" O TRP B 651 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 94 through 95 Processing sheet with id=AC8, first strand: chain 'B' and resid 180 through 182 removed outlier: 4.122A pdb=" N ALA B 180 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ASN B 182 " --> pdb=" O GLY B 185 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 258 through 260 Processing sheet with id=AD1, first strand: chain 'B' and resid 365 through 369 removed outlier: 6.230A pdb=" N GLN B 385 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 394 through 396 Processing sheet with id=AD3, first strand: chain 'B' and resid 468 through 469 removed outlier: 3.604A pdb=" N ILE B 468 " --> pdb=" O TRP B 592 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 508 through 510 removed outlier: 3.509A pdb=" N ASP B 491 " --> pdb=" O ILE B 520 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N GLU B 519 " --> pdb=" O ALA C 172 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ALA C 174 " --> pdb=" O GLU B 519 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLY B 521 " --> pdb=" O ALA C 174 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 508 through 510 removed outlier: 4.276A pdb=" N PHE C 272 " --> pdb=" O ILE B 496 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N ALA B 498 " --> pdb=" O MET C 270 " (cutoff:3.500A) removed outlier: 12.419A pdb=" N MET C 270 " --> pdb=" O ALA B 498 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY C 228 " --> pdb=" O TYR C 354 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N GLU C 356 " --> pdb=" O GLY C 228 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL C 230 " --> pdb=" O GLU C 356 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 709 through 712 Processing sheet with id=AD7, first strand: chain 'B' and resid 717 through 724 removed outlier: 4.044A pdb=" N GLY B 745 " --> pdb=" O GLU B 989 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 731 through 738 removed outlier: 4.388A pdb=" N SER B 737 " --> pdb=" O HIS B 967 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS B 967 " --> pdb=" O SER B 737 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 968 " --> pdb=" O PHE B 793 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B 793 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B 970 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE B 791 " --> pdb=" O ASP B 970 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 972 " --> pdb=" O VAL B 789 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 789 " --> pdb=" O THR B 972 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU B 974 " --> pdb=" O LYS B 787 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 731 through 738 removed outlier: 4.388A pdb=" N SER B 737 " --> pdb=" O HIS B 967 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N HIS B 967 " --> pdb=" O SER B 737 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ALA B 968 " --> pdb=" O PHE B 793 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N PHE B 793 " --> pdb=" O ALA B 968 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N ASP B 970 " --> pdb=" O ILE B 791 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N ILE B 791 " --> pdb=" O ASP B 970 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR B 972 " --> pdb=" O VAL B 789 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N VAL B 789 " --> pdb=" O THR B 972 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N GLU B 974 " --> pdb=" O LYS B 787 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'B' and resid 823 through 824 removed outlier: 4.454A pdb=" N MET B 829 " --> pdb=" O VAL B 824 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 867 through 874 Processing sheet with id=AE3, first strand: chain 'C' and resid 65 through 68 removed outlier: 6.836A pdb=" N ARG C 104 " --> pdb=" O ASP C 679 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ILE C 681 " --> pdb=" O ASP C 102 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ASP C 102 " --> pdb=" O ILE C 681 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N LEU C 683 " --> pdb=" O TYR C 100 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N TYR C 100 " --> pdb=" O LEU C 683 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY C 105 " --> pdb=" O PHE C 626 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.560A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 651 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 72 through 75 removed outlier: 3.560A pdb=" N ASP C 72 " --> pdb=" O ARG C 83 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N TRP C 651 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 94 through 95 Processing sheet with id=AE7, first strand: chain 'C' and resid 181 through 182 Processing sheet with id=AE8, first strand: chain 'C' and resid 257 through 260 Processing sheet with id=AE9, first strand: chain 'C' and resid 365 through 369 removed outlier: 6.235A pdb=" N GLN C 385 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 394 through 396 Processing sheet with id=AF2, first strand: chain 'C' and resid 468 through 469 removed outlier: 3.788A pdb=" N ILE C 468 " --> pdb=" O TRP C 592 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 709 through 712 Processing sheet with id=AF4, first strand: chain 'C' and resid 717 through 724 removed outlier: 4.064A pdb=" N GLY C 745 " --> pdb=" O GLU C 989 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 730 through 738 removed outlier: 4.381A pdb=" N SER C 737 " --> pdb=" O HIS C 967 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS C 967 " --> pdb=" O SER C 737 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ILE C 791 " --> pdb=" O TRP C 799 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 730 through 738 removed outlier: 4.381A pdb=" N SER C 737 " --> pdb=" O HIS C 967 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N HIS C 967 " --> pdb=" O SER C 737 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N THR C 972 " --> pdb=" O VAL C 789 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 789 " --> pdb=" O THR C 972 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N GLU C 974 " --> pdb=" O LYS C 787 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 823 through 824 removed outlier: 4.586A pdb=" N MET C 829 " --> pdb=" O VAL C 824 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 867 through 874 removed outlier: 3.550A pdb=" N LYS C 931 " --> pdb=" O MET C 869 " (cutoff:3.500A) 651 hydrogen bonds defined for protein. 1671 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.80 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3831 1.32 - 1.44: 6324 1.44 - 1.56: 12182 1.56 - 1.69: 0 1.69 - 1.81: 203 Bond restraints: 22540 Sorted by residual: bond pdb=" N ASN B 479 " pdb=" CA ASN B 479 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.23e-02 6.61e+03 1.03e+01 bond pdb=" C LEU A 477 " pdb=" N PRO A 478 " ideal model delta sigma weight residual 1.329 1.368 -0.038 1.25e-02 6.40e+03 9.36e+00 bond pdb=" N LEU C 484 " pdb=" CA LEU C 484 " ideal model delta sigma weight residual 1.458 1.496 -0.038 1.30e-02 5.92e+03 8.42e+00 bond pdb=" N PRO A 478 " pdb=" CD PRO A 478 " ideal model delta sigma weight residual 1.473 1.513 -0.040 1.40e-02 5.10e+03 8.15e+00 bond pdb=" N PHE B 482 " pdb=" CA PHE B 482 " ideal model delta sigma weight residual 1.452 1.482 -0.029 1.11e-02 8.12e+03 7.02e+00 ... (remaining 22535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.29: 30229 2.29 - 4.59: 380 4.59 - 6.88: 36 6.88 - 9.17: 3 9.17 - 11.47: 2 Bond angle restraints: 30650 Sorted by residual: angle pdb=" C CYS C 481 " pdb=" CA CYS C 481 " pdb=" CB CYS C 481 " ideal model delta sigma weight residual 110.16 98.69 11.47 1.66e+00 3.63e-01 4.77e+01 angle pdb=" N PHE A 482 " pdb=" CA PHE A 482 " pdb=" CB PHE A 482 " ideal model delta sigma weight residual 109.55 100.90 8.65 1.30e+00 5.92e-01 4.43e+01 angle pdb=" N PHE C 482 " pdb=" CA PHE C 482 " pdb=" CB PHE C 482 " ideal model delta sigma weight residual 109.88 100.50 9.38 1.42e+00 4.96e-01 4.36e+01 angle pdb=" CA ASN B 479 " pdb=" C ASN B 479 " pdb=" O ASN B 479 " ideal model delta sigma weight residual 120.70 116.06 4.64 1.08e+00 8.57e-01 1.85e+01 angle pdb=" N LYS B 921 " pdb=" CA LYS B 921 " pdb=" C LYS B 921 " ideal model delta sigma weight residual 113.50 108.33 5.17 1.23e+00 6.61e-01 1.76e+01 ... (remaining 30645 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12535 17.98 - 35.95: 628 35.95 - 53.93: 136 53.93 - 71.91: 24 71.91 - 89.88: 16 Dihedral angle restraints: 13339 sinusoidal: 5279 harmonic: 8060 Sorted by residual: dihedral pdb=" C CYS C 481 " pdb=" N CYS C 481 " pdb=" CA CYS C 481 " pdb=" CB CYS C 481 " ideal model delta harmonic sigma weight residual -122.60 -108.13 -14.47 0 2.50e+00 1.60e-01 3.35e+01 dihedral pdb=" CA THR B 3 " pdb=" C THR B 3 " pdb=" N PRO B 4 " pdb=" CA PRO B 4 " ideal model delta harmonic sigma weight residual 180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" C CYS B 481 " pdb=" N CYS B 481 " pdb=" CA CYS B 481 " pdb=" CB CYS B 481 " ideal model delta harmonic sigma weight residual -122.60 -111.49 -11.11 0 2.50e+00 1.60e-01 1.97e+01 ... (remaining 13336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2649 0.063 - 0.126: 545 0.126 - 0.189: 31 0.189 - 0.252: 2 0.252 - 0.315: 3 Chirality restraints: 3230 Sorted by residual: chirality pdb=" CA CYS B 481 " pdb=" N CYS B 481 " pdb=" C CYS B 481 " pdb=" CB CYS B 481 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA CYS C 481 " pdb=" N CYS C 481 " pdb=" C CYS C 481 " pdb=" CB CYS C 481 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" CA TYR C 480 " pdb=" N TYR C 480 " pdb=" C TYR C 480 " pdb=" CB TYR C 480 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3227 not shown) Planarity restraints: 4054 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 918 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" C LEU B 918 " -0.034 2.00e-02 2.50e+03 pdb=" O LEU B 918 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE B 919 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN B 867 " -0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO B 868 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 868 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 868 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 624 " 0.031 5.00e-02 4.00e+02 4.71e-02 3.56e+00 pdb=" N PRO C 625 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO C 625 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 625 " 0.026 5.00e-02 4.00e+02 ... (remaining 4051 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3385 2.76 - 3.29: 18177 3.29 - 3.83: 32893 3.83 - 4.36: 41669 4.36 - 4.90: 75908 Nonbonded interactions: 172032 Sorted by model distance: nonbonded pdb=" OD1 ASN C 719 " pdb=" OH TYR C 985 " model vdw 2.223 3.040 nonbonded pdb=" O SER A 861 " pdb=" ND2 ASN A 865 " model vdw 2.235 3.120 nonbonded pdb=" NH2 ARG B 905 " pdb=" O ASN C 525 " model vdw 2.251 3.120 nonbonded pdb=" OG SER B 543 " pdb=" OE1 GLU C 476 " model vdw 2.252 3.040 nonbonded pdb=" O GLY A 920 " pdb=" NH1 ARG C 622 " model vdw 2.255 3.120 ... (remaining 172027 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 6 through 346 or resid 348 through 1016)) selection = (chain 'B' and resid 6 through 1016) selection = (chain 'C' and (resid 6 through 346 or resid 348 through 1016)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.110 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 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 : 0.005 0.048 22540 Z= 0.243 Angle : 0.661 11.467 30650 Z= 0.394 Chirality : 0.049 0.315 3230 Planarity : 0.005 0.049 4054 Dihedral : 11.989 89.884 8205 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.15 % Allowed : 5.40 % Favored : 92.45 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 7.64 % 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: -1.36 (0.15), residues: 2746 helix: 0.50 (0.31), residues: 303 sheet: -0.89 (0.20), residues: 651 loop : -1.18 (0.13), residues: 1792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 614 TYR 0.016 0.002 TYR A 23 PHE 0.017 0.002 PHE A 943 TRP 0.015 0.002 TRP B 592 HIS 0.008 0.002 HIS C 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00546 / 0.24 (22540) covalent geometry : angle 0.66116 / 0.39 (30650) hydrogen bonds : bond 0.24833 / 16.22 ( 581) hydrogen bonds : angle 8.72819 / 6.04 ( 1671) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 376 time to evaluate : 0.765 Fit side-chains REVERT: A 9 GLN cc_start: 0.6460 (mm110) cc_final: 0.6003 (mt0) REVERT: A 63 ARG cc_start: 0.7280 (mtt180) cc_final: 0.6717 (mtp85) REVERT: A 66 LEU cc_start: 0.8252 (mt) cc_final: 0.7974 (mp) REVERT: A 67 ARG cc_start: 0.8626 (ttt180) cc_final: 0.8260 (ttt180) REVERT: A 73 ARG cc_start: 0.6894 (mtt180) cc_final: 0.6385 (mtm180) REVERT: A 183 LYS cc_start: 0.8433 (ttpm) cc_final: 0.7846 (ttmt) REVERT: A 373 LYS cc_start: 0.6664 (mttt) cc_final: 0.6322 (mmmt) REVERT: A 379 LYS cc_start: 0.7695 (tttt) cc_final: 0.7137 (tttm) REVERT: A 430 ASP cc_start: 0.8388 (p0) cc_final: 0.8108 (p0) REVERT: A 469 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7555 (mt-10) REVERT: A 475 ASP cc_start: 0.8116 (p0) cc_final: 0.7704 (p0) REVERT: A 497 LYS cc_start: 0.8204 (pttt) cc_final: 0.7849 (pttp) REVERT: A 570 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.6487 (t70) REVERT: A 712 ASN cc_start: 0.7940 (p0) cc_final: 0.7612 (p0) REVERT: A 758 SER cc_start: 0.7539 (t) cc_final: 0.7113 (p) REVERT: A 788 LYS cc_start: 0.7720 (pttt) cc_final: 0.7212 (ptpp) REVERT: A 859 MET cc_start: 0.8718 (ttm) cc_final: 0.8512 (ttp) REVERT: A 873 VAL cc_start: 0.7725 (m) cc_final: 0.7494 (p) REVERT: A 878 LYS cc_start: 0.8112 (mttt) cc_final: 0.7842 (mttm) REVERT: A 884 GLN cc_start: 0.8588 (tt0) cc_final: 0.8169 (tt0) REVERT: A 888 ILE cc_start: 0.7928 (mt) cc_final: 0.7680 (mp) REVERT: A 921 LYS cc_start: 0.7798 (mttt) cc_final: 0.7410 (mptp) REVERT: A 970 ASP cc_start: 0.7343 (m-30) cc_final: 0.7050 (m-30) REVERT: A 974 GLU cc_start: 0.7271 (tt0) cc_final: 0.6970 (tt0) REVERT: A 1011 THR cc_start: 0.8095 (t) cc_final: 0.7748 (p) REVERT: B 60 ARG cc_start: 0.6581 (mtt180) cc_final: 0.6266 (mtt180) REVERT: B 83 ARG cc_start: 0.6822 (ttm170) cc_final: 0.6192 (ttp80) REVERT: B 167 LYS cc_start: 0.7964 (mttt) cc_final: 0.7711 (mttm) REVERT: B 267 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7663 (mt0) REVERT: B 269 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7331 (mt-10) REVERT: B 370 LYS cc_start: 0.7923 (tttt) cc_final: 0.7670 (tttm) REVERT: B 519 GLU cc_start: 0.7448 (mm-30) cc_final: 0.7049 (mt-10) REVERT: B 803 ASP cc_start: 0.7155 (t0) cc_final: 0.6521 (t0) REVERT: B 816 SER cc_start: 0.8448 (m) cc_final: 0.8239 (p) REVERT: B 817 VAL cc_start: 0.8551 (t) cc_final: 0.8165 (p) REVERT: B 855 TYR cc_start: 0.7753 (p90) cc_final: 0.7168 (p90) REVERT: B 878 LYS cc_start: 0.7813 (mttt) cc_final: 0.7270 (mttp) REVERT: B 888 ILE cc_start: 0.8394 (mt) cc_final: 0.8052 (mm) REVERT: B 971 MET cc_start: 0.8604 (mtp) cc_final: 0.8371 (mtp) REVERT: B 978 MET cc_start: 0.8091 (mtp) cc_final: 0.7819 (mtp) REVERT: B 979 ASP cc_start: 0.7387 (p0) cc_final: 0.6888 (p0) REVERT: C 19 ASP cc_start: 0.7235 (m-30) cc_final: 0.7019 (m-30) REVERT: C 30 GLN cc_start: 0.6205 (tt0) cc_final: 0.5829 (mt0) REVERT: C 49 THR cc_start: 0.8619 (p) cc_final: 0.8325 (p) REVERT: C 60 ARG cc_start: 0.6882 (mtt180) cc_final: 0.6327 (mtt180) REVERT: C 137 GLU cc_start: 0.8291 (mt-10) cc_final: 0.8024 (mt-10) REVERT: C 166 LYS cc_start: 0.8342 (mmtt) cc_final: 0.8119 (mmtp) REVERT: C 179 GLU cc_start: 0.7997 (mt-10) cc_final: 0.7661 (mt-10) REVERT: C 233 LYS cc_start: 0.7781 (pttt) cc_final: 0.7569 (pttp) REVERT: C 264 LEU cc_start: 0.8427 (mt) cc_final: 0.8127 (mt) REVERT: C 269 GLU cc_start: 0.6995 (mt-10) cc_final: 0.6646 (tt0) REVERT: C 350 LYS cc_start: 0.7647 (tppp) cc_final: 0.6806 (tptp) REVERT: C 379 LYS cc_start: 0.7523 (tttt) cc_final: 0.7126 (tttp) REVERT: C 497 LYS cc_start: 0.8262 (pttt) cc_final: 0.7985 (pttt) REVERT: C 510 GLN cc_start: 0.7775 (tt0) cc_final: 0.7558 (tt0) REVERT: C 519 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7189 (mm-30) REVERT: C 528 MET cc_start: 0.8442 (mtt) cc_final: 0.8078 (mtt) REVERT: C 572 MET cc_start: 0.8627 (mtt) cc_final: 0.8396 (mtt) REVERT: C 616 MET cc_start: 0.7273 (mtm) cc_final: 0.6870 (mtp) REVERT: C 677 LYS cc_start: 0.6945 (tttm) cc_final: 0.6325 (ttpp) REVERT: C 681 ILE cc_start: 0.7817 (mt) cc_final: 0.7598 (tt) REVERT: C 704 ASN cc_start: 0.7598 (t0) cc_final: 0.7364 (m-40) REVERT: C 708 ASP cc_start: 0.7949 (m-30) cc_final: 0.7747 (m-30) REVERT: C 788 LYS cc_start: 0.7961 (pttt) cc_final: 0.7325 (ptpp) REVERT: C 816 SER cc_start: 0.8293 (m) cc_final: 0.8065 (p) REVERT: C 854 SER cc_start: 0.7145 (m) cc_final: 0.6922 (t) REVERT: C 878 LYS cc_start: 0.8050 (mttt) cc_final: 0.7568 (mttm) REVERT: C 881 ASP cc_start: 0.8047 (m-30) cc_final: 0.7832 (m-30) REVERT: C 888 ILE cc_start: 0.8323 (mt) cc_final: 0.8053 (mt) REVERT: C 921 LYS cc_start: 0.7864 (mttt) cc_final: 0.7610 (ttpt) REVERT: C 974 GLU cc_start: 0.7478 (tt0) cc_final: 0.6968 (tt0) outliers start: 51 outliers final: 36 residues processed: 422 average time/residue: 0.1347 time to fit residues: 86.4938 Evaluate side-chains 367 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 330 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 106 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 922 THR Chi-restraints excluded: chain B residue 925 ASP Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 584 CYS Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 876 ASP Chi-restraints excluded: chain C residue 925 ASP Chi-restraints excluded: chain C residue 937 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 197 optimal weight: 6.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 260 GLN B 30 GLN B 260 GLN B 267 GLN B 479 ASN C 254 GLN C 260 GLN C 267 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.085363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.066496 restraints weight = 27362.315| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 1.46 r_work: 0.2345 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2232 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9014 moved from start: 0.0893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22540 Z= 0.181 Angle : 0.579 6.119 30650 Z= 0.313 Chirality : 0.048 0.166 3230 Planarity : 0.005 0.061 4054 Dihedral : 6.426 85.562 3111 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.53 % Allowed : 8.52 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -1.21 (0.15), residues: 2746 helix: 0.51 (0.31), residues: 318 sheet: -0.64 (0.19), residues: 653 loop : -1.14 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 517 TYR 0.021 0.002 TYR A 23 PHE 0.016 0.002 PHE A 943 TRP 0.016 0.002 TRP B 592 HIS 0.007 0.001 HIS C 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00450 / 0.18 (22540) covalent geometry : angle 0.57901 / 0.31 (30650) hydrogen bonds : bond 0.05038 / 3.38 ( 581) hydrogen bonds : angle 6.04686 / 4.19 ( 1671) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 326 time to evaluate : 0.705 Fit side-chains REVERT: A 9 GLN cc_start: 0.7760 (mm110) cc_final: 0.7285 (mt0) REVERT: A 63 ARG cc_start: 0.8680 (mtt180) cc_final: 0.8276 (mtp85) REVERT: A 67 ARG cc_start: 0.9248 (ttt180) cc_final: 0.8929 (ttt90) REVERT: A 73 ARG cc_start: 0.8217 (mtt180) cc_final: 0.7730 (mtm180) REVERT: A 92 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7414 (mtp180) REVERT: A 183 LYS cc_start: 0.8750 (ttpm) cc_final: 0.8218 (ttmt) REVERT: A 267 GLN cc_start: 0.8813 (mt0) cc_final: 0.8537 (mt0) REVERT: A 271 GLN cc_start: 0.8940 (OUTLIER) cc_final: 0.8476 (pt0) REVERT: A 373 LYS cc_start: 0.7650 (mttt) cc_final: 0.7237 (mmmt) REVERT: A 434 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: A 469 GLU cc_start: 0.8789 (mt-10) cc_final: 0.8581 (mt-10) REVERT: A 475 ASP cc_start: 0.8799 (p0) cc_final: 0.8435 (p0) REVERT: A 497 LYS cc_start: 0.8719 (pttt) cc_final: 0.8386 (pttp) REVERT: A 570 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8075 (t70) REVERT: A 712 ASN cc_start: 0.8508 (p0) cc_final: 0.8293 (p0) REVERT: A 758 SER cc_start: 0.7881 (t) cc_final: 0.7638 (p) REVERT: A 859 MET cc_start: 0.9311 (ttm) cc_final: 0.9061 (ttp) REVERT: A 888 ILE cc_start: 0.8700 (mt) cc_final: 0.8487 (mp) REVERT: A 1011 THR cc_start: 0.8927 (t) cc_final: 0.8525 (p) REVERT: B 83 ARG cc_start: 0.8621 (ttm170) cc_final: 0.8168 (ttp80) REVERT: B 267 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: B 473 THR cc_start: 0.8811 (p) cc_final: 0.8606 (p) REVERT: B 519 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8174 (mm-30) REVERT: B 803 ASP cc_start: 0.8624 (t0) cc_final: 0.8007 (t0) REVERT: B 817 VAL cc_start: 0.8898 (t) cc_final: 0.8628 (p) REVERT: B 855 TYR cc_start: 0.8608 (p90) cc_final: 0.8090 (p90) REVERT: B 878 LYS cc_start: 0.8742 (mttt) cc_final: 0.8355 (mttp) REVERT: B 888 ILE cc_start: 0.9128 (mt) cc_final: 0.8917 (mm) REVERT: B 978 MET cc_start: 0.8984 (mtp) cc_final: 0.8774 (mtp) REVERT: C 30 GLN cc_start: 0.8018 (tt0) cc_final: 0.7677 (mt0) REVERT: C 60 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8072 (mtt180) REVERT: C 179 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8508 (mt-10) REVERT: C 202 TYR cc_start: 0.8955 (m-80) cc_final: 0.8422 (m-80) REVERT: C 233 LYS cc_start: 0.8455 (pttt) cc_final: 0.8177 (pttp) REVERT: C 257 MET cc_start: 0.8937 (mmm) cc_final: 0.8461 (mmt) REVERT: C 269 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7806 (tt0) REVERT: C 350 LYS cc_start: 0.8211 (tppp) cc_final: 0.7483 (tptp) REVERT: C 434 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7453 (mm-30) REVERT: C 497 LYS cc_start: 0.8457 (pttt) cc_final: 0.8227 (pttt) REVERT: C 510 GLN cc_start: 0.8267 (tt0) cc_final: 0.7734 (tt0) REVERT: C 519 GLU cc_start: 0.8497 (mm-30) cc_final: 0.8112 (mm-30) REVERT: C 528 MET cc_start: 0.8988 (mtt) cc_final: 0.8531 (mtt) REVERT: C 616 MET cc_start: 0.9044 (mtm) cc_final: 0.8619 (mtp) REVERT: C 677 LYS cc_start: 0.8129 (tttm) cc_final: 0.7679 (ttpp) REVERT: C 678 PHE cc_start: 0.8980 (m-80) cc_final: 0.8738 (m-80) REVERT: C 681 ILE cc_start: 0.8792 (mt) cc_final: 0.8543 (tt) REVERT: C 708 ASP cc_start: 0.8851 (m-30) cc_final: 0.8525 (m-30) REVERT: C 788 LYS cc_start: 0.8937 (pttt) cc_final: 0.8691 (ptpp) REVERT: C 816 SER cc_start: 0.8946 (m) cc_final: 0.8713 (p) REVERT: C 875 ASP cc_start: 0.9110 (t0) cc_final: 0.8758 (t0) REVERT: C 878 LYS cc_start: 0.8847 (mttt) cc_final: 0.8438 (mttm) REVERT: C 881 ASP cc_start: 0.8866 (m-30) cc_final: 0.8573 (m-30) REVERT: C 888 ILE cc_start: 0.8935 (mt) cc_final: 0.8660 (mt) REVERT: C 905 ARG cc_start: 0.8521 (pmt-80) cc_final: 0.8049 (pmt-80) REVERT: C 974 GLU cc_start: 0.8712 (tt0) cc_final: 0.8434 (tt0) outliers start: 60 outliers final: 45 residues processed: 373 average time/residue: 0.1420 time to fit residues: 81.1648 Evaluate side-chains 361 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 310 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 53 THR Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 117 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 856 LYS Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1019 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 59 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 17 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 28 optimal weight: 10.0000 chunk 200 optimal weight: 0.0270 chunk 150 optimal weight: 9.9990 chunk 156 optimal weight: 5.9990 chunk 229 optimal weight: 0.9990 overall best weight: 1.5442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 632 GLN B 30 GLN B 43 ASN B 260 GLN B 438 GLN C 184 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.087407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2458 r_free = 0.2458 target = 0.068558 restraints weight = 27185.344| |-----------------------------------------------------------------------------| r_work (start): 0.2469 rms_B_bonded: 1.44 r_work: 0.2380 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2267 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22540 Z= 0.103 Angle : 0.489 6.262 30650 Z= 0.266 Chirality : 0.045 0.143 3230 Planarity : 0.004 0.044 4054 Dihedral : 5.809 85.113 3096 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.15 % Allowed : 9.99 % Favored : 87.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -0.96 (0.15), residues: 2746 helix: 0.74 (0.31), residues: 325 sheet: -0.45 (0.19), residues: 665 loop : -0.99 (0.14), residues: 1756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.017 0.001 TYR A 23 PHE 0.011 0.001 PHE B 84 TRP 0.011 0.001 TRP B 592 HIS 0.006 0.001 HIS C 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (22540) covalent geometry : angle 0.48880 / 0.27 (30650) hydrogen bonds : bond 0.03841 / 2.58 ( 581) hydrogen bonds : angle 5.54651 / 3.83 ( 1671) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 320 time to evaluate : 0.822 Fit side-chains REVERT: A 9 GLN cc_start: 0.7650 (mm110) cc_final: 0.7221 (mt0) REVERT: A 63 ARG cc_start: 0.8679 (mtt180) cc_final: 0.8341 (mtp85) REVERT: A 66 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9051 (mp) REVERT: A 67 ARG cc_start: 0.9236 (ttt180) cc_final: 0.8946 (ttt180) REVERT: A 73 ARG cc_start: 0.8203 (mtt180) cc_final: 0.7716 (ttm170) REVERT: A 183 LYS cc_start: 0.8736 (ttpm) cc_final: 0.8193 (ttmt) REVERT: A 271 GLN cc_start: 0.8837 (OUTLIER) cc_final: 0.8530 (pt0) REVERT: A 373 LYS cc_start: 0.7749 (mttt) cc_final: 0.7229 (mmmt) REVERT: A 434 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7573 (mm-30) REVERT: A 469 GLU cc_start: 0.8768 (mt-10) cc_final: 0.8556 (mt-10) REVERT: A 497 LYS cc_start: 0.8720 (pttt) cc_final: 0.8411 (pttp) REVERT: A 570 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8101 (t70) REVERT: A 758 SER cc_start: 0.7729 (t) cc_final: 0.7502 (p) REVERT: A 838 MET cc_start: 0.9133 (mmm) cc_final: 0.8795 (mmt) REVERT: A 859 MET cc_start: 0.9270 (ttm) cc_final: 0.9032 (ttp) REVERT: A 1011 THR cc_start: 0.8895 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 83 ARG cc_start: 0.8549 (ttm170) cc_final: 0.8099 (ttp80) REVERT: B 519 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8215 (mm-30) REVERT: B 803 ASP cc_start: 0.8596 (t0) cc_final: 0.8333 (t70) REVERT: B 817 VAL cc_start: 0.8891 (t) cc_final: 0.8657 (p) REVERT: B 855 TYR cc_start: 0.8577 (p90) cc_final: 0.8060 (p90) REVERT: B 878 LYS cc_start: 0.8708 (mttt) cc_final: 0.8378 (mttp) REVERT: B 888 ILE cc_start: 0.9090 (mt) cc_final: 0.8852 (mm) REVERT: B 978 MET cc_start: 0.8977 (mtp) cc_final: 0.8763 (mtp) REVERT: C 30 GLN cc_start: 0.7711 (tt0) cc_final: 0.7412 (mt0) REVERT: C 60 ARG cc_start: 0.8422 (mtt180) cc_final: 0.8147 (mtt90) REVERT: C 179 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8481 (mt-10) REVERT: C 257 MET cc_start: 0.8942 (mmm) cc_final: 0.8452 (mmt) REVERT: C 269 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7735 (tt0) REVERT: C 350 LYS cc_start: 0.8075 (tppp) cc_final: 0.7347 (tptp) REVERT: C 434 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.7328 (mm-30) REVERT: C 497 LYS cc_start: 0.8289 (pttt) cc_final: 0.8082 (pttt) REVERT: C 511 ASP cc_start: 0.8205 (t0) cc_final: 0.7962 (t0) REVERT: C 519 GLU cc_start: 0.8440 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 612 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.8382 (mtm180) REVERT: C 616 MET cc_start: 0.8957 (mtm) cc_final: 0.8578 (mtp) REVERT: C 677 LYS cc_start: 0.8107 (tttm) cc_final: 0.7669 (ttpp) REVERT: C 678 PHE cc_start: 0.8923 (m-80) cc_final: 0.8695 (m-80) REVERT: C 708 ASP cc_start: 0.8832 (m-30) cc_final: 0.8397 (m-30) REVERT: C 737 SER cc_start: 0.9134 (t) cc_final: 0.8912 (m) REVERT: C 788 LYS cc_start: 0.8817 (pttt) cc_final: 0.8590 (ptpp) REVERT: C 816 SER cc_start: 0.8914 (m) cc_final: 0.8637 (p) REVERT: C 875 ASP cc_start: 0.9046 (t0) cc_final: 0.8718 (t0) REVERT: C 878 LYS cc_start: 0.8867 (mttt) cc_final: 0.8432 (mttm) REVERT: C 888 ILE cc_start: 0.8884 (mt) cc_final: 0.8602 (mt) REVERT: C 905 ARG cc_start: 0.8455 (pmt-80) cc_final: 0.8125 (pmt-80) REVERT: C 974 GLU cc_start: 0.8649 (tt0) cc_final: 0.8369 (tt0) outliers start: 51 outliers final: 33 residues processed: 364 average time/residue: 0.1525 time to fit residues: 85.5209 Evaluate side-chains 348 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 308 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 LEU Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 926 SER Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 212 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 35 optimal weight: 7.9990 chunk 234 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 chunk 150 optimal weight: 4.9990 chunk 237 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 181 optimal weight: 5.9990 chunk 201 optimal weight: 6.9990 chunk 214 optimal weight: 0.7980 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 ASN B 30 GLN B 260 GLN B 267 GLN B 712 ASN C 494 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.085976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2433 r_free = 0.2433 target = 0.067169 restraints weight = 27317.423| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 1.44 r_work: 0.2368 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9013 moved from start: 0.1206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 22540 Z= 0.157 Angle : 0.536 6.773 30650 Z= 0.288 Chirality : 0.046 0.149 3230 Planarity : 0.004 0.058 4054 Dihedral : 5.696 85.034 3084 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.70 % Allowed : 10.83 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.15), residues: 2746 helix: 0.75 (0.30), residues: 325 sheet: -0.37 (0.19), residues: 672 loop : -0.98 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 905 TYR 0.016 0.001 TYR A 23 PHE 0.013 0.002 PHE B 84 TRP 0.015 0.002 TRP B 592 HIS 0.007 0.001 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (22540) covalent geometry : angle 0.53619 / 0.29 (30650) hydrogen bonds : bond 0.04279 / 2.88 ( 581) hydrogen bonds : angle 5.48127 / 3.80 ( 1671) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 308 time to evaluate : 0.810 Fit side-chains REVERT: A 63 ARG cc_start: 0.8706 (mtt180) cc_final: 0.8472 (mtp85) REVERT: A 67 ARG cc_start: 0.9247 (ttt180) cc_final: 0.8949 (ttt180) REVERT: A 73 ARG cc_start: 0.8189 (mtt180) cc_final: 0.7691 (ttm170) REVERT: A 183 LYS cc_start: 0.8733 (ttpm) cc_final: 0.8217 (ttmt) REVERT: A 373 LYS cc_start: 0.7807 (mttt) cc_final: 0.7280 (mmmt) REVERT: A 434 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.7553 (mm-30) REVERT: A 469 GLU cc_start: 0.8757 (mt-10) cc_final: 0.8528 (mt-10) REVERT: A 497 LYS cc_start: 0.8733 (pttt) cc_final: 0.8447 (pttp) REVERT: A 570 ASP cc_start: 0.8789 (OUTLIER) cc_final: 0.8079 (t70) REVERT: A 758 SER cc_start: 0.7762 (t) cc_final: 0.7521 (p) REVERT: A 859 MET cc_start: 0.9305 (ttm) cc_final: 0.9046 (ttp) REVERT: A 1011 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8565 (p) REVERT: B 83 ARG cc_start: 0.8577 (ttm170) cc_final: 0.8128 (ttp80) REVERT: B 267 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: B 473 THR cc_start: 0.8827 (p) cc_final: 0.8618 (p) REVERT: B 519 GLU cc_start: 0.8633 (mm-30) cc_final: 0.8308 (mm-30) REVERT: B 561 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7629 (mm-30) REVERT: B 855 TYR cc_start: 0.8623 (p90) cc_final: 0.8153 (p90) REVERT: B 878 LYS cc_start: 0.8696 (mttt) cc_final: 0.8376 (mttp) REVERT: B 888 ILE cc_start: 0.9108 (mt) cc_final: 0.8871 (mm) REVERT: C 30 GLN cc_start: 0.7924 (tt0) cc_final: 0.7624 (mt0) REVERT: C 60 ARG cc_start: 0.8387 (mtt180) cc_final: 0.8109 (mtt90) REVERT: C 179 GLU cc_start: 0.8714 (mt-10) cc_final: 0.8463 (mt-10) REVERT: C 269 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7738 (tt0) REVERT: C 350 LYS cc_start: 0.8123 (tppp) cc_final: 0.7420 (tptp) REVERT: C 434 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.7426 (mm-30) REVERT: C 497 LYS cc_start: 0.8314 (pttt) cc_final: 0.8084 (pttt) REVERT: C 519 GLU cc_start: 0.8451 (mm-30) cc_final: 0.8158 (mm-30) REVERT: C 612 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.8444 (mtm180) REVERT: C 677 LYS cc_start: 0.8162 (tttm) cc_final: 0.7729 (ttpp) REVERT: C 708 ASP cc_start: 0.8878 (m-30) cc_final: 0.8429 (m-30) REVERT: C 788 LYS cc_start: 0.8935 (pttt) cc_final: 0.8710 (ptpp) REVERT: C 816 SER cc_start: 0.8923 (m) cc_final: 0.8640 (p) REVERT: C 875 ASP cc_start: 0.9068 (t0) cc_final: 0.8715 (t0) REVERT: C 878 LYS cc_start: 0.8896 (mttt) cc_final: 0.8428 (mttm) REVERT: C 888 ILE cc_start: 0.8901 (mt) cc_final: 0.8606 (mt) REVERT: C 905 ARG cc_start: 0.8565 (pmt-80) cc_final: 0.8016 (pmt-80) REVERT: C 974 GLU cc_start: 0.8586 (tt0) cc_final: 0.8242 (tt0) outliers start: 64 outliers final: 46 residues processed: 361 average time/residue: 0.1553 time to fit residues: 87.0625 Evaluate side-chains 360 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 308 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 588 LEU Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1019 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 172 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 60 optimal weight: 0.0670 chunk 250 optimal weight: 0.0570 chunk 193 optimal weight: 0.0970 chunk 49 optimal weight: 0.9980 chunk 198 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 chunk 162 optimal weight: 0.9980 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 overall best weight: 0.4034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 184 ASN A 739 ASN B 30 GLN B 260 GLN B 418 GLN B 712 ASN C 494 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.091034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2515 r_free = 0.2515 target = 0.071917 restraints weight = 26612.767| |-----------------------------------------------------------------------------| r_work (start): 0.2526 rms_B_bonded: 1.47 r_work: 0.2435 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.2320 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8937 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.033 22540 Z= 0.072 Angle : 0.435 6.215 30650 Z= 0.237 Chirality : 0.043 0.140 3230 Planarity : 0.004 0.038 4054 Dihedral : 5.120 85.142 3083 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.94 % Allowed : 12.52 % Favored : 85.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -0.66 (0.15), residues: 2746 helix: 0.97 (0.31), residues: 325 sheet: -0.18 (0.20), residues: 656 loop : -0.82 (0.14), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.017 0.001 TYR A 23 PHE 0.011 0.001 PHE A 748 TRP 0.010 0.001 TRP A 537 HIS 0.005 0.001 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00149 / 0.07 (22540) covalent geometry : angle 0.43536 / 0.24 (30650) hydrogen bonds : bond 0.02796 / 1.88 ( 581) hydrogen bonds : angle 5.09510 / 3.52 ( 1671) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 340 time to evaluate : 0.861 Fit side-chains REVERT: A 9 GLN cc_start: 0.7614 (mm110) cc_final: 0.7207 (mt0) REVERT: A 63 ARG cc_start: 0.8648 (mtt180) cc_final: 0.8417 (mtp85) REVERT: A 67 ARG cc_start: 0.9208 (ttt180) cc_final: 0.8943 (ttt180) REVERT: A 73 ARG cc_start: 0.8165 (mtt180) cc_final: 0.7948 (mtm180) REVERT: A 183 LYS cc_start: 0.8681 (ttpm) cc_final: 0.8164 (ttmt) REVERT: A 373 LYS cc_start: 0.7698 (mttt) cc_final: 0.7169 (mmmt) REVERT: A 434 GLU cc_start: 0.8509 (OUTLIER) cc_final: 0.7424 (mm-30) REVERT: A 497 LYS cc_start: 0.8553 (pttt) cc_final: 0.8264 (pttp) REVERT: A 758 SER cc_start: 0.7609 (t) cc_final: 0.7350 (p) REVERT: A 810 GLU cc_start: 0.8557 (pt0) cc_final: 0.8296 (pt0) REVERT: A 838 MET cc_start: 0.9120 (mmm) cc_final: 0.8786 (mmt) REVERT: A 1011 THR cc_start: 0.8840 (OUTLIER) cc_final: 0.8568 (p) REVERT: B 7 MET cc_start: 0.8231 (mmt) cc_final: 0.7687 (mmm) REVERT: B 11 SER cc_start: 0.9131 (t) cc_final: 0.8606 (m) REVERT: B 83 ARG cc_start: 0.8468 (ttm170) cc_final: 0.7978 (ttp80) REVERT: B 96 MET cc_start: 0.9089 (mmm) cc_final: 0.8755 (mmt) REVERT: B 109 ARG cc_start: 0.8966 (OUTLIER) cc_final: 0.7278 (mtt180) REVERT: B 519 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8266 (mm-30) REVERT: B 561 GLU cc_start: 0.8017 (mm-30) cc_final: 0.7576 (mm-30) REVERT: B 855 TYR cc_start: 0.8588 (p90) cc_final: 0.8062 (p90) REVERT: B 878 LYS cc_start: 0.8612 (mttt) cc_final: 0.8259 (mttp) REVERT: C 11 SER cc_start: 0.9288 (t) cc_final: 0.8983 (m) REVERT: C 30 GLN cc_start: 0.7540 (tt0) cc_final: 0.7281 (mt0) REVERT: C 60 ARG cc_start: 0.8344 (mtt180) cc_final: 0.8098 (mtt90) REVERT: C 179 GLU cc_start: 0.8672 (mt-10) cc_final: 0.8421 (mt-10) REVERT: C 257 MET cc_start: 0.8523 (mmt) cc_final: 0.8049 (mmt) REVERT: C 269 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7601 (tt0) REVERT: C 350 LYS cc_start: 0.8082 (tppp) cc_final: 0.7252 (tptp) REVERT: C 381 MET cc_start: 0.8931 (mmm) cc_final: 0.8653 (mmt) REVERT: C 434 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.7174 (mm-30) REVERT: C 497 LYS cc_start: 0.8182 (pttt) cc_final: 0.7974 (pttt) REVERT: C 519 GLU cc_start: 0.8422 (mm-30) cc_final: 0.7987 (mm-30) REVERT: C 612 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.8401 (mtm180) REVERT: C 677 LYS cc_start: 0.8126 (tttm) cc_final: 0.7701 (ttpp) REVERT: C 708 ASP cc_start: 0.8844 (m-30) cc_final: 0.8436 (m-30) REVERT: C 737 SER cc_start: 0.9081 (t) cc_final: 0.8854 (m) REVERT: C 816 SER cc_start: 0.8959 (m) cc_final: 0.8661 (p) REVERT: C 875 ASP cc_start: 0.8986 (t0) cc_final: 0.8654 (t0) REVERT: C 878 LYS cc_start: 0.8856 (mttt) cc_final: 0.8424 (mttm) REVERT: C 888 ILE cc_start: 0.8815 (mt) cc_final: 0.8508 (mt) REVERT: C 904 MET cc_start: 0.8742 (ttp) cc_final: 0.8526 (ttp) REVERT: C 905 ARG cc_start: 0.8310 (pmt-80) cc_final: 0.7860 (pmt-80) REVERT: C 974 GLU cc_start: 0.8591 (tt0) cc_final: 0.8301 (tt0) REVERT: C 992 ASP cc_start: 0.8396 (t0) cc_final: 0.8167 (t0) outliers start: 46 outliers final: 27 residues processed: 377 average time/residue: 0.1443 time to fit residues: 83.5396 Evaluate side-chains 353 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 321 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 857 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 193 optimal weight: 5.9990 chunk 39 optimal weight: 10.0000 chunk 258 optimal weight: 7.9990 chunk 257 optimal weight: 3.9990 chunk 146 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 157 optimal weight: 8.9990 chunk 219 optimal weight: 8.9990 chunk 240 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 211 optimal weight: 3.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 739 ASN B 30 GLN B 260 GLN B 267 GLN C 494 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.085131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.066245 restraints weight = 27340.405| |-----------------------------------------------------------------------------| r_work (start): 0.2426 rms_B_bonded: 1.45 r_work: 0.2338 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2225 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 22540 Z= 0.232 Angle : 0.598 6.951 30650 Z= 0.318 Chirality : 0.049 0.170 3230 Planarity : 0.005 0.072 4054 Dihedral : 5.263 85.065 3067 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.61 % Allowed : 12.56 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.80 (0.15), residues: 2746 helix: 0.96 (0.31), residues: 313 sheet: -0.23 (0.19), residues: 685 loop : -0.94 (0.14), residues: 1748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 73 TYR 0.017 0.002 TYR B 766 PHE 0.017 0.002 PHE A 943 TRP 0.019 0.002 TRP B 592 HIS 0.008 0.002 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.23 (22540) covalent geometry : angle 0.59763 / 0.32 (30650) hydrogen bonds : bond 0.04799 / 3.22 ( 581) hydrogen bonds : angle 5.40452 / 3.75 ( 1671) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 305 time to evaluate : 0.829 Fit side-chains REVERT: A 63 ARG cc_start: 0.8719 (mtt180) cc_final: 0.8467 (mtp85) REVERT: A 67 ARG cc_start: 0.9267 (ttt180) cc_final: 0.8970 (ttt180) REVERT: A 73 ARG cc_start: 0.8223 (mtt180) cc_final: 0.7820 (ttm170) REVERT: A 92 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7414 (mtp180) REVERT: A 183 LYS cc_start: 0.8730 (ttpm) cc_final: 0.8193 (ttmt) REVERT: A 373 LYS cc_start: 0.7782 (mttt) cc_final: 0.7259 (mmmt) REVERT: A 381 MET cc_start: 0.9004 (mmm) cc_final: 0.8015 (ttm) REVERT: A 434 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: A 497 LYS cc_start: 0.8575 (pttt) cc_final: 0.8263 (pttp) REVERT: A 758 SER cc_start: 0.7673 (t) cc_final: 0.7386 (p) REVERT: A 1011 THR cc_start: 0.8938 (t) cc_final: 0.8539 (p) REVERT: B 83 ARG cc_start: 0.8572 (ttm170) cc_final: 0.8108 (ttp80) REVERT: B 109 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7131 (mtt180) REVERT: B 210 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: B 473 THR cc_start: 0.8840 (p) cc_final: 0.8636 (p) REVERT: B 519 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8330 (mt-10) REVERT: B 561 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7680 (mm-30) REVERT: B 855 TYR cc_start: 0.8613 (p90) cc_final: 0.8126 (p90) REVERT: B 878 LYS cc_start: 0.8701 (mttt) cc_final: 0.8342 (mttp) REVERT: C 30 GLN cc_start: 0.7969 (tt0) cc_final: 0.7637 (mt0) REVERT: C 60 ARG cc_start: 0.8408 (mtt180) cc_final: 0.8123 (mtt90) REVERT: C 179 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8404 (mt-10) REVERT: C 257 MET cc_start: 0.8520 (mmt) cc_final: 0.8111 (mmt) REVERT: C 350 LYS cc_start: 0.8182 (tppp) cc_final: 0.7435 (tptp) REVERT: C 434 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.7572 (mm-30) REVERT: C 497 LYS cc_start: 0.8340 (pttt) cc_final: 0.8109 (pttt) REVERT: C 519 GLU cc_start: 0.8427 (mm-30) cc_final: 0.7952 (mm-30) REVERT: C 612 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8075 (mtp180) REVERT: C 677 LYS cc_start: 0.8198 (tttm) cc_final: 0.7742 (ttpp) REVERT: C 681 ILE cc_start: 0.8781 (mt) cc_final: 0.8551 (tt) REVERT: C 708 ASP cc_start: 0.8935 (m-30) cc_final: 0.8551 (m-30) REVERT: C 816 SER cc_start: 0.8980 (m) cc_final: 0.8681 (p) REVERT: C 875 ASP cc_start: 0.9093 (t0) cc_final: 0.8700 (t0) REVERT: C 878 LYS cc_start: 0.8921 (mttt) cc_final: 0.8459 (mttm) REVERT: C 888 ILE cc_start: 0.8900 (mt) cc_final: 0.8600 (mt) REVERT: C 974 GLU cc_start: 0.8579 (tt0) cc_final: 0.8216 (tt0) outliers start: 62 outliers final: 49 residues processed: 353 average time/residue: 0.1502 time to fit residues: 81.2390 Evaluate side-chains 356 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 301 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 92 ARG Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 706 THR Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 558 THR Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 206 THR Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 753 THR Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 223 optimal weight: 2.9990 chunk 147 optimal weight: 4.9990 chunk 136 optimal weight: 0.9990 chunk 196 optimal weight: 9.9990 chunk 256 optimal weight: 1.9990 chunk 227 optimal weight: 3.9990 chunk 79 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 39 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 ASN B 30 GLN C 267 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.087748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2464 r_free = 0.2464 target = 0.068896 restraints weight = 26960.520| |-----------------------------------------------------------------------------| r_work (start): 0.2480 rms_B_bonded: 1.43 r_work: 0.2389 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2274 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.2274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22540 Z= 0.104 Angle : 0.480 6.673 30650 Z= 0.259 Chirality : 0.044 0.149 3230 Planarity : 0.004 0.042 4054 Dihedral : 4.968 84.857 3067 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.28 % Allowed : 13.07 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -0.68 (0.15), residues: 2746 helix: 0.99 (0.31), residues: 319 sheet: -0.16 (0.19), residues: 663 loop : -0.85 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.017 0.001 TYR B 23 PHE 0.012 0.001 PHE B 84 TRP 0.011 0.001 TRP B 592 HIS 0.006 0.001 HIS C 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.10 (22540) covalent geometry : angle 0.47986 / 0.26 (30650) hydrogen bonds : bond 0.03415 / 2.31 ( 581) hydrogen bonds : angle 5.17400 / 3.58 ( 1671) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 312 time to evaluate : 0.722 Fit side-chains REVERT: A 6 MET cc_start: 0.6192 (OUTLIER) cc_final: 0.4988 (tpt) REVERT: A 63 ARG cc_start: 0.8692 (mtt180) cc_final: 0.8346 (mtp85) REVERT: A 67 ARG cc_start: 0.9263 (ttt180) cc_final: 0.8976 (ttt180) REVERT: A 73 ARG cc_start: 0.8208 (mtt180) cc_final: 0.7931 (mtm180) REVERT: A 183 LYS cc_start: 0.8720 (ttpm) cc_final: 0.8218 (ttmt) REVERT: A 373 LYS cc_start: 0.7714 (mttt) cc_final: 0.7196 (mmmt) REVERT: A 434 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.7566 (mm-30) REVERT: A 497 LYS cc_start: 0.8564 (pttt) cc_final: 0.8271 (pttp) REVERT: A 758 SER cc_start: 0.7534 (t) cc_final: 0.7264 (p) REVERT: A 1011 THR cc_start: 0.8890 (OUTLIER) cc_final: 0.8566 (p) REVERT: B 11 SER cc_start: 0.9335 (t) cc_final: 0.8790 (m) REVERT: B 83 ARG cc_start: 0.8508 (ttm170) cc_final: 0.8060 (ttp80) REVERT: B 109 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.7078 (mtt180) REVERT: B 210 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8464 (mt-10) REVERT: B 267 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.7624 (mt0) REVERT: B 473 THR cc_start: 0.8964 (p) cc_final: 0.8732 (p) REVERT: B 519 GLU cc_start: 0.8619 (mm-30) cc_final: 0.8315 (mt-10) REVERT: B 561 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7730 (mm-30) REVERT: B 855 TYR cc_start: 0.8612 (p90) cc_final: 0.8093 (p90) REVERT: B 872 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8386 (mm-40) REVERT: B 878 LYS cc_start: 0.8649 (mttt) cc_final: 0.8291 (mttp) REVERT: C 11 SER cc_start: 0.9343 (t) cc_final: 0.8961 (m) REVERT: C 30 GLN cc_start: 0.7934 (tt0) cc_final: 0.7636 (mt0) REVERT: C 60 ARG cc_start: 0.8379 (mtt180) cc_final: 0.8117 (mtt90) REVERT: C 179 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8395 (mt-10) REVERT: C 257 MET cc_start: 0.8607 (mmt) cc_final: 0.8049 (mmt) REVERT: C 350 LYS cc_start: 0.8135 (tppp) cc_final: 0.7387 (tptp) REVERT: C 373 LYS cc_start: 0.8025 (ptpp) cc_final: 0.7550 (pttp) REVERT: C 434 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7320 (mm-30) REVERT: C 497 LYS cc_start: 0.8304 (pttt) cc_final: 0.8052 (pttt) REVERT: C 519 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7938 (mm-30) REVERT: C 612 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.8355 (mtm180) REVERT: C 677 LYS cc_start: 0.8201 (tttm) cc_final: 0.7769 (ttpp) REVERT: C 681 ILE cc_start: 0.8725 (mt) cc_final: 0.8514 (tt) REVERT: C 708 ASP cc_start: 0.8886 (m-30) cc_final: 0.8456 (m-30) REVERT: C 737 SER cc_start: 0.9122 (t) cc_final: 0.8906 (m) REVERT: C 816 SER cc_start: 0.8994 (m) cc_final: 0.8692 (p) REVERT: C 875 ASP cc_start: 0.9047 (t0) cc_final: 0.8670 (t0) REVERT: C 878 LYS cc_start: 0.8902 (mttt) cc_final: 0.8445 (mttm) REVERT: C 888 ILE cc_start: 0.8854 (mt) cc_final: 0.8546 (mt) REVERT: C 974 GLU cc_start: 0.8650 (tt0) cc_final: 0.8328 (tt0) REVERT: C 992 ASP cc_start: 0.8516 (t0) cc_final: 0.8209 (t0) outliers start: 54 outliers final: 40 residues processed: 349 average time/residue: 0.1539 time to fit residues: 82.8059 Evaluate side-chains 360 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 311 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1019 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 130 optimal weight: 0.7980 chunk 95 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 124 optimal weight: 0.0980 chunk 65 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 150 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 126 optimal weight: 4.9990 chunk 216 optimal weight: 5.9990 chunk 252 optimal weight: 4.9990 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 GLN C 494 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.086890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2450 r_free = 0.2450 target = 0.068034 restraints weight = 26999.087| |-----------------------------------------------------------------------------| r_work (start): 0.2457 rms_B_bonded: 1.44 r_work: 0.2368 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.2255 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22540 Z= 0.133 Angle : 0.507 6.730 30650 Z= 0.272 Chirality : 0.045 0.149 3230 Planarity : 0.004 0.067 4054 Dihedral : 4.995 84.918 3066 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 2.57 % Allowed : 12.90 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.67 (0.15), residues: 2746 helix: 0.98 (0.31), residues: 319 sheet: -0.15 (0.19), residues: 670 loop : -0.84 (0.14), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.016 0.001 TYR A 23 PHE 0.013 0.001 PHE B 84 TRP 0.013 0.001 TRP B 592 HIS 0.006 0.001 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (22540) covalent geometry : angle 0.50691 / 0.27 (30650) hydrogen bonds : bond 0.03796 / 2.55 ( 581) hydrogen bonds : angle 5.19079 / 3.59 ( 1671) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 308 time to evaluate : 0.822 Fit side-chains REVERT: A 6 MET cc_start: 0.6162 (OUTLIER) cc_final: 0.5006 (tpt) REVERT: A 63 ARG cc_start: 0.8690 (mtt180) cc_final: 0.8439 (mtp85) REVERT: A 67 ARG cc_start: 0.9270 (ttt180) cc_final: 0.8984 (ttt180) REVERT: A 73 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7693 (mtm180) REVERT: A 183 LYS cc_start: 0.8686 (ttpm) cc_final: 0.8207 (ttmt) REVERT: A 373 LYS cc_start: 0.7741 (mttt) cc_final: 0.7229 (mmmt) REVERT: A 434 GLU cc_start: 0.8583 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: A 497 LYS cc_start: 0.8573 (pttt) cc_final: 0.8281 (pttp) REVERT: A 570 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8136 (t70) REVERT: A 758 SER cc_start: 0.7704 (t) cc_final: 0.7424 (p) REVERT: A 1011 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8558 (p) REVERT: B 11 SER cc_start: 0.9310 (t) cc_final: 0.8789 (m) REVERT: B 53 THR cc_start: 0.9332 (OUTLIER) cc_final: 0.9033 (m) REVERT: B 83 ARG cc_start: 0.8527 (ttm170) cc_final: 0.8082 (ttp80) REVERT: B 109 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.7091 (mtt180) REVERT: B 210 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8487 (mt-10) REVERT: B 267 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: B 473 THR cc_start: 0.8829 (p) cc_final: 0.8623 (p) REVERT: B 519 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8328 (mt-10) REVERT: B 561 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 878 LYS cc_start: 0.8652 (mttt) cc_final: 0.8286 (mttp) REVERT: C 11 SER cc_start: 0.9214 (t) cc_final: 0.8889 (m) REVERT: C 30 GLN cc_start: 0.7956 (tt0) cc_final: 0.7648 (mt0) REVERT: C 60 ARG cc_start: 0.8393 (mtt180) cc_final: 0.8119 (mtt90) REVERT: C 179 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8403 (mt-10) REVERT: C 257 MET cc_start: 0.8587 (mmt) cc_final: 0.8089 (mmt) REVERT: C 350 LYS cc_start: 0.8155 (tppp) cc_final: 0.7407 (tptp) REVERT: C 434 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.7378 (mm-30) REVERT: C 497 LYS cc_start: 0.8329 (pttt) cc_final: 0.8058 (pttt) REVERT: C 519 GLU cc_start: 0.8405 (mm-30) cc_final: 0.7937 (mm-30) REVERT: C 612 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8396 (mtm180) REVERT: C 677 LYS cc_start: 0.8217 (tttm) cc_final: 0.7781 (ttpp) REVERT: C 681 ILE cc_start: 0.8750 (mt) cc_final: 0.8544 (tt) REVERT: C 708 ASP cc_start: 0.8895 (m-30) cc_final: 0.8463 (m-30) REVERT: C 737 SER cc_start: 0.9089 (t) cc_final: 0.8833 (m) REVERT: C 816 SER cc_start: 0.8981 (m) cc_final: 0.8694 (p) REVERT: C 875 ASP cc_start: 0.9066 (t0) cc_final: 0.8685 (t0) REVERT: C 878 LYS cc_start: 0.8849 (mttt) cc_final: 0.8413 (mttm) REVERT: C 888 ILE cc_start: 0.8868 (mt) cc_final: 0.8558 (mt) REVERT: C 974 GLU cc_start: 0.8531 (tt0) cc_final: 0.8140 (tt0) REVERT: C 992 ASP cc_start: 0.8527 (t0) cc_final: 0.8224 (t0) outliers start: 61 outliers final: 49 residues processed: 352 average time/residue: 0.1493 time to fit residues: 81.0808 Evaluate side-chains 365 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 306 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 869 MET Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1014 SER Chi-restraints excluded: chain C residue 1019 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 163 optimal weight: 8.9990 chunk 247 optimal weight: 10.0000 chunk 6 optimal weight: 0.0050 chunk 126 optimal weight: 0.9980 chunk 263 optimal weight: 7.9990 chunk 145 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 232 optimal weight: 1.9990 chunk 240 optimal weight: 9.9990 chunk 220 optimal weight: 3.9990 chunk 193 optimal weight: 2.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.087771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2463 r_free = 0.2463 target = 0.068688 restraints weight = 27050.494| |-----------------------------------------------------------------------------| r_work (start): 0.2470 rms_B_bonded: 1.47 r_work: 0.2379 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2264 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22540 Z= 0.117 Angle : 0.488 6.404 30650 Z= 0.263 Chirality : 0.045 0.146 3230 Planarity : 0.004 0.058 4054 Dihedral : 4.924 84.919 3066 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 12.73 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -0.65 (0.15), residues: 2746 helix: 0.95 (0.31), residues: 325 sheet: -0.13 (0.19), residues: 672 loop : -0.82 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.016 0.001 TYR A 23 PHE 0.012 0.001 PHE B 84 TRP 0.011 0.001 TRP B 592 HIS 0.006 0.001 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.12 (22540) covalent geometry : angle 0.48774 / 0.26 (30650) hydrogen bonds : bond 0.03525 / 2.37 ( 581) hydrogen bonds : angle 5.13450 / 3.55 ( 1671) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 306 time to evaluate : 0.760 Fit side-chains REVERT: A 6 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.4934 (tpt) REVERT: A 63 ARG cc_start: 0.8668 (mtt180) cc_final: 0.8349 (mtp85) REVERT: A 67 ARG cc_start: 0.9273 (ttt180) cc_final: 0.8976 (ttt180) REVERT: A 73 ARG cc_start: 0.7922 (mtt180) cc_final: 0.7694 (mtm180) REVERT: A 183 LYS cc_start: 0.8704 (ttpm) cc_final: 0.8207 (ttmt) REVERT: A 373 LYS cc_start: 0.7694 (mttt) cc_final: 0.7173 (mmmt) REVERT: A 434 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: A 497 LYS cc_start: 0.8539 (pttt) cc_final: 0.8253 (pttp) REVERT: A 570 ASP cc_start: 0.8781 (OUTLIER) cc_final: 0.8122 (t70) REVERT: A 758 SER cc_start: 0.7531 (t) cc_final: 0.7244 (p) REVERT: A 1011 THR cc_start: 0.8906 (OUTLIER) cc_final: 0.8601 (p) REVERT: B 7 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7762 (mmm) REVERT: B 11 SER cc_start: 0.9297 (t) cc_final: 0.8778 (m) REVERT: B 53 THR cc_start: 0.9318 (OUTLIER) cc_final: 0.9017 (m) REVERT: B 83 ARG cc_start: 0.8517 (ttm170) cc_final: 0.8053 (ttp80) REVERT: B 109 ARG cc_start: 0.9026 (OUTLIER) cc_final: 0.7081 (mtt180) REVERT: B 210 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8467 (mt-10) REVERT: B 267 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.7661 (mt0) REVERT: B 473 THR cc_start: 0.8962 (p) cc_final: 0.8729 (p) REVERT: B 519 GLU cc_start: 0.8623 (mm-30) cc_final: 0.8316 (mt-10) REVERT: B 561 GLU cc_start: 0.8239 (mm-30) cc_final: 0.7712 (mm-30) REVERT: B 872 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.8421 (mm-40) REVERT: B 878 LYS cc_start: 0.8637 (mttt) cc_final: 0.8278 (mttp) REVERT: C 11 SER cc_start: 0.9344 (t) cc_final: 0.8965 (m) REVERT: C 30 GLN cc_start: 0.7929 (tt0) cc_final: 0.7617 (mt0) REVERT: C 60 ARG cc_start: 0.8380 (mtt180) cc_final: 0.8105 (mtt90) REVERT: C 179 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8398 (mt-10) REVERT: C 257 MET cc_start: 0.8588 (mmt) cc_final: 0.8106 (mmt) REVERT: C 350 LYS cc_start: 0.8139 (tppp) cc_final: 0.7386 (tptp) REVERT: C 373 LYS cc_start: 0.7979 (ptpp) cc_final: 0.7485 (pttp) REVERT: C 381 MET cc_start: 0.8997 (mmm) cc_final: 0.8739 (mmt) REVERT: C 434 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7322 (mm-30) REVERT: C 497 LYS cc_start: 0.8288 (pttt) cc_final: 0.8034 (pttt) REVERT: C 519 GLU cc_start: 0.8380 (mm-30) cc_final: 0.7907 (mm-30) REVERT: C 612 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8351 (mtm180) REVERT: C 677 LYS cc_start: 0.8195 (tttm) cc_final: 0.7752 (ttpp) REVERT: C 708 ASP cc_start: 0.8889 (m-30) cc_final: 0.8456 (m-30) REVERT: C 737 SER cc_start: 0.9066 (t) cc_final: 0.8826 (m) REVERT: C 816 SER cc_start: 0.9005 (m) cc_final: 0.8710 (p) REVERT: C 875 ASP cc_start: 0.9054 (t0) cc_final: 0.8665 (t0) REVERT: C 878 LYS cc_start: 0.8845 (mttt) cc_final: 0.8415 (mttm) REVERT: C 888 ILE cc_start: 0.8854 (mt) cc_final: 0.8543 (mt) REVERT: C 974 GLU cc_start: 0.8524 (tt0) cc_final: 0.8125 (tt0) REVERT: C 992 ASP cc_start: 0.8503 (t0) cc_final: 0.8209 (t0) outliers start: 70 outliers final: 52 residues processed: 356 average time/residue: 0.1566 time to fit residues: 85.5729 Evaluate side-chains 369 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 305 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain B residue 7 MET Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 577 VAL Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1014 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 160 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 114 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 130 optimal weight: 0.9980 chunk 260 optimal weight: 3.9990 chunk 189 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.086855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2448 r_free = 0.2448 target = 0.067846 restraints weight = 27158.391| |-----------------------------------------------------------------------------| r_work (start): 0.2460 rms_B_bonded: 1.47 r_work: 0.2369 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.2254 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.2254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22540 Z= 0.141 Angle : 0.514 6.531 30650 Z= 0.276 Chirality : 0.046 0.153 3230 Planarity : 0.004 0.067 4054 Dihedral : 4.992 84.855 3066 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.82 % Allowed : 12.86 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -0.69 (0.15), residues: 2746 helix: 0.80 (0.30), residues: 331 sheet: -0.13 (0.19), residues: 673 loop : -0.84 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 517 TYR 0.016 0.001 TYR A 23 PHE 0.013 0.001 PHE C 84 TRP 0.014 0.001 TRP B 592 HIS 0.006 0.001 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.14 (22540) covalent geometry : angle 0.51429 / 0.28 (30650) hydrogen bonds : bond 0.03861 / 2.60 ( 581) hydrogen bonds : angle 5.18304 / 3.59 ( 1671) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5492 Ramachandran restraints generated. 2746 Oldfield, 0 Emsley, 2746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 304 time to evaluate : 0.614 Fit side-chains REVERT: A 6 MET cc_start: 0.6079 (OUTLIER) cc_final: 0.4924 (tpt) REVERT: A 63 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8427 (mtp85) REVERT: A 67 ARG cc_start: 0.9277 (ttt180) cc_final: 0.8985 (ttt180) REVERT: A 73 ARG cc_start: 0.7935 (mtt180) cc_final: 0.7695 (mtm180) REVERT: A 183 LYS cc_start: 0.8715 (ttpm) cc_final: 0.8206 (ttmt) REVERT: A 373 LYS cc_start: 0.7726 (mttt) cc_final: 0.7208 (mmmt) REVERT: A 434 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7517 (mm-30) REVERT: A 497 LYS cc_start: 0.8541 (pttt) cc_final: 0.8252 (pttp) REVERT: A 570 ASP cc_start: 0.8795 (OUTLIER) cc_final: 0.8144 (t70) REVERT: A 758 SER cc_start: 0.7698 (t) cc_final: 0.7415 (p) REVERT: A 1011 THR cc_start: 0.8916 (OUTLIER) cc_final: 0.8589 (p) REVERT: B 11 SER cc_start: 0.9298 (t) cc_final: 0.8776 (m) REVERT: B 53 THR cc_start: 0.9328 (OUTLIER) cc_final: 0.9015 (m) REVERT: B 83 ARG cc_start: 0.8530 (ttm170) cc_final: 0.8068 (ttp80) REVERT: B 109 ARG cc_start: 0.9039 (OUTLIER) cc_final: 0.7119 (mtt180) REVERT: B 210 GLU cc_start: 0.8771 (OUTLIER) cc_final: 0.8485 (mt-10) REVERT: B 267 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.7719 (mt0) REVERT: B 473 THR cc_start: 0.8825 (p) cc_final: 0.8616 (p) REVERT: B 519 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8325 (mt-10) REVERT: B 872 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8450 (mm-40) REVERT: B 878 LYS cc_start: 0.8635 (mttt) cc_final: 0.8272 (mttp) REVERT: C 11 SER cc_start: 0.9223 (t) cc_final: 0.8893 (m) REVERT: C 30 GLN cc_start: 0.7955 (tt0) cc_final: 0.7620 (mt0) REVERT: C 60 ARG cc_start: 0.8389 (mtt180) cc_final: 0.8109 (mtt90) REVERT: C 179 GLU cc_start: 0.8633 (mt-10) cc_final: 0.8388 (mt-10) REVERT: C 257 MET cc_start: 0.8573 (mmt) cc_final: 0.8053 (mmt) REVERT: C 350 LYS cc_start: 0.8159 (tppp) cc_final: 0.7406 (tptp) REVERT: C 373 LYS cc_start: 0.8070 (ptpp) cc_final: 0.7583 (pttp) REVERT: C 434 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7395 (mm-30) REVERT: C 497 LYS cc_start: 0.8306 (pttt) cc_final: 0.8051 (pttt) REVERT: C 519 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7902 (mm-30) REVERT: C 612 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.8374 (mtm180) REVERT: C 677 LYS cc_start: 0.8192 (tttm) cc_final: 0.7763 (ttpp) REVERT: C 737 SER cc_start: 0.9088 (t) cc_final: 0.8838 (m) REVERT: C 816 SER cc_start: 0.9009 (m) cc_final: 0.8718 (p) REVERT: C 875 ASP cc_start: 0.9075 (t0) cc_final: 0.8666 (t0) REVERT: C 878 LYS cc_start: 0.8848 (mttt) cc_final: 0.8414 (mttm) REVERT: C 888 ILE cc_start: 0.8866 (mt) cc_final: 0.8556 (mt) REVERT: C 974 GLU cc_start: 0.8547 (tt0) cc_final: 0.8152 (tt0) outliers start: 67 outliers final: 54 residues processed: 355 average time/residue: 0.1522 time to fit residues: 83.0900 Evaluate side-chains 370 residues out of total 2372 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 305 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 MET Chi-restraints excluded: chain A residue 7 MET Chi-restraints excluded: chain A residue 133 CYS Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 422 LEU Chi-restraints excluded: chain A residue 434 GLU Chi-restraints excluded: chain A residue 510 GLN Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain A residue 576 VAL Chi-restraints excluded: chain A residue 582 VAL Chi-restraints excluded: chain A residue 660 VAL Chi-restraints excluded: chain A residue 710 SER Chi-restraints excluded: chain A residue 720 MET Chi-restraints excluded: chain A residue 824 VAL Chi-restraints excluded: chain A residue 914 VAL Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 982 THR Chi-restraints excluded: chain A residue 993 VAL Chi-restraints excluded: chain A residue 1004 ILE Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1014 SER Chi-restraints excluded: chain B residue 43 ASN Chi-restraints excluded: chain B residue 53 THR Chi-restraints excluded: chain B residue 90 ASP Chi-restraints excluded: chain B residue 109 ARG Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 196 GLU Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain B residue 267 GLN Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 275 THR Chi-restraints excluded: chain B residue 348 THR Chi-restraints excluded: chain B residue 386 SER Chi-restraints excluded: chain B residue 710 SER Chi-restraints excluded: chain B residue 810 GLU Chi-restraints excluded: chain B residue 816 SER Chi-restraints excluded: chain B residue 817 VAL Chi-restraints excluded: chain B residue 824 VAL Chi-restraints excluded: chain B residue 870 SER Chi-restraints excluded: chain B residue 872 GLN Chi-restraints excluded: chain B residue 873 VAL Chi-restraints excluded: chain B residue 965 SER Chi-restraints excluded: chain B residue 982 THR Chi-restraints excluded: chain B residue 993 VAL Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 133 CYS Chi-restraints excluded: chain C residue 196 GLU Chi-restraints excluded: chain C residue 271 GLN Chi-restraints excluded: chain C residue 386 SER Chi-restraints excluded: chain C residue 427 ASP Chi-restraints excluded: chain C residue 434 GLU Chi-restraints excluded: chain C residue 452 SER Chi-restraints excluded: chain C residue 489 VAL Chi-restraints excluded: chain C residue 588 LEU Chi-restraints excluded: chain C residue 612 ARG Chi-restraints excluded: chain C residue 657 VAL Chi-restraints excluded: chain C residue 710 SER Chi-restraints excluded: chain C residue 789 VAL Chi-restraints excluded: chain C residue 854 SER Chi-restraints excluded: chain C residue 857 ASP Chi-restraints excluded: chain C residue 982 THR Chi-restraints excluded: chain C residue 1004 ILE Chi-restraints excluded: chain C residue 1014 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 276 random chunks: chunk 255 optimal weight: 5.9990 chunk 272 optimal weight: 10.0000 chunk 77 optimal weight: 0.0070 chunk 164 optimal weight: 3.9990 chunk 256 optimal weight: 0.3980 chunk 262 optimal weight: 8.9990 chunk 87 optimal weight: 0.9990 chunk 8 optimal weight: 8.9990 chunk 231 optimal weight: 7.9990 chunk 116 optimal weight: 0.8980 chunk 145 optimal weight: 2.9990 overall best weight: 1.0602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.089268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2488 r_free = 0.2488 target = 0.070264 restraints weight = 26887.559| |-----------------------------------------------------------------------------| r_work (start): 0.2502 rms_B_bonded: 1.46 r_work: 0.2411 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2297 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8963 moved from start: 0.1676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22540 Z= 0.084 Angle : 0.451 6.076 30650 Z= 0.244 Chirality : 0.043 0.147 3230 Planarity : 0.004 0.041 4054 Dihedral : 4.733 84.922 3066 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.61 % Allowed : 13.15 % Favored : 84.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.64 % 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: -0.54 (0.15), residues: 2746 helix: 0.94 (0.31), residues: 331 sheet: -0.05 (0.20), residues: 660 loop : -0.74 (0.14), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 517 TYR 0.016 0.001 TYR A 23 PHE 0.011 0.001 PHE B 84 TRP 0.012 0.001 TRP A 537 HIS 0.005 0.001 HIS A 891 Details of bonding type rmsd/Z covalent geometry : bond 0.00188 / 0.08 (22540) covalent geometry : angle 0.45144 / 0.24 (30650) hydrogen bonds : bond 0.03033 / 2.04 ( 581) hydrogen bonds : angle 5.00172 / 3.46 ( 1671) =============================================================================== Job complete usr+sys time: 4404.32 seconds wall clock time: 76 minutes 9.47 seconds (4569.47 seconds total)