Starting phenix.real_space_refine on Tue Aug 26 01:36:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk8_16092/08_2025/8bk8_16092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk8_16092/08_2025/8bk8_16092.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bk8_16092/08_2025/8bk8_16092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk8_16092/08_2025/8bk8_16092.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bk8_16092/08_2025/8bk8_16092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk8_16092/08_2025/8bk8_16092.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 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 152 5.16 5 C 20552 2.51 5 N 5760 2.21 5 O 6036 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 100 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32500 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8125 Classifications: {'peptide': 1011} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 945} Restraints were copied for chains: B, C, D Time building chain proxies: 9.09, per 1000 atoms: 0.28 Number of scatterers: 32500 At special positions: 0 Unit cell: (195.825, 148.827, 101.829, 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 152 16.00 O 6036 8.00 N 5760 7.00 C 20552 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.65 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7520 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 52 sheets defined 16.9% alpha, 36.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.53 Creating SS restraints... Processing helix chain 'A' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 44 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 70 through 75 Processing helix chain 'A' and resid 89 through 93 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU A 136 " --> pdb=" O SER A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 198 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 400 " --> pdb=" O PRO A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 Processing helix chain 'A' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 619 " --> pdb=" O PRO A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 794 Processing helix chain 'A' and resid 805 through 813 Processing helix chain 'A' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR A 926 " --> pdb=" O SER A 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 923 through 926' Processing helix chain 'A' and resid 963 through 970 Processing helix chain 'A' and resid 972 through 976 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'B' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 44 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 70 through 75 Processing helix chain 'B' and resid 89 through 93 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 136 " --> pdb=" O SER B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 198 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 400 " --> pdb=" O PRO B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG B 442 " --> pdb=" O GLU B 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 Processing helix chain 'B' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU B 619 " --> pdb=" O PRO B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 789 through 794 Processing helix chain 'B' and resid 805 through 813 Processing helix chain 'B' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR B 926 " --> pdb=" O SER B 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 923 through 926' Processing helix chain 'B' and resid 963 through 970 Processing helix chain 'B' and resid 972 through 976 Processing helix chain 'B' and resid 1004 through 1008 Processing helix chain 'C' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 44 Processing helix chain 'C' and resid 65 through 69 Processing helix chain 'C' and resid 70 through 75 Processing helix chain 'C' and resid 89 through 93 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU C 136 " --> pdb=" O SER C 132 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 198 Processing helix chain 'C' and resid 368 through 382 Processing helix chain 'C' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR C 400 " --> pdb=" O PRO C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 429 through 431 No H-bonds generated for 'chain 'C' and resid 429 through 431' Processing helix chain 'C' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG C 442 " --> pdb=" O GLU C 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 Processing helix chain 'C' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR C 618 " --> pdb=" O HIS C 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU C 619 " --> pdb=" O PRO C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 789 through 794 Processing helix chain 'C' and resid 805 through 813 Processing helix chain 'C' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR C 926 " --> pdb=" O SER C 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 923 through 926' Processing helix chain 'C' and resid 963 through 970 Processing helix chain 'C' and resid 972 through 976 Processing helix chain 'C' and resid 1004 through 1008 Processing helix chain 'D' and resid 14 through 18 removed outlier: 3.582A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 44 Processing helix chain 'D' and resid 65 through 69 Processing helix chain 'D' and resid 70 through 75 Processing helix chain 'D' and resid 89 through 93 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.776A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU D 136 " --> pdb=" O SER D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 198 Processing helix chain 'D' and resid 368 through 382 Processing helix chain 'D' and resid 395 through 406 removed outlier: 3.838A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR D 400 " --> pdb=" O PRO D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 429 through 431 No H-bonds generated for 'chain 'D' and resid 429 through 431' Processing helix chain 'D' and resid 432 through 448 removed outlier: 4.218A pdb=" N ARG D 442 " --> pdb=" O GLU D 438 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.581A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 3.606A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 Processing helix chain 'D' and resid 614 through 624 removed outlier: 4.229A pdb=" N THR D 618 " --> pdb=" O HIS D 614 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU D 619 " --> pdb=" O PRO D 615 " (cutoff:3.500A) Processing helix chain 'D' and resid 789 through 794 Processing helix chain 'D' and resid 805 through 813 Processing helix chain 'D' and resid 923 through 926 removed outlier: 3.522A pdb=" N TYR D 926 " --> pdb=" O SER D 923 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 923 through 926' Processing helix chain 'D' and resid 963 through 970 Processing helix chain 'D' and resid 972 through 976 Processing helix chain 'D' and resid 1004 through 1008 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA A 149 " --> pdb=" O LEU A 189 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 129 " --> pdb=" O GLY A 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU A 57 " --> pdb=" O THR A 126 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 53 Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 265 through 273 removed outlier: 6.907A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU A 254 " --> pdb=" O PRO A 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA7, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL A 409 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP A 456 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP A 411 " --> pdb=" O TRP A 456 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU A 412 " --> pdb=" O CYS A 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AA9, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU A 658 " --> pdb=" O PRO A 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 664 " --> pdb=" O VAL A 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS A 754 " --> pdb=" O LEU A 751 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE A 850 " --> pdb=" O TRP A 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY A 940 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU A 900 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU A 898 " --> pdb=" O ARG A 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU A 944 " --> pdb=" O ASN A 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN A 896 " --> pdb=" O LEU A 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR A 946 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG A 894 " --> pdb=" O TYR A 946 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA B 149 " --> pdb=" O LEU B 189 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 129 " --> pdb=" O GLY B 180 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB7, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 265 through 273 removed outlier: 6.906A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU B 254 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC2, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL B 409 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP B 456 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP B 411 " --> pdb=" O TRP B 456 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU B 412 " --> pdb=" O CYS B 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC4, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC5, first strand: chain 'B' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU B 658 " --> pdb=" O PRO B 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 664 " --> pdb=" O VAL B 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS B 754 " --> pdb=" O LEU B 751 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 850 " --> pdb=" O TRP B 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY B 940 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU B 900 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU B 898 " --> pdb=" O ARG B 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU B 944 " --> pdb=" O ASN B 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN B 896 " --> pdb=" O LEU B 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR B 946 " --> pdb=" O ARG B 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG B 894 " --> pdb=" O TYR B 946 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 149 " --> pdb=" O LEU C 189 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL C 129 " --> pdb=" O GLY C 180 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD2, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 265 through 273 removed outlier: 6.906A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 8.409A pdb=" N LEU C 254 " --> pdb=" O PRO C 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD6, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL C 409 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP C 456 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP C 411 " --> pdb=" O TRP C 456 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLU C 412 " --> pdb=" O CYS C 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AD8, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AD9, first strand: chain 'C' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU C 658 " --> pdb=" O PRO C 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA C 664 " --> pdb=" O VAL C 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS C 754 " --> pdb=" O LEU C 751 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE C 850 " --> pdb=" O TRP C 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY C 940 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU C 900 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU C 898 " --> pdb=" O ARG C 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU C 944 " --> pdb=" O ASN C 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN C 896 " --> pdb=" O LEU C 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR C 946 " --> pdb=" O ARG C 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG C 894 " --> pdb=" O TYR C 946 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.757A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA D 149 " --> pdb=" O LEU D 189 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL D 129 " --> pdb=" O GLY D 180 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.420A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE6, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.122A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.591A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 265 through 273 removed outlier: 6.907A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 8.410A pdb=" N LEU D 254 " --> pdb=" O PRO D 273 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF1, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.140A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N VAL D 409 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N TRP D 456 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ASP D 411 " --> pdb=" O TRP D 456 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU D 412 " --> pdb=" O CYS D 389 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.338A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.616A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF3, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF4, first strand: chain 'D' and resid 661 through 669 removed outlier: 5.945A pdb=" N LEU D 658 " --> pdb=" O PRO D 662 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA D 664 " --> pdb=" O VAL D 656 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'D' and resid 739 through 742 removed outlier: 4.127A pdb=" N LYS D 754 " --> pdb=" O LEU D 751 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.416A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.526A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.496A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.403A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE D 850 " --> pdb=" O TRP D 842 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.533A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.733A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 12.029A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLY D 940 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU D 900 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LEU D 898 " --> pdb=" O ARG D 942 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU D 944 " --> pdb=" O ASN D 896 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ASN D 896 " --> pdb=" O LEU D 944 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TYR D 946 " --> pdb=" O ARG D 894 " (cutoff:3.500A) removed outlier: 8.674A pdb=" N ARG D 894 " --> pdb=" O TYR D 946 " (cutoff:3.500A) 1216 hydrogen bonds defined for protein. 3180 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: 8.34 Time building geometry restraints manager: 3.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10030 1.33 - 1.45: 5842 1.45 - 1.57: 17356 1.57 - 1.69: 0 1.69 - 1.81: 240 Bond restraints: 33468 Sorted by residual: bond pdb=" C LEU C 433 " pdb=" N PRO C 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" C LEU A 433 " pdb=" N PRO A 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" C LEU D 433 " pdb=" N PRO D 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" C LEU B 433 " pdb=" N PRO B 434 " ideal model delta sigma weight residual 1.335 1.368 -0.033 1.30e-02 5.92e+03 6.29e+00 bond pdb=" CB TYR A 472 " pdb=" CG TYR A 472 " ideal model delta sigma weight residual 1.512 1.480 0.032 2.20e-02 2.07e+03 2.17e+00 ... (remaining 33463 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 43880 1.45 - 2.90: 1424 2.90 - 4.36: 260 4.36 - 5.81: 80 5.81 - 7.26: 16 Bond angle restraints: 45660 Sorted by residual: angle pdb=" C ASN A 394 " pdb=" N HIS A 395 " pdb=" CA HIS A 395 " ideal model delta sigma weight residual 120.65 127.91 -7.26 1.36e+00 5.41e-01 2.85e+01 angle pdb=" C ASN D 394 " pdb=" N HIS D 395 " pdb=" CA HIS D 395 " ideal model delta sigma weight residual 120.65 127.91 -7.26 1.36e+00 5.41e-01 2.85e+01 angle pdb=" C ASN B 394 " pdb=" N HIS B 395 " pdb=" CA HIS B 395 " ideal model delta sigma weight residual 120.65 127.90 -7.25 1.36e+00 5.41e-01 2.84e+01 angle pdb=" C ASN C 394 " pdb=" N HIS C 395 " pdb=" CA HIS C 395 " ideal model delta sigma weight residual 120.65 127.90 -7.25 1.36e+00 5.41e-01 2.84e+01 angle pdb=" C SER D 545 " pdb=" N LEU D 546 " pdb=" CA LEU D 546 " ideal model delta sigma weight residual 122.36 127.49 -5.13 1.47e+00 4.63e-01 1.22e+01 ... (remaining 45655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 17960 17.74 - 35.47: 1360 35.47 - 53.21: 184 53.21 - 70.95: 68 70.95 - 88.69: 24 Dihedral angle restraints: 19596 sinusoidal: 7912 harmonic: 11684 Sorted by residual: dihedral pdb=" CA ASP B 598 " pdb=" C ASP B 598 " pdb=" N ARG B 599 " pdb=" CA ARG B 599 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASP A 598 " pdb=" C ASP A 598 " pdb=" N ARG A 599 " pdb=" CA ARG A 599 " ideal model delta harmonic sigma weight residual -180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASP D 598 " pdb=" C ASP D 598 " pdb=" N ARG D 599 " pdb=" CA ARG D 599 " ideal model delta harmonic sigma weight residual 180.00 -151.33 -28.67 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 19593 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3680 0.051 - 0.101: 810 0.101 - 0.152: 250 0.152 - 0.203: 8 0.203 - 0.253: 4 Chirality restraints: 4752 Sorted by residual: chirality pdb=" CA ARG C 599 " pdb=" N ARG C 599 " pdb=" C ARG C 599 " pdb=" CB ARG C 599 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG A 599 " pdb=" N ARG A 599 " pdb=" C ARG A 599 " pdb=" CB ARG A 599 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA ARG B 599 " pdb=" N ARG B 599 " pdb=" C ARG B 599 " pdb=" CB ARG B 599 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.61e+00 ... (remaining 4749 not shown) Planarity restraints: 6036 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 403 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" CG ASP D 403 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP D 403 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP D 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 403 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" CG ASP A 403 " -0.049 2.00e-02 2.50e+03 pdb=" OD1 ASP A 403 " 0.018 2.00e-02 2.50e+03 pdb=" OD2 ASP A 403 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 403 " -0.014 2.00e-02 2.50e+03 2.80e-02 7.82e+00 pdb=" CG ASP B 403 " 0.048 2.00e-02 2.50e+03 pdb=" OD1 ASP B 403 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP B 403 " -0.017 2.00e-02 2.50e+03 ... (remaining 6033 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 6422 2.78 - 3.31: 27788 3.31 - 3.84: 58261 3.84 - 4.37: 70107 4.37 - 4.90: 119448 Nonbonded interactions: 282026 Sorted by model distance: nonbonded pdb=" O PRO A 434 " pdb=" OG SER A 437 " model vdw 2.252 3.040 nonbonded pdb=" O PRO C 434 " pdb=" OG SER C 437 " model vdw 2.252 3.040 nonbonded pdb=" O PRO B 434 " pdb=" OG SER B 437 " model vdw 2.252 3.040 nonbonded pdb=" O PRO D 434 " pdb=" OG SER D 437 " model vdw 2.252 3.040 nonbonded pdb=" OH TYR A 105 " pdb=" O TYR A 196 " model vdw 2.260 3.040 ... (remaining 282021 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 0.040 Extract box with map and model: 0.370 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 32.440 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 33468 Z= 0.150 Angle : 0.657 7.262 45660 Z= 0.369 Chirality : 0.047 0.253 4752 Planarity : 0.005 0.046 6036 Dihedral : 13.276 88.687 12076 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: -0.31 (0.13), residues: 4036 helix: -0.98 (0.21), residues: 496 sheet: 0.74 (0.14), residues: 1300 loop : -0.55 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 336 TYR 0.022 0.002 TYR B 100 PHE 0.019 0.001 PHE B 549 TRP 0.025 0.002 TRP A 523 HIS 0.006 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00308 (33468) covalent geometry : angle 0.65735 (45660) hydrogen bonds : bond 0.14755 ( 1160) hydrogen bonds : angle 6.44523 ( 3180) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 682 time to evaluate : 1.315 Fit side-chains REVERT: A 46 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6874 (mtt180) REVERT: A 102 ASN cc_start: 0.7754 (t0) cc_final: 0.7370 (t0) REVERT: A 221 GLN cc_start: 0.8002 (mt0) cc_final: 0.7770 (mt0) REVERT: A 281 GLU cc_start: 0.7913 (mp0) cc_final: 0.7609 (mp0) REVERT: A 584 PRO cc_start: 0.7550 (Cg_endo) cc_final: 0.7066 (Cg_exo) REVERT: A 782 ASP cc_start: 0.8059 (m-30) cc_final: 0.7722 (m-30) REVERT: A 925 MET cc_start: 0.8214 (mmm) cc_final: 0.7812 (mmm) REVERT: B 46 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6871 (mtt180) REVERT: B 102 ASN cc_start: 0.7760 (t0) cc_final: 0.7378 (t0) REVERT: B 221 GLN cc_start: 0.7998 (mt0) cc_final: 0.7763 (mt0) REVERT: B 245 GLN cc_start: 0.7042 (mt0) cc_final: 0.6839 (mt0) REVERT: B 281 GLU cc_start: 0.7913 (mp0) cc_final: 0.7608 (mp0) REVERT: B 584 PRO cc_start: 0.7545 (Cg_endo) cc_final: 0.7061 (Cg_exo) REVERT: B 782 ASP cc_start: 0.8066 (m-30) cc_final: 0.7729 (m-30) REVERT: B 925 MET cc_start: 0.8213 (mmm) cc_final: 0.7812 (mmm) REVERT: C 46 ARG cc_start: 0.7088 (mtt90) cc_final: 0.6871 (mtt180) REVERT: C 102 ASN cc_start: 0.7759 (t0) cc_final: 0.7375 (t0) REVERT: C 221 GLN cc_start: 0.8001 (mt0) cc_final: 0.7766 (mt0) REVERT: C 245 GLN cc_start: 0.7042 (mt0) cc_final: 0.6838 (mt0) REVERT: C 281 GLU cc_start: 0.7914 (mp0) cc_final: 0.7613 (mp0) REVERT: C 584 PRO cc_start: 0.7545 (Cg_endo) cc_final: 0.7059 (Cg_exo) REVERT: C 782 ASP cc_start: 0.8058 (m-30) cc_final: 0.7722 (m-30) REVERT: C 925 MET cc_start: 0.8210 (mmm) cc_final: 0.7814 (mmm) REVERT: D 46 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6873 (mtt180) REVERT: D 102 ASN cc_start: 0.7763 (t0) cc_final: 0.7377 (t0) REVERT: D 221 GLN cc_start: 0.8002 (mt0) cc_final: 0.7772 (mt0) REVERT: D 245 GLN cc_start: 0.7041 (mt0) cc_final: 0.6840 (mt0) REVERT: D 281 GLU cc_start: 0.7915 (mp0) cc_final: 0.7609 (mp0) REVERT: D 584 PRO cc_start: 0.7546 (Cg_endo) cc_final: 0.7060 (Cg_exo) REVERT: D 782 ASP cc_start: 0.8058 (m-30) cc_final: 0.7721 (m-30) REVERT: D 925 MET cc_start: 0.8213 (mmm) cc_final: 0.7810 (mmm) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 0.8935 time to fit residues: 697.5866 Evaluate side-chains 534 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 534 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.0970 chunk 401 optimal weight: 9.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 510 GLN A 623 GLN A 739 HIS A 761 GLN A 903 GLN B 395 HIS B 510 GLN B 623 GLN B 739 HIS B 761 GLN B 903 GLN C 395 HIS C 510 GLN C 623 GLN C 739 HIS C 761 GLN C 903 GLN D 395 HIS D 510 GLN D 623 GLN D 739 HIS D 761 GLN D 903 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.127034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.109296 restraints weight = 38787.813| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 1.40 r_work: 0.3000 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33468 Z= 0.130 Angle : 0.528 5.592 45660 Z= 0.279 Chirality : 0.043 0.147 4752 Planarity : 0.004 0.039 6036 Dihedral : 4.646 26.738 4428 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.86 % Allowed : 9.78 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.08 (0.14), residues: 4036 helix: -0.12 (0.23), residues: 520 sheet: 0.69 (0.14), residues: 1360 loop : -0.25 (0.14), residues: 2156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.022 0.002 TYR B 100 PHE 0.007 0.001 PHE B 143 TRP 0.020 0.001 TRP A 553 HIS 0.007 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00291 (33468) covalent geometry : angle 0.52838 (45660) hydrogen bonds : bond 0.03514 ( 1160) hydrogen bonds : angle 4.94669 ( 3180) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 574 time to evaluate : 1.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7434 (ttm170) REVERT: A 77 ASP cc_start: 0.6348 (p0) cc_final: 0.6098 (p0) REVERT: A 102 ASN cc_start: 0.8145 (t0) cc_final: 0.7459 (t0) REVERT: A 170 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7947 (mt-10) REVERT: A 281 GLU cc_start: 0.7776 (mp0) cc_final: 0.7549 (mp0) REVERT: A 296 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6877 (mm-30) REVERT: A 338 GLU cc_start: 0.8032 (OUTLIER) cc_final: 0.7797 (pp20) REVERT: A 584 PRO cc_start: 0.7742 (Cg_endo) cc_final: 0.7307 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7466 (m-30) cc_final: 0.7078 (m-30) REVERT: A 724 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7149 (tt0) REVERT: A 925 MET cc_start: 0.8260 (mmm) cc_final: 0.7848 (mmm) REVERT: A 965 GLN cc_start: 0.8032 (tp40) cc_final: 0.7642 (tp40) REVERT: B 52 ARG cc_start: 0.7645 (mtp180) cc_final: 0.7441 (ttm170) REVERT: B 77 ASP cc_start: 0.6350 (p0) cc_final: 0.6104 (p0) REVERT: B 102 ASN cc_start: 0.8151 (t0) cc_final: 0.7466 (t0) REVERT: B 170 GLU cc_start: 0.8387 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: B 245 GLN cc_start: 0.7263 (mt0) cc_final: 0.7021 (mt0) REVERT: B 281 GLU cc_start: 0.7796 (mp0) cc_final: 0.7579 (mp0) REVERT: B 296 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6896 (mm-30) REVERT: B 338 GLU cc_start: 0.8039 (OUTLIER) cc_final: 0.7804 (pp20) REVERT: B 584 PRO cc_start: 0.7740 (Cg_endo) cc_final: 0.7305 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7471 (m-30) cc_final: 0.7076 (m-30) REVERT: B 724 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7141 (tt0) REVERT: B 745 MET cc_start: 0.4978 (OUTLIER) cc_final: 0.4740 (tpp) REVERT: B 925 MET cc_start: 0.8269 (mmm) cc_final: 0.7859 (mmm) REVERT: B 942 ARG cc_start: 0.8598 (mmt90) cc_final: 0.8296 (mmm-85) REVERT: B 965 GLN cc_start: 0.8037 (tp40) cc_final: 0.7647 (tp40) REVERT: C 52 ARG cc_start: 0.7646 (mtp180) cc_final: 0.7443 (ttm170) REVERT: C 77 ASP cc_start: 0.6352 (p0) cc_final: 0.6102 (p0) REVERT: C 102 ASN cc_start: 0.8148 (t0) cc_final: 0.7458 (t0) REVERT: C 170 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: C 245 GLN cc_start: 0.7265 (mt0) cc_final: 0.7023 (mt0) REVERT: C 281 GLU cc_start: 0.7790 (mp0) cc_final: 0.7569 (mp0) REVERT: C 296 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6900 (mm-30) REVERT: C 338 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7800 (pp20) REVERT: C 584 PRO cc_start: 0.7737 (Cg_endo) cc_final: 0.7298 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7464 (m-30) cc_final: 0.7066 (m-30) REVERT: C 724 GLU cc_start: 0.7584 (OUTLIER) cc_final: 0.7137 (tt0) REVERT: C 745 MET cc_start: 0.4987 (OUTLIER) cc_final: 0.4744 (tpp) REVERT: C 925 MET cc_start: 0.8264 (mmm) cc_final: 0.7854 (mmm) REVERT: C 942 ARG cc_start: 0.8600 (mmt90) cc_final: 0.8302 (mmm-85) REVERT: C 965 GLN cc_start: 0.8036 (tp40) cc_final: 0.7649 (tp40) REVERT: D 52 ARG cc_start: 0.7644 (mtp180) cc_final: 0.7438 (ttm170) REVERT: D 77 ASP cc_start: 0.6341 (p0) cc_final: 0.6088 (p0) REVERT: D 102 ASN cc_start: 0.8144 (t0) cc_final: 0.7457 (t0) REVERT: D 170 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: D 245 GLN cc_start: 0.7277 (mt0) cc_final: 0.7056 (mt0) REVERT: D 281 GLU cc_start: 0.7791 (mp0) cc_final: 0.7570 (mp0) REVERT: D 296 GLU cc_start: 0.7234 (mm-30) cc_final: 0.6865 (mm-30) REVERT: D 338 GLU cc_start: 0.8030 (OUTLIER) cc_final: 0.7797 (pp20) REVERT: D 584 PRO cc_start: 0.7743 (Cg_endo) cc_final: 0.7311 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7468 (m-30) cc_final: 0.7068 (m-30) REVERT: D 724 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7150 (tt0) REVERT: D 925 MET cc_start: 0.8260 (mmm) cc_final: 0.7850 (mmm) REVERT: D 965 GLN cc_start: 0.8028 (tp40) cc_final: 0.7640 (tp40) outliers start: 99 outliers final: 28 residues processed: 606 average time/residue: 0.8677 time to fit residues: 607.5770 Evaluate side-chains 573 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 531 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 ARG Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 338 GLU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 59 ARG Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 338 GLU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 59 ARG Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 338 GLU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 59 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 338 GLU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 400 optimal weight: 10.0000 chunk 165 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 362 optimal weight: 7.9990 chunk 64 optimal weight: 7.9990 chunk 164 optimal weight: 9.9990 chunk 170 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 387 optimal weight: 10.0000 chunk 172 optimal weight: 0.1980 chunk 147 optimal weight: 5.9990 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 ASN ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 753 ASN A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 89 ASN ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 753 ASN B 761 GLN B 903 GLN B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 761 GLN C 903 GLN C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 89 ASN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 753 ASN D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.122313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.104348 restraints weight = 39111.173| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.40 r_work: 0.2929 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 33468 Z= 0.211 Angle : 0.596 7.215 45660 Z= 0.315 Chirality : 0.046 0.162 4752 Planarity : 0.005 0.049 6036 Dihedral : 5.097 27.241 4428 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.65 % Allowed : 10.68 % Favored : 85.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.07 (0.13), residues: 4036 helix: -0.30 (0.22), residues: 496 sheet: 0.59 (0.14), residues: 1340 loop : -0.12 (0.14), residues: 2200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 237 TYR 0.020 0.002 TYR A 100 PHE 0.012 0.002 PHE C 143 TRP 0.021 0.002 TRP C 553 HIS 0.006 0.001 HIS A 226 Details of bonding type rmsd covalent geometry : bond 0.00485 (33468) covalent geometry : angle 0.59641 (45660) hydrogen bonds : bond 0.04166 ( 1160) hydrogen bonds : angle 5.13472 ( 3180) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 538 time to evaluate : 1.371 Fit side-chains REVERT: A 18 ASN cc_start: 0.8066 (t0) cc_final: 0.7635 (t0) REVERT: A 77 ASP cc_start: 0.6380 (p0) cc_final: 0.6057 (p0) REVERT: A 102 ASN cc_start: 0.8164 (t0) cc_final: 0.7486 (t0) REVERT: A 170 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8152 (mt-10) REVERT: A 281 GLU cc_start: 0.7785 (mp0) cc_final: 0.7555 (mp0) REVERT: A 291 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8212 (mm) REVERT: A 296 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6654 (mm-30) REVERT: A 447 ASP cc_start: 0.8912 (m-30) cc_final: 0.8698 (m-30) REVERT: A 584 PRO cc_start: 0.7846 (Cg_endo) cc_final: 0.7375 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7509 (m-30) cc_final: 0.7162 (m-30) REVERT: A 693 GLN cc_start: 0.8436 (tp40) cc_final: 0.8216 (tm-30) REVERT: A 724 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 770 ILE cc_start: 0.8254 (OUTLIER) cc_final: 0.7858 (mp) REVERT: A 925 MET cc_start: 0.8115 (mmm) cc_final: 0.7655 (mmm) REVERT: A 1006 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: B 18 ASN cc_start: 0.8060 (t0) cc_final: 0.7628 (t0) REVERT: B 77 ASP cc_start: 0.6363 (p0) cc_final: 0.6045 (p0) REVERT: B 102 ASN cc_start: 0.8164 (t0) cc_final: 0.7478 (t0) REVERT: B 170 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: B 245 GLN cc_start: 0.7312 (mt0) cc_final: 0.7085 (mt0) REVERT: B 281 GLU cc_start: 0.7795 (mp0) cc_final: 0.7572 (mp0) REVERT: B 291 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8214 (mm) REVERT: B 296 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6668 (mm-30) REVERT: B 447 ASP cc_start: 0.8907 (m-30) cc_final: 0.8695 (m-30) REVERT: B 584 PRO cc_start: 0.7850 (Cg_endo) cc_final: 0.7381 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7511 (m-30) cc_final: 0.7162 (m-30) REVERT: B 693 GLN cc_start: 0.8441 (tp40) cc_final: 0.8217 (tm-30) REVERT: B 724 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.7343 (tt0) REVERT: B 770 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7864 (mp) REVERT: B 925 MET cc_start: 0.8106 (mmm) cc_final: 0.7654 (mmm) REVERT: B 1006 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7602 (pt0) REVERT: C 18 ASN cc_start: 0.8070 (t0) cc_final: 0.7637 (t0) REVERT: C 77 ASP cc_start: 0.6376 (p0) cc_final: 0.6054 (p0) REVERT: C 102 ASN cc_start: 0.8160 (t0) cc_final: 0.7481 (t0) REVERT: C 170 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: C 245 GLN cc_start: 0.7307 (mt0) cc_final: 0.7079 (mt0) REVERT: C 281 GLU cc_start: 0.7791 (mp0) cc_final: 0.7568 (mp0) REVERT: C 291 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8215 (mm) REVERT: C 296 GLU cc_start: 0.7257 (mm-30) cc_final: 0.6665 (mm-30) REVERT: C 447 ASP cc_start: 0.8906 (m-30) cc_final: 0.8696 (m-30) REVERT: C 584 PRO cc_start: 0.7854 (Cg_endo) cc_final: 0.7381 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7511 (m-30) cc_final: 0.7166 (m-30) REVERT: C 693 GLN cc_start: 0.8435 (tp40) cc_final: 0.8208 (tm-30) REVERT: C 724 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7335 (tt0) REVERT: C 770 ILE cc_start: 0.8291 (OUTLIER) cc_final: 0.7879 (mp) REVERT: C 925 MET cc_start: 0.8118 (mmm) cc_final: 0.7658 (mmm) REVERT: C 1006 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: D 18 ASN cc_start: 0.8069 (t0) cc_final: 0.7637 (t0) REVERT: D 77 ASP cc_start: 0.6386 (p0) cc_final: 0.6056 (p0) REVERT: D 102 ASN cc_start: 0.8161 (t0) cc_final: 0.7478 (t0) REVERT: D 170 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8158 (mt-10) REVERT: D 245 GLN cc_start: 0.7312 (mt0) cc_final: 0.7087 (mt0) REVERT: D 281 GLU cc_start: 0.7803 (mp0) cc_final: 0.7580 (mp0) REVERT: D 291 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8214 (mm) REVERT: D 296 GLU cc_start: 0.7240 (mm-30) cc_final: 0.6640 (mm-30) REVERT: D 447 ASP cc_start: 0.8912 (m-30) cc_final: 0.8698 (m-30) REVERT: D 584 PRO cc_start: 0.7847 (Cg_endo) cc_final: 0.7375 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7499 (m-30) cc_final: 0.7153 (m-30) REVERT: D 693 GLN cc_start: 0.8435 (tp40) cc_final: 0.8212 (tm-30) REVERT: D 724 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7350 (tt0) REVERT: D 770 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7857 (mp) REVERT: D 925 MET cc_start: 0.8120 (mmm) cc_final: 0.7662 (mmm) REVERT: D 1006 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7602 (pt0) outliers start: 126 outliers final: 54 residues processed: 588 average time/residue: 0.8548 time to fit residues: 585.8378 Evaluate side-chains 592 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 518 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 345 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 62 optimal weight: 6.9990 chunk 124 optimal weight: 8.9990 chunk 136 optimal weight: 9.9990 chunk 170 optimal weight: 0.0570 chunk 142 optimal weight: 2.9990 chunk 393 optimal weight: 9.9990 chunk 197 optimal weight: 1.9990 chunk 390 optimal weight: 0.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 739 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.125464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.107877 restraints weight = 39086.806| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.39 r_work: 0.2982 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 33468 Z= 0.101 Angle : 0.488 6.255 45660 Z= 0.258 Chirality : 0.043 0.149 4752 Planarity : 0.004 0.051 6036 Dihedral : 4.631 24.484 4428 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.26 % Allowed : 12.93 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.25 (0.14), residues: 4036 helix: 0.12 (0.23), residues: 520 sheet: 0.63 (0.14), residues: 1380 loop : -0.03 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 404 TYR 0.018 0.001 TYR B 100 PHE 0.008 0.001 PHE A 143 TRP 0.025 0.001 TRP D 553 HIS 0.005 0.001 HIS D 226 Details of bonding type rmsd covalent geometry : bond 0.00225 (33468) covalent geometry : angle 0.48771 (45660) hydrogen bonds : bond 0.03040 ( 1160) hydrogen bonds : angle 4.80343 ( 3180) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 556 time to evaluate : 1.249 Fit side-chains REVERT: A 18 ASN cc_start: 0.7933 (t0) cc_final: 0.7515 (t0) REVERT: A 77 ASP cc_start: 0.6197 (p0) cc_final: 0.5843 (p0) REVERT: A 102 ASN cc_start: 0.8099 (t0) cc_final: 0.7450 (t0) REVERT: A 170 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7938 (mt-10) REVERT: A 187 MET cc_start: 0.9047 (ttm) cc_final: 0.8615 (ttm) REVERT: A 281 GLU cc_start: 0.7675 (mp0) cc_final: 0.7294 (mp0) REVERT: A 530 THR cc_start: 0.7671 (t) cc_final: 0.7385 (p) REVERT: A 584 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7236 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7479 (m-30) cc_final: 0.7256 (m-30) REVERT: A 693 GLN cc_start: 0.8452 (tp40) cc_final: 0.8195 (tm-30) REVERT: A 724 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7283 (tt0) REVERT: A 770 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 857 ARG cc_start: 0.8283 (ttt-90) cc_final: 0.8028 (tmt170) REVERT: A 925 MET cc_start: 0.8102 (mmm) cc_final: 0.7601 (mmm) REVERT: A 1006 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.7467 (pt0) REVERT: B 18 ASN cc_start: 0.7933 (t0) cc_final: 0.7517 (t0) REVERT: B 77 ASP cc_start: 0.6199 (p0) cc_final: 0.5839 (p0) REVERT: B 102 ASN cc_start: 0.8105 (t0) cc_final: 0.7453 (t0) REVERT: B 170 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7949 (mt-10) REVERT: B 187 MET cc_start: 0.9044 (ttm) cc_final: 0.8613 (ttm) REVERT: B 281 GLU cc_start: 0.7699 (mp0) cc_final: 0.7331 (mp0) REVERT: B 530 THR cc_start: 0.7670 (t) cc_final: 0.7382 (p) REVERT: B 584 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7236 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7469 (m-30) cc_final: 0.7250 (m-30) REVERT: B 693 GLN cc_start: 0.8441 (tp40) cc_final: 0.8182 (tm-30) REVERT: B 724 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: B 770 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7849 (mp) REVERT: B 857 ARG cc_start: 0.8276 (ttt-90) cc_final: 0.8024 (tmt170) REVERT: B 925 MET cc_start: 0.8108 (mmm) cc_final: 0.7612 (mmm) REVERT: B 1006 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7465 (pt0) REVERT: C 18 ASN cc_start: 0.7929 (t0) cc_final: 0.7508 (t0) REVERT: C 77 ASP cc_start: 0.6210 (p0) cc_final: 0.5847 (p0) REVERT: C 102 ASN cc_start: 0.8096 (t0) cc_final: 0.7443 (t0) REVERT: C 170 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.7943 (mt-10) REVERT: C 187 MET cc_start: 0.9038 (ttm) cc_final: 0.8603 (ttm) REVERT: C 281 GLU cc_start: 0.7690 (mp0) cc_final: 0.7319 (mp0) REVERT: C 530 THR cc_start: 0.7676 (t) cc_final: 0.7389 (p) REVERT: C 584 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7237 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7483 (m-30) cc_final: 0.7264 (m-30) REVERT: C 693 GLN cc_start: 0.8450 (tp40) cc_final: 0.8190 (tm-30) REVERT: C 724 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7291 (tt0) REVERT: C 770 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7848 (mp) REVERT: C 857 ARG cc_start: 0.8274 (ttt-90) cc_final: 0.8022 (tmt170) REVERT: C 925 MET cc_start: 0.8102 (mmm) cc_final: 0.7604 (mmm) REVERT: C 1006 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7461 (pt0) REVERT: D 18 ASN cc_start: 0.7931 (t0) cc_final: 0.7512 (t0) REVERT: D 77 ASP cc_start: 0.6219 (p0) cc_final: 0.5860 (p0) REVERT: D 102 ASN cc_start: 0.8107 (t0) cc_final: 0.7456 (t0) REVERT: D 170 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.7940 (mt-10) REVERT: D 187 MET cc_start: 0.9031 (ttm) cc_final: 0.8597 (ttm) REVERT: D 245 GLN cc_start: 0.7057 (mt0) cc_final: 0.6855 (mt0) REVERT: D 281 GLU cc_start: 0.7691 (mp0) cc_final: 0.7322 (mp0) REVERT: D 530 THR cc_start: 0.7670 (t) cc_final: 0.7382 (p) REVERT: D 584 PRO cc_start: 0.7692 (Cg_endo) cc_final: 0.7238 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7474 (m-30) cc_final: 0.7250 (m-30) REVERT: D 693 GLN cc_start: 0.8454 (tp40) cc_final: 0.8197 (tm-30) REVERT: D 724 GLU cc_start: 0.7650 (OUTLIER) cc_final: 0.7281 (tt0) REVERT: D 770 ILE cc_start: 0.8228 (OUTLIER) cc_final: 0.7842 (mp) REVERT: D 857 ARG cc_start: 0.8277 (ttt-90) cc_final: 0.8025 (tmt170) REVERT: D 925 MET cc_start: 0.8100 (mmm) cc_final: 0.7601 (mmm) REVERT: D 1006 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7448 (pt0) outliers start: 78 outliers final: 36 residues processed: 588 average time/residue: 0.8600 time to fit residues: 585.0426 Evaluate side-chains 567 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 515 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 177 optimal weight: 10.0000 chunk 307 optimal weight: 9.9990 chunk 358 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 132 optimal weight: 5.9990 chunk 210 optimal weight: 9.9990 chunk 312 optimal weight: 0.5980 chunk 191 optimal weight: 6.9990 chunk 166 optimal weight: 2.9990 chunk 241 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 221 GLN ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 221 GLN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.122071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.103737 restraints weight = 38969.180| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.46 r_work: 0.2915 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 33468 Z= 0.223 Angle : 0.602 8.138 45660 Z= 0.316 Chirality : 0.047 0.155 4752 Planarity : 0.005 0.054 6036 Dihedral : 5.105 25.569 4428 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 3.53 % Allowed : 13.40 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.20 (0.13), residues: 4036 helix: 0.09 (0.23), residues: 464 sheet: 0.58 (0.14), residues: 1340 loop : -0.04 (0.14), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 52 TYR 0.020 0.002 TYR B 100 PHE 0.013 0.002 PHE B 143 TRP 0.022 0.002 TRP D 553 HIS 0.005 0.001 HIS C 226 Details of bonding type rmsd covalent geometry : bond 0.00517 (33468) covalent geometry : angle 0.60190 (45660) hydrogen bonds : bond 0.04028 ( 1160) hydrogen bonds : angle 5.12412 ( 3180) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 536 time to evaluate : 1.383 Fit side-chains REVERT: A 18 ASN cc_start: 0.8025 (t0) cc_final: 0.7595 (t0) REVERT: A 77 ASP cc_start: 0.6312 (p0) cc_final: 0.5930 (p0) REVERT: A 102 ASN cc_start: 0.8149 (t0) cc_final: 0.7428 (t0) REVERT: A 128 ASN cc_start: 0.7848 (OUTLIER) cc_final: 0.7573 (m110) REVERT: A 170 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8172 (mt-10) REVERT: A 277 GLU cc_start: 0.7103 (mm-30) cc_final: 0.5997 (pp20) REVERT: A 278 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7620 (mp) REVERT: A 280 ASP cc_start: 0.6465 (m-30) cc_final: 0.6184 (m-30) REVERT: A 281 GLU cc_start: 0.7682 (mp0) cc_final: 0.7437 (mp0) REVERT: A 296 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6689 (mm-30) REVERT: A 530 THR cc_start: 0.7861 (t) cc_final: 0.7534 (p) REVERT: A 584 PRO cc_start: 0.7790 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7458 (m-30) cc_final: 0.7173 (m-30) REVERT: A 693 GLN cc_start: 0.8436 (tp40) cc_final: 0.8217 (tm-30) REVERT: A 724 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: A 770 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7836 (mp) REVERT: A 925 MET cc_start: 0.8146 (mmm) cc_final: 0.7772 (mmm) REVERT: A 1006 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7593 (pt0) REVERT: B 18 ASN cc_start: 0.8023 (t0) cc_final: 0.7599 (t0) REVERT: B 77 ASP cc_start: 0.6321 (p0) cc_final: 0.5942 (p0) REVERT: B 102 ASN cc_start: 0.8145 (t0) cc_final: 0.7413 (t0) REVERT: B 128 ASN cc_start: 0.7851 (OUTLIER) cc_final: 0.7576 (m110) REVERT: B 170 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: B 278 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7688 (mp) REVERT: B 280 ASP cc_start: 0.6476 (m-30) cc_final: 0.6194 (m-30) REVERT: B 281 GLU cc_start: 0.7745 (mp0) cc_final: 0.7506 (mp0) REVERT: B 296 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6704 (mm-30) REVERT: B 530 THR cc_start: 0.7859 (t) cc_final: 0.7528 (p) REVERT: B 584 PRO cc_start: 0.7790 (Cg_endo) cc_final: 0.7312 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7457 (m-30) cc_final: 0.7164 (m-30) REVERT: B 693 GLN cc_start: 0.8438 (tp40) cc_final: 0.8214 (tm-30) REVERT: B 724 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: B 770 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7843 (mp) REVERT: B 925 MET cc_start: 0.8157 (mmm) cc_final: 0.7789 (mmm) REVERT: B 1006 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: C 18 ASN cc_start: 0.8024 (t0) cc_final: 0.7588 (t0) REVERT: C 77 ASP cc_start: 0.6326 (p0) cc_final: 0.5937 (p0) REVERT: C 102 ASN cc_start: 0.8144 (t0) cc_final: 0.7418 (t0) REVERT: C 128 ASN cc_start: 0.7853 (OUTLIER) cc_final: 0.7576 (m110) REVERT: C 170 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: C 278 ILE cc_start: 0.8193 (OUTLIER) cc_final: 0.7679 (mp) REVERT: C 280 ASP cc_start: 0.6468 (m-30) cc_final: 0.6187 (m-30) REVERT: C 281 GLU cc_start: 0.7736 (mp0) cc_final: 0.7493 (mp0) REVERT: C 296 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6706 (mm-30) REVERT: C 530 THR cc_start: 0.7866 (t) cc_final: 0.7536 (p) REVERT: C 584 PRO cc_start: 0.7792 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7456 (m-30) cc_final: 0.7170 (m-30) REVERT: C 693 GLN cc_start: 0.8436 (tp40) cc_final: 0.8209 (tm-30) REVERT: C 724 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: C 770 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7838 (mp) REVERT: C 925 MET cc_start: 0.8146 (mmm) cc_final: 0.7770 (mmm) REVERT: C 1006 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: D 18 ASN cc_start: 0.8037 (t0) cc_final: 0.7616 (t0) REVERT: D 77 ASP cc_start: 0.6317 (p0) cc_final: 0.5928 (p0) REVERT: D 102 ASN cc_start: 0.8147 (t0) cc_final: 0.7419 (t0) REVERT: D 128 ASN cc_start: 0.7856 (OUTLIER) cc_final: 0.7583 (m110) REVERT: D 170 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: D 245 GLN cc_start: 0.7279 (mt0) cc_final: 0.7019 (mt0) REVERT: D 277 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6026 (pp20) REVERT: D 278 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7627 (mp) REVERT: D 280 ASP cc_start: 0.6489 (m-30) cc_final: 0.6207 (m-30) REVERT: D 281 GLU cc_start: 0.7735 (mp0) cc_final: 0.7497 (mp0) REVERT: D 296 GLU cc_start: 0.7290 (mm-30) cc_final: 0.6660 (mm-30) REVERT: D 530 THR cc_start: 0.7859 (t) cc_final: 0.7533 (p) REVERT: D 584 PRO cc_start: 0.7792 (Cg_endo) cc_final: 0.7312 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7456 (m-30) cc_final: 0.7165 (m-30) REVERT: D 693 GLN cc_start: 0.8437 (tp40) cc_final: 0.8214 (tm-30) REVERT: D 724 GLU cc_start: 0.7789 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: D 770 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7841 (mp) REVERT: D 925 MET cc_start: 0.8153 (mmm) cc_final: 0.7782 (mmm) REVERT: D 1006 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7583 (pt0) outliers start: 122 outliers final: 66 residues processed: 596 average time/residue: 0.8154 time to fit residues: 564.0266 Evaluate side-chains 605 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 515 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 127 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 318 optimal weight: 10.0000 chunk 133 optimal weight: 2.9990 chunk 283 optimal weight: 10.0000 chunk 383 optimal weight: 10.0000 chunk 167 optimal weight: 10.0000 chunk 351 optimal weight: 9.9990 chunk 122 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 chunk 372 optimal weight: 0.2980 overall best weight: 5.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.121617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.103310 restraints weight = 39109.824| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.45 r_work: 0.2903 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 33468 Z= 0.259 Angle : 0.632 8.533 45660 Z= 0.333 Chirality : 0.048 0.156 4752 Planarity : 0.005 0.057 6036 Dihedral : 5.303 26.833 4428 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 4.28 % Allowed : 13.08 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: -0.01 (0.13), residues: 4036 helix: -0.18 (0.23), residues: 464 sheet: 0.44 (0.14), residues: 1344 loop : -0.16 (0.14), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 699 TYR 0.022 0.002 TYR B 100 PHE 0.015 0.002 PHE B 143 TRP 0.026 0.002 TRP D 553 HIS 0.005 0.001 HIS B 226 Details of bonding type rmsd covalent geometry : bond 0.00603 (33468) covalent geometry : angle 0.63202 (45660) hydrogen bonds : bond 0.04225 ( 1160) hydrogen bonds : angle 5.26546 ( 3180) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 148 poor density : 518 time to evaluate : 1.405 Fit side-chains REVERT: A 77 ASP cc_start: 0.6371 (p0) cc_final: 0.5957 (p0) REVERT: A 82 ASP cc_start: 0.6705 (OUTLIER) cc_final: 0.6329 (t70) REVERT: A 102 ASN cc_start: 0.8175 (t0) cc_final: 0.7451 (t0) REVERT: A 128 ASN cc_start: 0.7779 (OUTLIER) cc_final: 0.7502 (m110) REVERT: A 170 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: A 277 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6052 (pp20) REVERT: A 278 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7666 (mp) REVERT: A 280 ASP cc_start: 0.6486 (m-30) cc_final: 0.6200 (m-30) REVERT: A 281 GLU cc_start: 0.7781 (mp0) cc_final: 0.7381 (mp0) REVERT: A 296 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6752 (mm-30) REVERT: A 336 ARG cc_start: 0.8405 (ptt-90) cc_final: 0.8158 (ptt-90) REVERT: A 530 THR cc_start: 0.7888 (t) cc_final: 0.7416 (p) REVERT: A 584 PRO cc_start: 0.7823 (Cg_endo) cc_final: 0.7342 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7481 (m-30) cc_final: 0.7188 (m-30) REVERT: A 693 GLN cc_start: 0.8439 (tp40) cc_final: 0.8183 (tm-30) REVERT: A 724 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7488 (tt0) REVERT: A 770 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7845 (mp) REVERT: A 1006 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7678 (pt0) REVERT: B 77 ASP cc_start: 0.6366 (p0) cc_final: 0.5932 (p0) REVERT: B 82 ASP cc_start: 0.6714 (OUTLIER) cc_final: 0.6324 (t70) REVERT: B 102 ASN cc_start: 0.8174 (t0) cc_final: 0.7442 (t0) REVERT: B 128 ASN cc_start: 0.7781 (OUTLIER) cc_final: 0.7507 (m110) REVERT: B 170 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: B 277 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6093 (pp20) REVERT: B 278 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7670 (mp) REVERT: B 280 ASP cc_start: 0.6500 (m-30) cc_final: 0.6209 (m-30) REVERT: B 281 GLU cc_start: 0.7796 (mp0) cc_final: 0.7504 (mp0) REVERT: B 296 GLU cc_start: 0.7316 (mm-30) cc_final: 0.6766 (mm-30) REVERT: B 336 ARG cc_start: 0.8393 (ptt-90) cc_final: 0.8147 (ptt-90) REVERT: B 530 THR cc_start: 0.7886 (t) cc_final: 0.7408 (p) REVERT: B 584 PRO cc_start: 0.7826 (Cg_endo) cc_final: 0.7342 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7480 (m-30) cc_final: 0.7192 (m-30) REVERT: B 693 GLN cc_start: 0.8436 (tp40) cc_final: 0.8181 (tm-30) REVERT: B 724 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7477 (tt0) REVERT: B 770 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 1006 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7675 (pt0) REVERT: C 77 ASP cc_start: 0.6371 (p0) cc_final: 0.5929 (p0) REVERT: C 82 ASP cc_start: 0.6706 (OUTLIER) cc_final: 0.6319 (t70) REVERT: C 102 ASN cc_start: 0.8173 (t0) cc_final: 0.7442 (t0) REVERT: C 170 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8232 (mt-10) REVERT: C 277 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6076 (pp20) REVERT: C 278 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7659 (mp) REVERT: C 280 ASP cc_start: 0.6487 (m-30) cc_final: 0.6196 (m-30) REVERT: C 281 GLU cc_start: 0.7776 (mp0) cc_final: 0.7477 (mp0) REVERT: C 296 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6762 (mm-30) REVERT: C 336 ARG cc_start: 0.8391 (ptt-90) cc_final: 0.8149 (ptt-90) REVERT: C 530 THR cc_start: 0.7886 (t) cc_final: 0.7410 (p) REVERT: C 584 PRO cc_start: 0.7826 (Cg_endo) cc_final: 0.7342 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7501 (m-30) cc_final: 0.7203 (m-30) REVERT: C 693 GLN cc_start: 0.8437 (tp40) cc_final: 0.8180 (tm-30) REVERT: C 724 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: C 770 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7862 (mp) REVERT: C 1006 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7655 (pt0) REVERT: D 77 ASP cc_start: 0.6372 (p0) cc_final: 0.5953 (p0) REVERT: D 82 ASP cc_start: 0.6743 (OUTLIER) cc_final: 0.6385 (t70) REVERT: D 102 ASN cc_start: 0.8173 (t0) cc_final: 0.7444 (t0) REVERT: D 128 ASN cc_start: 0.7788 (OUTLIER) cc_final: 0.7515 (m110) REVERT: D 170 GLU cc_start: 0.8445 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: D 245 GLN cc_start: 0.7451 (mt0) cc_final: 0.7236 (mt0) REVERT: D 277 GLU cc_start: 0.7142 (mm-30) cc_final: 0.6068 (pp20) REVERT: D 278 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7670 (mp) REVERT: D 280 ASP cc_start: 0.6510 (m-30) cc_final: 0.6222 (m-30) REVERT: D 281 GLU cc_start: 0.7795 (mp0) cc_final: 0.7505 (mp0) REVERT: D 296 GLU cc_start: 0.7288 (mm-30) cc_final: 0.6729 (mm-30) REVERT: D 336 ARG cc_start: 0.8398 (ptt-90) cc_final: 0.8153 (ptt-90) REVERT: D 530 THR cc_start: 0.7886 (t) cc_final: 0.7410 (p) REVERT: D 584 PRO cc_start: 0.7828 (Cg_endo) cc_final: 0.7343 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7495 (m-30) cc_final: 0.7194 (m-30) REVERT: D 693 GLN cc_start: 0.8440 (tp40) cc_final: 0.8185 (tm-30) REVERT: D 724 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7474 (tt0) REVERT: D 770 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7846 (mp) REVERT: D 1006 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7679 (pt0) outliers start: 148 outliers final: 81 residues processed: 578 average time/residue: 0.8712 time to fit residues: 582.5505 Evaluate side-chains 616 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 508 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 499 ILE Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 230 ARG Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 499 ILE Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 111 optimal weight: 6.9990 chunk 14 optimal weight: 9.9990 chunk 332 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 385 optimal weight: 10.0000 chunk 358 optimal weight: 2.9990 chunk 45 optimal weight: 20.0000 chunk 61 optimal weight: 4.9990 chunk 340 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 HIS A 739 HIS A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 HIS B 739 HIS B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 HIS D 739 HIS D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.122044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.103799 restraints weight = 39034.244| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.46 r_work: 0.2914 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 33468 Z= 0.202 Angle : 0.588 7.830 45660 Z= 0.310 Chirality : 0.046 0.156 4752 Planarity : 0.005 0.056 6036 Dihedral : 5.205 25.984 4428 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.88 % Allowed : 14.18 % Favored : 81.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.06 (0.13), residues: 4036 helix: 0.00 (0.23), residues: 464 sheet: 0.57 (0.14), residues: 1288 loop : -0.19 (0.14), residues: 2284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 404 TYR 0.022 0.002 TYR C 100 PHE 0.013 0.002 PHE B 143 TRP 0.028 0.002 TRP C 553 HIS 0.003 0.001 HIS C 949 Details of bonding type rmsd covalent geometry : bond 0.00467 (33468) covalent geometry : angle 0.58780 (45660) hydrogen bonds : bond 0.03857 ( 1160) hydrogen bonds : angle 5.18091 ( 3180) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 656 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 522 time to evaluate : 1.428 Fit side-chains REVERT: A 18 ASN cc_start: 0.8007 (t0) cc_final: 0.7602 (t0) REVERT: A 52 ARG cc_start: 0.7679 (OUTLIER) cc_final: 0.6997 (ttm170) REVERT: A 77 ASP cc_start: 0.6321 (p0) cc_final: 0.5880 (p0) REVERT: A 102 ASN cc_start: 0.8167 (t0) cc_final: 0.7432 (t0) REVERT: A 128 ASN cc_start: 0.7815 (OUTLIER) cc_final: 0.7532 (m110) REVERT: A 170 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: A 278 ILE cc_start: 0.8218 (OUTLIER) cc_final: 0.7969 (mm) REVERT: A 280 ASP cc_start: 0.6479 (m-30) cc_final: 0.6212 (m-30) REVERT: A 281 GLU cc_start: 0.7752 (mp0) cc_final: 0.7407 (mp0) REVERT: A 296 GLU cc_start: 0.7262 (mm-30) cc_final: 0.6770 (mm-30) REVERT: A 530 THR cc_start: 0.7850 (t) cc_final: 0.7476 (p) REVERT: A 542 MET cc_start: 0.8605 (ttt) cc_final: 0.8260 (ttt) REVERT: A 584 PRO cc_start: 0.7823 (Cg_endo) cc_final: 0.7344 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7372 (m-30) cc_final: 0.7100 (m-30) REVERT: A 693 GLN cc_start: 0.8432 (tp40) cc_final: 0.8183 (tm-30) REVERT: A 724 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7482 (tt0) REVERT: A 770 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7853 (mp) REVERT: A 1006 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: B 18 ASN cc_start: 0.8006 (t0) cc_final: 0.7606 (t0) REVERT: B 52 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6982 (ttm170) REVERT: B 77 ASP cc_start: 0.6331 (p0) cc_final: 0.5888 (p0) REVERT: B 82 ASP cc_start: 0.6682 (OUTLIER) cc_final: 0.6326 (t70) REVERT: B 102 ASN cc_start: 0.8161 (t0) cc_final: 0.7420 (t0) REVERT: B 128 ASN cc_start: 0.7808 (OUTLIER) cc_final: 0.7523 (m110) REVERT: B 170 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: B 278 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7968 (mm) REVERT: B 280 ASP cc_start: 0.6485 (m-30) cc_final: 0.6217 (m-30) REVERT: B 281 GLU cc_start: 0.7768 (mp0) cc_final: 0.7426 (mp0) REVERT: B 296 GLU cc_start: 0.7311 (mm-30) cc_final: 0.6816 (mm-30) REVERT: B 530 THR cc_start: 0.7850 (t) cc_final: 0.7480 (p) REVERT: B 542 MET cc_start: 0.8610 (ttt) cc_final: 0.8275 (ttt) REVERT: B 584 PRO cc_start: 0.7821 (Cg_endo) cc_final: 0.7343 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7366 (m-30) cc_final: 0.7091 (m-30) REVERT: B 693 GLN cc_start: 0.8429 (tp40) cc_final: 0.8183 (tm-30) REVERT: B 724 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7469 (tt0) REVERT: B 770 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 1006 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: C 18 ASN cc_start: 0.8012 (t0) cc_final: 0.7611 (t0) REVERT: C 52 ARG cc_start: 0.7668 (OUTLIER) cc_final: 0.6982 (ttm170) REVERT: C 77 ASP cc_start: 0.6327 (p0) cc_final: 0.5870 (p0) REVERT: C 82 ASP cc_start: 0.6681 (OUTLIER) cc_final: 0.6321 (t70) REVERT: C 102 ASN cc_start: 0.8163 (t0) cc_final: 0.7426 (t0) REVERT: C 128 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7461 (m110) REVERT: C 170 GLU cc_start: 0.8453 (OUTLIER) cc_final: 0.8207 (mt-10) REVERT: C 278 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7965 (mm) REVERT: C 280 ASP cc_start: 0.6481 (m-30) cc_final: 0.6215 (m-30) REVERT: C 281 GLU cc_start: 0.7759 (mp0) cc_final: 0.7418 (mp0) REVERT: C 296 GLU cc_start: 0.7274 (mm-30) cc_final: 0.6780 (mm-30) REVERT: C 530 THR cc_start: 0.7853 (t) cc_final: 0.7479 (p) REVERT: C 542 MET cc_start: 0.8613 (ttt) cc_final: 0.8275 (ttt) REVERT: C 584 PRO cc_start: 0.7823 (Cg_endo) cc_final: 0.7343 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7368 (m-30) cc_final: 0.7096 (m-30) REVERT: C 693 GLN cc_start: 0.8427 (tp40) cc_final: 0.8180 (tm-30) REVERT: C 724 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7476 (tt0) REVERT: C 770 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7862 (mp) REVERT: C 1006 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7636 (pt0) REVERT: D 18 ASN cc_start: 0.8014 (t0) cc_final: 0.7619 (t0) REVERT: D 52 ARG cc_start: 0.7670 (OUTLIER) cc_final: 0.6985 (ttm170) REVERT: D 77 ASP cc_start: 0.6329 (p0) cc_final: 0.5876 (p0) REVERT: D 82 ASP cc_start: 0.6728 (OUTLIER) cc_final: 0.6380 (t70) REVERT: D 102 ASN cc_start: 0.8168 (t0) cc_final: 0.7429 (t0) REVERT: D 128 ASN cc_start: 0.7814 (OUTLIER) cc_final: 0.7530 (m110) REVERT: D 170 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: D 278 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7966 (mm) REVERT: D 280 ASP cc_start: 0.6502 (m-30) cc_final: 0.6237 (m-30) REVERT: D 281 GLU cc_start: 0.7767 (mp0) cc_final: 0.7429 (mp0) REVERT: D 296 GLU cc_start: 0.7281 (mm-30) cc_final: 0.6778 (mm-30) REVERT: D 530 THR cc_start: 0.7850 (t) cc_final: 0.7480 (p) REVERT: D 542 MET cc_start: 0.8608 (ttt) cc_final: 0.8262 (ttt) REVERT: D 584 PRO cc_start: 0.7824 (Cg_endo) cc_final: 0.7346 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7369 (m-30) cc_final: 0.7091 (m-30) REVERT: D 693 GLN cc_start: 0.8439 (tp40) cc_final: 0.8192 (tm-30) REVERT: D 724 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: D 770 ILE cc_start: 0.8285 (OUTLIER) cc_final: 0.7859 (mp) REVERT: D 1006 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7655 (pt0) outliers start: 134 outliers final: 77 residues processed: 584 average time/residue: 0.8672 time to fit residues: 584.6057 Evaluate side-chains 622 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 514 time to evaluate : 1.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 436 MET Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 82 ASP Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 436 MET Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 82 ASP Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 82 ASP Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 436 MET Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 942 ARG Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 98 optimal weight: 9.9990 chunk 382 optimal weight: 1.9990 chunk 326 optimal weight: 20.0000 chunk 378 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 112 optimal weight: 6.9990 chunk 317 optimal weight: 6.9990 chunk 45 optimal weight: 20.0000 chunk 207 optimal weight: 0.0870 chunk 46 optimal weight: 0.9980 chunk 228 optimal weight: 0.4980 overall best weight: 0.8760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 739 HIS A 903 GLN A 945 ASN A 956 GLN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 739 HIS B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 739 HIS C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 245 GLN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN D 739 HIS D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.125064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.107456 restraints weight = 39084.377| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.39 r_work: 0.2973 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 33468 Z= 0.099 Angle : 0.502 6.370 45660 Z= 0.266 Chirality : 0.043 0.149 4752 Planarity : 0.004 0.053 6036 Dihedral : 4.767 23.024 4428 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.07 % Allowed : 15.22 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.25 (0.14), residues: 4036 helix: 0.30 (0.24), residues: 496 sheet: 0.52 (0.14), residues: 1380 loop : 0.01 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 404 TYR 0.018 0.001 TYR D 100 PHE 0.009 0.001 PHE A 143 TRP 0.033 0.001 TRP C 553 HIS 0.004 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00221 (33468) covalent geometry : angle 0.50235 (45660) hydrogen bonds : bond 0.02983 ( 1160) hydrogen bonds : angle 4.87029 ( 3180) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 559 time to evaluate : 1.409 Fit side-chains REVERT: A 77 ASP cc_start: 0.6281 (p0) cc_final: 0.5810 (p0) REVERT: A 102 ASN cc_start: 0.8132 (t0) cc_final: 0.7427 (t0) REVERT: A 170 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.7971 (mt-10) REVERT: A 187 MET cc_start: 0.9050 (ttm) cc_final: 0.8708 (ttm) REVERT: A 277 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6212 (mm-30) REVERT: A 296 GLU cc_start: 0.7309 (mm-30) cc_final: 0.6814 (mm-30) REVERT: A 336 ARG cc_start: 0.8347 (ptt-90) cc_final: 0.8126 (ptt-90) REVERT: A 530 THR cc_start: 0.7876 (t) cc_final: 0.7530 (p) REVERT: A 542 MET cc_start: 0.8593 (ttt) cc_final: 0.8248 (ttt) REVERT: A 584 PRO cc_start: 0.7711 (Cg_endo) cc_final: 0.7223 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7467 (m-30) cc_final: 0.7198 (m-30) REVERT: A 599 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.6686 (pmt-80) REVERT: A 693 GLN cc_start: 0.8422 (tp40) cc_final: 0.8157 (tm-30) REVERT: A 724 GLU cc_start: 0.7664 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: A 745 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.5460 (tpp) REVERT: A 770 ILE cc_start: 0.8271 (OUTLIER) cc_final: 0.7911 (mp) REVERT: A 1006 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: B 77 ASP cc_start: 0.6286 (p0) cc_final: 0.5822 (p0) REVERT: B 102 ASN cc_start: 0.8128 (t0) cc_final: 0.7422 (t0) REVERT: B 170 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7984 (mt-10) REVERT: B 187 MET cc_start: 0.9054 (ttm) cc_final: 0.8706 (ttm) REVERT: B 277 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6226 (mm-30) REVERT: B 296 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6799 (mm-30) REVERT: B 530 THR cc_start: 0.7874 (t) cc_final: 0.7523 (p) REVERT: B 542 MET cc_start: 0.8594 (ttt) cc_final: 0.8277 (ttt) REVERT: B 584 PRO cc_start: 0.7704 (Cg_endo) cc_final: 0.7215 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7454 (m-30) cc_final: 0.7190 (m-30) REVERT: B 599 ARG cc_start: 0.7472 (OUTLIER) cc_final: 0.6697 (pmt-80) REVERT: B 693 GLN cc_start: 0.8422 (tp40) cc_final: 0.8159 (tm-30) REVERT: B 724 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7317 (tt0) REVERT: B 770 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7939 (mp) REVERT: B 1006 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: C 77 ASP cc_start: 0.6299 (p0) cc_final: 0.5834 (p0) REVERT: C 102 ASN cc_start: 0.8127 (t0) cc_final: 0.7416 (t0) REVERT: C 128 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7549 (m110) REVERT: C 170 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.7986 (mt-10) REVERT: C 187 MET cc_start: 0.9050 (ttm) cc_final: 0.8709 (ttm) REVERT: C 277 GLU cc_start: 0.7102 (mm-30) cc_final: 0.6216 (mm-30) REVERT: C 296 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6812 (mm-30) REVERT: C 336 ARG cc_start: 0.8347 (ptt-90) cc_final: 0.8130 (ptt-90) REVERT: C 530 THR cc_start: 0.7876 (t) cc_final: 0.7533 (p) REVERT: C 542 MET cc_start: 0.8600 (ttt) cc_final: 0.8282 (ttt) REVERT: C 584 PRO cc_start: 0.7709 (Cg_endo) cc_final: 0.7219 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7461 (m-30) cc_final: 0.7184 (m-30) REVERT: C 693 GLN cc_start: 0.8417 (tp40) cc_final: 0.8149 (tm-30) REVERT: C 724 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7323 (tt0) REVERT: C 770 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.7931 (mp) REVERT: C 1006 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.7586 (pt0) REVERT: D 77 ASP cc_start: 0.6293 (p0) cc_final: 0.5823 (p0) REVERT: D 102 ASN cc_start: 0.8132 (t0) cc_final: 0.7427 (t0) REVERT: D 170 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.7980 (mt-10) REVERT: D 187 MET cc_start: 0.9053 (ttm) cc_final: 0.8713 (ttm) REVERT: D 277 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6225 (mm-30) REVERT: D 281 GLU cc_start: 0.7681 (mp0) cc_final: 0.7330 (mp0) REVERT: D 296 GLU cc_start: 0.7285 (mm-30) cc_final: 0.6776 (mm-30) REVERT: D 530 THR cc_start: 0.7873 (t) cc_final: 0.7525 (p) REVERT: D 542 MET cc_start: 0.8602 (ttt) cc_final: 0.8287 (ttt) REVERT: D 584 PRO cc_start: 0.7706 (Cg_endo) cc_final: 0.7219 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7431 (m-30) cc_final: 0.7222 (m-30) REVERT: D 599 ARG cc_start: 0.7464 (OUTLIER) cc_final: 0.6656 (pmt-80) REVERT: D 693 GLN cc_start: 0.8422 (tp40) cc_final: 0.8144 (tm-30) REVERT: D 724 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: D 745 MET cc_start: 0.6371 (OUTLIER) cc_final: 0.5453 (tpp) REVERT: D 770 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7925 (mp) REVERT: D 942 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8329 (mmm-85) REVERT: D 1006 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7593 (pt0) outliers start: 106 outliers final: 42 residues processed: 617 average time/residue: 0.8555 time to fit residues: 611.2591 Evaluate side-chains 590 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 525 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 942 ARG Chi-restraints excluded: chain D residue 996 ASP Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 188 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 249 optimal weight: 9.9990 chunk 252 optimal weight: 0.0030 chunk 375 optimal weight: 0.0770 chunk 283 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 126 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 323 optimal weight: 8.9990 overall best weight: 3.4154 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 GLN C 226 HIS ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 739 HIS C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1022 GLN D 226 HIS D 245 GLN ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.123098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.104917 restraints weight = 38719.285| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.45 r_work: 0.2949 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 33468 Z= 0.181 Angle : 0.575 8.070 45660 Z= 0.302 Chirality : 0.045 0.151 4752 Planarity : 0.005 0.055 6036 Dihedral : 5.022 23.479 4428 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.89 % Allowed : 15.60 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.25 (0.14), residues: 4036 helix: 0.30 (0.23), residues: 472 sheet: 0.51 (0.14), residues: 1380 loop : 0.02 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 404 TYR 0.020 0.002 TYR D 100 PHE 0.012 0.001 PHE B 143 TRP 0.023 0.002 TRP C 553 HIS 0.003 0.001 HIS A 840 Details of bonding type rmsd covalent geometry : bond 0.00422 (33468) covalent geometry : angle 0.57488 (45660) hydrogen bonds : bond 0.03622 ( 1160) hydrogen bonds : angle 5.02727 ( 3180) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 512 time to evaluate : 1.387 Fit side-chains REVERT: A 52 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6948 (ttm170) REVERT: A 77 ASP cc_start: 0.6366 (p0) cc_final: 0.5910 (p0) REVERT: A 102 ASN cc_start: 0.8179 (t0) cc_final: 0.7467 (t0) REVERT: A 128 ASN cc_start: 0.7777 (OUTLIER) cc_final: 0.7491 (m110) REVERT: A 170 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: A 277 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6245 (mm-30) REVERT: A 278 ILE cc_start: 0.8201 (OUTLIER) cc_final: 0.7922 (mm) REVERT: A 280 ASP cc_start: 0.6528 (m-30) cc_final: 0.6309 (m-30) REVERT: A 296 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6819 (mm-30) REVERT: A 530 THR cc_start: 0.7864 (t) cc_final: 0.7526 (p) REVERT: A 542 MET cc_start: 0.8611 (ttt) cc_final: 0.8272 (ttt) REVERT: A 584 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7554 (m-30) cc_final: 0.7284 (m-30) REVERT: A 599 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6734 (pmt-80) REVERT: A 693 GLN cc_start: 0.8420 (tp40) cc_final: 0.8179 (tm-30) REVERT: A 724 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7428 (tt0) REVERT: A 770 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 18 ASN cc_start: 0.7989 (t0) cc_final: 0.7590 (t0) REVERT: B 52 ARG cc_start: 0.7598 (OUTLIER) cc_final: 0.6951 (ttm170) REVERT: B 77 ASP cc_start: 0.6372 (p0) cc_final: 0.5897 (p0) REVERT: B 102 ASN cc_start: 0.8172 (t0) cc_final: 0.7458 (t0) REVERT: B 128 ASN cc_start: 0.7773 (OUTLIER) cc_final: 0.7490 (m110) REVERT: B 170 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8169 (mt-10) REVERT: B 187 MET cc_start: 0.9045 (ttm) cc_final: 0.8746 (ttm) REVERT: B 277 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6258 (mm-30) REVERT: B 278 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7921 (mm) REVERT: B 280 ASP cc_start: 0.6540 (m-30) cc_final: 0.6316 (m-30) REVERT: B 296 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6831 (mm-30) REVERT: B 530 THR cc_start: 0.7865 (t) cc_final: 0.7518 (p) REVERT: B 542 MET cc_start: 0.8618 (ttt) cc_final: 0.8289 (ttt) REVERT: B 584 PRO cc_start: 0.7795 (Cg_endo) cc_final: 0.7309 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7549 (m-30) cc_final: 0.7281 (m-30) REVERT: B 599 ARG cc_start: 0.7519 (OUTLIER) cc_final: 0.6740 (pmt-80) REVERT: B 693 GLN cc_start: 0.8428 (tp40) cc_final: 0.8193 (tm-30) REVERT: B 724 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7430 (tt0) REVERT: B 760 ARG cc_start: 0.7605 (mtp180) cc_final: 0.7274 (mmm-85) REVERT: B 770 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7856 (mp) REVERT: C 52 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6928 (ttm170) REVERT: C 77 ASP cc_start: 0.6383 (p0) cc_final: 0.5933 (p0) REVERT: C 102 ASN cc_start: 0.8179 (t0) cc_final: 0.7463 (t0) REVERT: C 128 ASN cc_start: 0.7757 (OUTLIER) cc_final: 0.7461 (m110) REVERT: C 170 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: C 277 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6244 (mm-30) REVERT: C 278 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7918 (mm) REVERT: C 280 ASP cc_start: 0.6542 (m-30) cc_final: 0.6322 (m-30) REVERT: C 296 GLU cc_start: 0.7340 (mm-30) cc_final: 0.6858 (mm-30) REVERT: C 530 THR cc_start: 0.7863 (t) cc_final: 0.7526 (p) REVERT: C 542 MET cc_start: 0.8623 (ttt) cc_final: 0.8291 (ttt) REVERT: C 584 PRO cc_start: 0.7804 (Cg_endo) cc_final: 0.7318 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7572 (m-30) cc_final: 0.7301 (m-30) REVERT: C 599 ARG cc_start: 0.7502 (OUTLIER) cc_final: 0.6671 (pmt-80) REVERT: C 693 GLN cc_start: 0.8425 (tp40) cc_final: 0.8184 (tm-30) REVERT: C 724 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7427 (tt0) REVERT: C 760 ARG cc_start: 0.7619 (mtp180) cc_final: 0.7280 (mmm-85) REVERT: C 770 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7846 (mp) REVERT: D 18 ASN cc_start: 0.7991 (t0) cc_final: 0.7590 (t0) REVERT: D 52 ARG cc_start: 0.7593 (OUTLIER) cc_final: 0.6940 (ttm170) REVERT: D 77 ASP cc_start: 0.6361 (p0) cc_final: 0.5900 (p0) REVERT: D 102 ASN cc_start: 0.8177 (t0) cc_final: 0.7461 (t0) REVERT: D 128 ASN cc_start: 0.7778 (OUTLIER) cc_final: 0.7498 (m110) REVERT: D 170 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8171 (mt-10) REVERT: D 277 GLU cc_start: 0.7155 (mm-30) cc_final: 0.6252 (mm-30) REVERT: D 278 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7931 (mm) REVERT: D 280 ASP cc_start: 0.6487 (m-30) cc_final: 0.6225 (m-30) REVERT: D 281 GLU cc_start: 0.7758 (mp0) cc_final: 0.7325 (mp0) REVERT: D 296 GLU cc_start: 0.7300 (mm-30) cc_final: 0.6806 (mm-30) REVERT: D 530 THR cc_start: 0.7859 (t) cc_final: 0.7515 (p) REVERT: D 542 MET cc_start: 0.8618 (ttt) cc_final: 0.8282 (ttt) REVERT: D 584 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7312 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7557 (m-30) cc_final: 0.7282 (m-30) REVERT: D 599 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.6737 (pmt-80) REVERT: D 693 GLN cc_start: 0.8434 (tp40) cc_final: 0.8196 (tm-30) REVERT: D 724 GLU cc_start: 0.7759 (OUTLIER) cc_final: 0.7422 (tt0) REVERT: D 770 ILE cc_start: 0.8202 (OUTLIER) cc_final: 0.7840 (mp) outliers start: 100 outliers final: 49 residues processed: 565 average time/residue: 0.8643 time to fit residues: 565.4058 Evaluate side-chains 577 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 500 time to evaluate : 1.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 305 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 128 ASN Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 599 ARG Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 969 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 79 optimal weight: 2.9990 chunk 246 optimal weight: 7.9990 chunk 358 optimal weight: 4.9990 chunk 289 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 263 optimal weight: 3.9990 chunk 236 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 205 optimal weight: 0.0050 chunk 284 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 739 HIS C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN D 956 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.123614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.105960 restraints weight = 39206.874| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 1.39 r_work: 0.2953 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 33468 Z= 0.151 Angle : 0.553 7.595 45660 Z= 0.291 Chirality : 0.044 0.151 4752 Planarity : 0.004 0.054 6036 Dihedral : 4.976 22.896 4428 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.95 % Allowed : 15.62 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.26 (0.14), residues: 4036 helix: 0.31 (0.23), residues: 472 sheet: 0.53 (0.14), residues: 1380 loop : 0.01 (0.14), residues: 2184 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 237 TYR 0.020 0.002 TYR C 100 PHE 0.012 0.001 PHE A 143 TRP 0.029 0.002 TRP C 553 HIS 0.003 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00350 (33468) covalent geometry : angle 0.55265 (45660) hydrogen bonds : bond 0.03431 ( 1160) hydrogen bonds : angle 4.97315 ( 3180) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8072 Ramachandran restraints generated. 4036 Oldfield, 0 Emsley, 4036 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 521 time to evaluate : 1.650 Fit side-chains REVERT: A 52 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6923 (ttm170) REVERT: A 77 ASP cc_start: 0.6362 (p0) cc_final: 0.5876 (p0) REVERT: A 102 ASN cc_start: 0.8154 (t0) cc_final: 0.7442 (t0) REVERT: A 128 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7457 (m110) REVERT: A 170 GLU cc_start: 0.8420 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: A 277 GLU cc_start: 0.7130 (mm-30) cc_final: 0.6229 (mm-30) REVERT: A 278 ILE cc_start: 0.8188 (OUTLIER) cc_final: 0.7899 (mm) REVERT: A 296 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6782 (mm-30) REVERT: A 530 THR cc_start: 0.7763 (t) cc_final: 0.7340 (p) REVERT: A 542 MET cc_start: 0.8598 (ttt) cc_final: 0.8262 (ttt) REVERT: A 584 PRO cc_start: 0.7778 (Cg_endo) cc_final: 0.7293 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7518 (m-30) cc_final: 0.7231 (m-30) REVERT: A 599 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6668 (pmt-80) REVERT: A 693 GLN cc_start: 0.8429 (tp40) cc_final: 0.8184 (tm-30) REVERT: A 724 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: A 760 ARG cc_start: 0.7653 (mtp180) cc_final: 0.7343 (mmm-85) REVERT: A 770 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7828 (mp) REVERT: B 52 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6921 (ttm170) REVERT: B 77 ASP cc_start: 0.6363 (p0) cc_final: 0.5878 (p0) REVERT: B 102 ASN cc_start: 0.8140 (t0) cc_final: 0.7426 (t0) REVERT: B 128 ASN cc_start: 0.7727 (OUTLIER) cc_final: 0.7462 (m110) REVERT: B 170 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: B 187 MET cc_start: 0.9043 (ttm) cc_final: 0.8750 (ttm) REVERT: B 277 GLU cc_start: 0.7115 (mm-30) cc_final: 0.6239 (mm-30) REVERT: B 278 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7895 (mm) REVERT: B 296 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6766 (mm-30) REVERT: B 530 THR cc_start: 0.7770 (t) cc_final: 0.7349 (p) REVERT: B 542 MET cc_start: 0.8614 (ttt) cc_final: 0.8287 (ttt) REVERT: B 584 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7510 (m-30) cc_final: 0.7227 (m-30) REVERT: B 599 ARG cc_start: 0.7499 (OUTLIER) cc_final: 0.6669 (pmt-80) REVERT: B 693 GLN cc_start: 0.8434 (tp40) cc_final: 0.8196 (tm-30) REVERT: B 724 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7364 (tt0) REVERT: B 770 ILE cc_start: 0.8216 (OUTLIER) cc_final: 0.7854 (mp) REVERT: C 52 ARG cc_start: 0.7571 (OUTLIER) cc_final: 0.6913 (ttm170) REVERT: C 77 ASP cc_start: 0.6365 (p0) cc_final: 0.5884 (p0) REVERT: C 102 ASN cc_start: 0.8147 (t0) cc_final: 0.7430 (t0) REVERT: C 170 GLU cc_start: 0.8432 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: C 277 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6233 (mm-30) REVERT: C 278 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7895 (mm) REVERT: C 296 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6794 (mm-30) REVERT: C 530 THR cc_start: 0.7767 (t) cc_final: 0.7348 (p) REVERT: C 542 MET cc_start: 0.8614 (ttt) cc_final: 0.8283 (ttt) REVERT: C 584 PRO cc_start: 0.7776 (Cg_endo) cc_final: 0.7289 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7536 (m-30) cc_final: 0.7234 (m-30) REVERT: C 693 GLN cc_start: 0.8429 (tp40) cc_final: 0.8182 (tm-30) REVERT: C 724 GLU cc_start: 0.7700 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: C 760 ARG cc_start: 0.7583 (mtp180) cc_final: 0.7260 (mmm-85) REVERT: C 770 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7928 (mp) REVERT: D 52 ARG cc_start: 0.7578 (OUTLIER) cc_final: 0.6928 (ttm170) REVERT: D 77 ASP cc_start: 0.6318 (p0) cc_final: 0.5823 (p0) REVERT: D 102 ASN cc_start: 0.8150 (t0) cc_final: 0.7436 (t0) REVERT: D 128 ASN cc_start: 0.7728 (OUTLIER) cc_final: 0.7467 (m110) REVERT: D 170 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8133 (mt-10) REVERT: D 277 GLU cc_start: 0.7133 (mm-30) cc_final: 0.6239 (mm-30) REVERT: D 278 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7907 (mm) REVERT: D 280 ASP cc_start: 0.6410 (m-30) cc_final: 0.6157 (m-30) REVERT: D 281 GLU cc_start: 0.7743 (mp0) cc_final: 0.7323 (mp0) REVERT: D 296 GLU cc_start: 0.7305 (mm-30) cc_final: 0.6759 (mm-30) REVERT: D 530 THR cc_start: 0.7765 (t) cc_final: 0.7346 (p) REVERT: D 542 MET cc_start: 0.8612 (ttt) cc_final: 0.8278 (ttt) REVERT: D 584 PRO cc_start: 0.7776 (Cg_endo) cc_final: 0.7290 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7524 (m-30) cc_final: 0.7233 (m-30) REVERT: D 599 ARG cc_start: 0.7471 (OUTLIER) cc_final: 0.6623 (pmt-80) REVERT: D 693 GLN cc_start: 0.8439 (tp40) cc_final: 0.8196 (tm-30) REVERT: D 724 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: D 760 ARG cc_start: 0.7648 (mtp180) cc_final: 0.7333 (mmm-85) REVERT: D 770 ILE cc_start: 0.8290 (OUTLIER) cc_final: 0.7895 (mp) outliers start: 102 outliers final: 51 residues processed: 573 average time/residue: 0.8820 time to fit residues: 583.1128 Evaluate side-chains 581 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 504 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ARG Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 599 ARG Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 745 MET Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 128 ASN Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 599 ARG Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 969 GLU Chi-restraints excluded: chain D residue 52 ARG Chi-restraints excluded: chain D residue 128 ASN Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 305 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 484 VAL Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 599 ARG Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 745 MET Chi-restraints excluded: chain D residue 770 ILE Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 969 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 234 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 0.0670 chunk 84 optimal weight: 6.9990 chunk 176 optimal weight: 8.9990 chunk 403 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 212 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 292 optimal weight: 6.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 GLN A 226 HIS ** A 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 GLN B 226 HIS ** B 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN B 956 GLN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1022 GLN C 163 GLN C 226 HIS ** C 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 739 HIS C 945 ASN C 956 GLN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 GLN D 226 HIS ** D 395 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1022 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.125063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.107421 restraints weight = 39000.169| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.39 r_work: 0.2973 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 3.19 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 33468 Z= 0.118 Angle : 0.526 7.642 45660 Z= 0.277 Chirality : 0.043 0.149 4752 Planarity : 0.004 0.053 6036 Dihedral : 4.823 21.218 4428 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.40 % Allowed : 16.46 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % 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 aren not related in a simple way. whole: 0.28 (0.14), residues: 4036 helix: 0.31 (0.23), residues: 496 sheet: 0.56 (0.14), residues: 1380 loop : 0.01 (0.14), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 237 TYR 0.019 0.001 TYR C 100 PHE 0.009 0.001 PHE D 143 TRP 0.030 0.001 TRP D 553 HIS 0.004 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00271 (33468) covalent geometry : angle 0.52628 (45660) hydrogen bonds : bond 0.03133 ( 1160) hydrogen bonds : angle 4.84428 ( 3180) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12764.13 seconds wall clock time: 218 minutes 19.43 seconds (13099.43 seconds total)