Starting phenix.real_space_refine on Sat Jun 28 00:06:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk8_16092/06_2025/8bk8_16092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk8_16092/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bk8_16092/06_2025/8bk8_16092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk8_16092/06_2025/8bk8_16092.map" model { file = "/net/cci-nas-00/data/ceres_data/8bk8_16092/06_2025/8bk8_16092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk8_16092/06_2025/8bk8_16092.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, D Time building chain proxies: 22.20, per 1000 atoms: 0.68 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: 7.21 Conformation dependent library (CDL) restraints added in 4.2 seconds 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: 5.07 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: 15.98 Time building geometry restraints manager: 8.38 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: 0.21 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 1.260 Check model and map are aligned: 0.250 Set scattering table: 0.330 Process input model: 78.410 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.080 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:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.210 ------------------------------------------------------------------------------- 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 : 5.52 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.025 0.002 TRP A 523 HIS 0.006 0.001 HIS C 395 PHE 0.019 0.001 PHE B 549 TYR 0.022 0.002 TYR B 100 ARG 0.008 0.000 ARG B 336 Details of bonding type rmsd hydrogen bonds : bond 0.14755 ( 1160) hydrogen bonds : angle 6.44523 ( 3180) covalent geometry : bond 0.00308 (33468) covalent geometry : angle 0.65735 (45660) *********************** 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 : 4.498 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: 0.6838 (mt0) REVERT: B 281 GLU cc_start: 0.7913 (mp0) cc_final: 0.7607 (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: 0.6870 (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: 0.7765 (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: 0.7612 (mp0) REVERT: C 584 PRO cc_start: 0.7545 (Cg_endo) cc_final: 0.7058 (Cg_exo) REVERT: C 782 ASP cc_start: 0.8058 (m-30) cc_final: 0.7723 (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: 0.7811 (mmm) outliers start: 0 outliers final: 0 residues processed: 682 average time/residue: 1.7973 time to fit residues: 1408.8260 Evaluate side-chains 538 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 538 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 341 optimal weight: 4.9990 chunk 306 optimal weight: 8.9990 chunk 169 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 10.0000 chunk 316 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 192 optimal weight: 9.9990 chunk 235 optimal weight: 4.9990 chunk 366 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 A 510 GLN A 623 GLN A 739 HIS A 761 GLN A 903 GLN B 89 ASN B 395 HIS B 510 GLN B 623 GLN B 739 HIS B 761 GLN B 903 GLN C 89 ASN C 395 HIS C 510 GLN C 623 GLN C 739 HIS C 761 GLN C 903 GLN D 89 ASN 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: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.121647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.103230 restraints weight = 39073.030| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 1.45 r_work: 0.2912 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 33468 Z= 0.308 Angle : 0.697 8.010 45660 Z= 0.368 Chirality : 0.050 0.170 4752 Planarity : 0.006 0.045 6036 Dihedral : 5.410 30.970 4428 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.56 % Allowed : 8.91 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.13), residues: 4036 helix: -0.69 (0.22), residues: 488 sheet: 0.45 (0.14), residues: 1344 loop : -0.21 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 553 HIS 0.009 0.001 HIS B 395 PHE 0.013 0.002 PHE D 143 TYR 0.026 0.003 TYR B 588 ARG 0.005 0.001 ARG D 599 Details of bonding type rmsd hydrogen bonds : bond 0.05037 ( 1160) hydrogen bonds : angle 5.42832 ( 3180) covalent geometry : bond 0.00714 (33468) covalent geometry : angle 0.69694 (45660) *********************** 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 648 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 525 time to evaluate : 3.592 Fit side-chains REVERT: A 77 ASP cc_start: 0.6312 (p0) cc_final: 0.6078 (p0) REVERT: A 102 ASN cc_start: 0.8229 (t0) cc_final: 0.7537 (t0) REVERT: A 170 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: A 221 GLN cc_start: 0.8346 (mt0) cc_final: 0.8020 (mt0) REVERT: A 280 ASP cc_start: 0.6604 (m-30) cc_final: 0.6282 (m-30) REVERT: A 281 GLU cc_start: 0.7826 (mp0) cc_final: 0.7561 (mp0) REVERT: A 336 ARG cc_start: 0.8343 (ptt-90) cc_final: 0.7978 (ptt-90) REVERT: A 584 PRO cc_start: 0.7860 (Cg_endo) cc_final: 0.7389 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7766 (m-30) cc_final: 0.7287 (m-30) REVERT: A 693 GLN cc_start: 0.8394 (tp40) cc_final: 0.8157 (tm-30) REVERT: A 724 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: A 925 MET cc_start: 0.8185 (mmm) cc_final: 0.7745 (mmm) REVERT: B 77 ASP cc_start: 0.6319 (p0) cc_final: 0.6089 (p0) REVERT: B 102 ASN cc_start: 0.8226 (t0) cc_final: 0.7532 (t0) REVERT: B 170 GLU cc_start: 0.8409 (OUTLIER) cc_final: 0.8198 (mt-10) REVERT: B 245 GLN cc_start: 0.7697 (mt0) cc_final: 0.7288 (mt0) REVERT: B 280 ASP cc_start: 0.6605 (m-30) cc_final: 0.6277 (m-30) REVERT: B 281 GLU cc_start: 0.7830 (mp0) cc_final: 0.7568 (mp0) REVERT: B 336 ARG cc_start: 0.8334 (ptt-90) cc_final: 0.7967 (ptt-90) REVERT: B 584 PRO cc_start: 0.7852 (Cg_endo) cc_final: 0.7380 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7757 (m-30) cc_final: 0.7282 (m-30) REVERT: B 693 GLN cc_start: 0.8393 (tp40) cc_final: 0.8151 (tm-30) REVERT: B 724 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: B 925 MET cc_start: 0.8182 (mmm) cc_final: 0.7745 (mmm) REVERT: C 77 ASP cc_start: 0.6331 (p0) cc_final: 0.6100 (p0) REVERT: C 102 ASN cc_start: 0.8219 (t0) cc_final: 0.7529 (t0) REVERT: C 170 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8205 (mt-10) REVERT: C 245 GLN cc_start: 0.7679 (mt0) cc_final: 0.7274 (mt0) REVERT: C 280 ASP cc_start: 0.6614 (m-30) cc_final: 0.6285 (m-30) REVERT: C 281 GLU cc_start: 0.7826 (mp0) cc_final: 0.7561 (mp0) REVERT: C 336 ARG cc_start: 0.8326 (ptt-90) cc_final: 0.7961 (ptt-90) REVERT: C 584 PRO cc_start: 0.7855 (Cg_endo) cc_final: 0.7380 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7761 (m-30) cc_final: 0.7290 (m-30) REVERT: C 693 GLN cc_start: 0.8389 (tp40) cc_final: 0.8142 (tm-30) REVERT: C 724 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: C 925 MET cc_start: 0.8179 (mmm) cc_final: 0.7740 (mmm) REVERT: D 77 ASP cc_start: 0.6322 (p0) cc_final: 0.6086 (p0) REVERT: D 102 ASN cc_start: 0.8223 (t0) cc_final: 0.7526 (t0) REVERT: D 170 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8211 (mt-10) REVERT: D 245 GLN cc_start: 0.7702 (mt0) cc_final: 0.7306 (mt0) REVERT: D 280 ASP cc_start: 0.6625 (m-30) cc_final: 0.6304 (m-30) REVERT: D 281 GLU cc_start: 0.7832 (mp0) cc_final: 0.7577 (mp0) REVERT: D 336 ARG cc_start: 0.8335 (ptt-90) cc_final: 0.7969 (ptt-90) REVERT: D 584 PRO cc_start: 0.7861 (Cg_endo) cc_final: 0.7390 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7761 (m-30) cc_final: 0.7282 (m-30) REVERT: D 693 GLN cc_start: 0.8392 (tp40) cc_final: 0.8153 (tm-30) REVERT: D 724 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: D 925 MET cc_start: 0.8182 (mmm) cc_final: 0.7745 (mmm) outliers start: 123 outliers final: 44 residues processed: 573 average time/residue: 1.6476 time to fit residues: 1095.5420 Evaluate side-chains 552 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 500 time to evaluate : 3.637 ------------------------------------------------------------------------------- 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 484 VAL Chi-restraints excluded: chain A residue 530 THR Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 754 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 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 484 VAL Chi-restraints excluded: chain B residue 530 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 754 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 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 484 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 754 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 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 484 VAL Chi-restraints excluded: chain D residue 530 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 754 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 315 optimal weight: 0.5980 chunk 129 optimal weight: 10.0000 chunk 354 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 chunk 108 optimal weight: 6.9990 chunk 60 optimal weight: 20.0000 chunk 231 optimal weight: 10.0000 chunk 237 optimal weight: 8.9990 chunk 68 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 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 395 HIS A 739 HIS A 903 GLN A 945 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 GLN B 395 HIS B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 GLN C 395 HIS C 739 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS D 739 HIS D 903 GLN D 945 ASN ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3243 r_free = 0.3243 target = 0.122066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.104505 restraints weight = 39339.751| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.35 r_work: 0.2917 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 33468 Z= 0.223 Angle : 0.613 7.325 45660 Z= 0.323 Chirality : 0.047 0.162 4752 Planarity : 0.005 0.044 6036 Dihedral : 5.315 30.213 4428 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.15 % Allowed : 11.89 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.13), residues: 4036 helix: -0.57 (0.22), residues: 488 sheet: 0.45 (0.14), residues: 1336 loop : -0.16 (0.14), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 553 HIS 0.009 0.001 HIS D 395 PHE 0.014 0.002 PHE D 143 TYR 0.023 0.002 TYR C 100 ARG 0.003 0.001 ARG A 531 Details of bonding type rmsd hydrogen bonds : bond 0.04257 ( 1160) hydrogen bonds : angle 5.28421 ( 3180) covalent geometry : bond 0.00515 (33468) covalent geometry : angle 0.61306 (45660) *********************** 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 631 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 522 time to evaluate : 3.763 Fit side-chains REVERT: A 18 ASN cc_start: 0.8069 (t0) cc_final: 0.7645 (t0) REVERT: A 77 ASP cc_start: 0.6452 (p0) cc_final: 0.6134 (p0) REVERT: A 102 ASN cc_start: 0.8124 (t0) cc_final: 0.7414 (t0) REVERT: A 170 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8175 (mt-10) REVERT: A 245 GLN cc_start: 0.7446 (mt0) cc_final: 0.7205 (mt0) REVERT: A 278 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7939 (mm) REVERT: A 280 ASP cc_start: 0.6623 (m-30) cc_final: 0.6313 (m-30) REVERT: A 281 GLU cc_start: 0.7791 (mp0) cc_final: 0.7572 (mp0) REVERT: A 319 ASP cc_start: 0.6580 (OUTLIER) cc_final: 0.6243 (t0) REVERT: A 336 ARG cc_start: 0.8198 (ptt-90) cc_final: 0.7890 (ptt-90) REVERT: A 584 PRO cc_start: 0.7794 (Cg_endo) cc_final: 0.7311 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7678 (m-30) cc_final: 0.7331 (m-30) REVERT: A 693 GLN cc_start: 0.8429 (tp40) cc_final: 0.8145 (tm-30) REVERT: A 724 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7357 (tt0) REVERT: A 770 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7916 (mp) REVERT: A 925 MET cc_start: 0.8085 (mmm) cc_final: 0.7703 (mmm) REVERT: A 1006 GLU cc_start: 0.7886 (OUTLIER) cc_final: 0.7572 (pt0) REVERT: B 18 ASN cc_start: 0.8072 (t0) cc_final: 0.7648 (t0) REVERT: B 77 ASP cc_start: 0.6456 (p0) cc_final: 0.6143 (p0) REVERT: B 102 ASN cc_start: 0.8125 (t0) cc_final: 0.7411 (t0) REVERT: B 170 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: B 245 GLN cc_start: 0.7683 (mt0) cc_final: 0.7291 (mt0) REVERT: B 278 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7939 (mm) REVERT: B 280 ASP cc_start: 0.6629 (m-30) cc_final: 0.6322 (m-30) REVERT: B 281 GLU cc_start: 0.7841 (mp0) cc_final: 0.7629 (mp0) REVERT: B 319 ASP cc_start: 0.6571 (OUTLIER) cc_final: 0.6236 (t0) REVERT: B 336 ARG cc_start: 0.8183 (ptt-90) cc_final: 0.7872 (ptt-90) REVERT: B 584 PRO cc_start: 0.7795 (Cg_endo) cc_final: 0.7316 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7678 (m-30) cc_final: 0.7325 (m-30) REVERT: B 693 GLN cc_start: 0.8407 (tp40) cc_final: 0.8116 (tm-30) REVERT: B 724 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7358 (tt0) REVERT: B 770 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (mp) REVERT: B 925 MET cc_start: 0.8087 (mmm) cc_final: 0.7711 (mmm) REVERT: B 1006 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7576 (pt0) REVERT: C 18 ASN cc_start: 0.8075 (t0) cc_final: 0.7665 (t0) REVERT: C 77 ASP cc_start: 0.6459 (p0) cc_final: 0.6142 (p0) REVERT: C 102 ASN cc_start: 0.8124 (t0) cc_final: 0.7413 (t0) REVERT: C 170 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8185 (mt-10) REVERT: C 245 GLN cc_start: 0.7675 (mt0) cc_final: 0.7282 (mt0) REVERT: C 278 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7940 (mm) REVERT: C 280 ASP cc_start: 0.6628 (m-30) cc_final: 0.6318 (m-30) REVERT: C 281 GLU cc_start: 0.7838 (mp0) cc_final: 0.7622 (mp0) REVERT: C 319 ASP cc_start: 0.6575 (OUTLIER) cc_final: 0.6242 (t0) REVERT: C 336 ARG cc_start: 0.8190 (ptt-90) cc_final: 0.7882 (ptt-90) REVERT: C 584 PRO cc_start: 0.7796 (Cg_endo) cc_final: 0.7314 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7673 (m-30) cc_final: 0.7327 (m-30) REVERT: C 693 GLN cc_start: 0.8406 (tp40) cc_final: 0.8112 (tm-30) REVERT: C 724 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: C 770 ILE cc_start: 0.8264 (OUTLIER) cc_final: 0.7917 (mp) REVERT: C 925 MET cc_start: 0.8086 (mmm) cc_final: 0.7707 (mmm) REVERT: C 1006 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7557 (pt0) REVERT: D 18 ASN cc_start: 0.8076 (t0) cc_final: 0.7650 (t0) REVERT: D 77 ASP cc_start: 0.6453 (p0) cc_final: 0.6130 (p0) REVERT: D 102 ASN cc_start: 0.8120 (t0) cc_final: 0.7409 (t0) REVERT: D 170 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: D 245 GLN cc_start: 0.7677 (mt0) cc_final: 0.7270 (mt0) REVERT: D 278 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7934 (mm) REVERT: D 280 ASP cc_start: 0.6645 (m-30) cc_final: 0.6337 (m-30) REVERT: D 281 GLU cc_start: 0.7842 (mp0) cc_final: 0.7635 (mp0) REVERT: D 319 ASP cc_start: 0.6582 (OUTLIER) cc_final: 0.6248 (t0) REVERT: D 336 ARG cc_start: 0.8193 (ptt-90) cc_final: 0.7882 (ptt-90) REVERT: D 584 PRO cc_start: 0.7798 (Cg_endo) cc_final: 0.7315 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7675 (m-30) cc_final: 0.7331 (m-30) REVERT: D 693 GLN cc_start: 0.8431 (tp40) cc_final: 0.8144 (tm-30) REVERT: D 724 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7359 (tt0) REVERT: D 770 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7914 (mp) REVERT: D 925 MET cc_start: 0.8084 (mmm) cc_final: 0.7705 (mmm) REVERT: D 1006 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7581 (pt0) outliers start: 109 outliers final: 62 residues processed: 569 average time/residue: 1.8409 time to fit residues: 1221.4362 Evaluate side-chains 594 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 508 time to evaluate : 3.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 227 VAL Chi-restraints excluded: chain A residue 230 ARG Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 319 ASP 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 754 LYS Chi-restraints excluded: chain A residue 770 ILE 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 85 VAL 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 227 VAL Chi-restraints excluded: chain B residue 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 319 ASP 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 745 MET Chi-restraints excluded: chain B residue 754 LYS Chi-restraints excluded: chain B residue 770 ILE 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 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 319 ASP 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 745 MET Chi-restraints excluded: chain C residue 754 LYS Chi-restraints excluded: chain C residue 770 ILE 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 85 VAL 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 227 VAL Chi-restraints excluded: chain D residue 230 ARG Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 319 ASP 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 754 LYS Chi-restraints excluded: chain D residue 770 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 324 optimal weight: 2.9990 chunk 195 optimal weight: 0.9980 chunk 187 optimal weight: 4.9990 chunk 228 optimal weight: 9.9990 chunk 387 optimal weight: 10.0000 chunk 216 optimal weight: 2.9990 chunk 341 optimal weight: 4.9990 chunk 27 optimal weight: 9.9990 chunk 177 optimal weight: 9.9990 chunk 283 optimal weight: 6.9990 chunk 188 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** A 563 GLN ** 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 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 395 HIS ** D 563 GLN ** 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 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.122818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.104961 restraints weight = 39145.530| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.39 r_work: 0.2939 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33468 Z= 0.149 Angle : 0.537 6.258 45660 Z= 0.283 Chirality : 0.044 0.156 4752 Planarity : 0.004 0.043 6036 Dihedral : 4.999 27.777 4428 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 4.22 % Allowed : 12.33 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.14), residues: 4036 helix: -0.01 (0.23), residues: 472 sheet: 0.50 (0.14), residues: 1376 loop : -0.08 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 553 HIS 0.008 0.001 HIS B 395 PHE 0.011 0.001 PHE D 143 TYR 0.021 0.002 TYR B 100 ARG 0.004 0.000 ARG C 404 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 1160) hydrogen bonds : angle 5.03531 ( 3180) covalent geometry : bond 0.00341 (33468) covalent geometry : angle 0.53663 (45660) *********************** 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 680 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 534 time to evaluate : 3.527 Fit side-chains REVERT: A 18 ASN cc_start: 0.8027 (t0) cc_final: 0.7639 (t0) REVERT: A 77 ASP cc_start: 0.6319 (p0) cc_final: 0.5939 (p0) REVERT: A 102 ASN cc_start: 0.8116 (t0) cc_final: 0.7398 (t0) REVERT: A 170 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 187 MET cc_start: 0.9054 (OUTLIER) cc_final: 0.8659 (ttm) REVERT: A 245 GLN cc_start: 0.7401 (mt0) cc_final: 0.7141 (mt0) REVERT: A 277 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6038 (pp20) REVERT: A 278 ILE cc_start: 0.8166 (OUTLIER) cc_final: 0.7874 (mm) REVERT: A 280 ASP cc_start: 0.6544 (m-30) cc_final: 0.6242 (m-30) REVERT: A 281 GLU cc_start: 0.7801 (mp0) cc_final: 0.7391 (mp0) REVERT: A 296 GLU cc_start: 0.7193 (mm-30) cc_final: 0.6668 (mm-30) REVERT: A 336 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7884 (ptt-90) REVERT: A 530 THR cc_start: 0.7756 (t) cc_final: 0.7350 (p) REVERT: A 584 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7279 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7404 (m-30) cc_final: 0.7138 (m-30) REVERT: A 693 GLN cc_start: 0.8436 (tp40) cc_final: 0.8165 (tm-30) REVERT: A 724 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7351 (tt0) REVERT: A 770 ILE cc_start: 0.8283 (OUTLIER) cc_final: 0.7886 (mp) REVERT: A 925 MET cc_start: 0.8144 (mmm) cc_final: 0.7823 (mmm) REVERT: A 1006 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7615 (pt0) REVERT: B 18 ASN cc_start: 0.8032 (t0) cc_final: 0.7645 (t0) REVERT: B 77 ASP cc_start: 0.6324 (p0) cc_final: 0.5948 (p0) REVERT: B 102 ASN cc_start: 0.8109 (t0) cc_final: 0.7382 (t0) REVERT: B 170 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8150 (mt-10) REVERT: B 187 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: B 245 GLN cc_start: 0.7520 (mt0) cc_final: 0.7191 (mt0) REVERT: B 278 ILE cc_start: 0.8171 (OUTLIER) cc_final: 0.7943 (mm) REVERT: B 280 ASP cc_start: 0.6540 (m-30) cc_final: 0.6243 (m-30) REVERT: B 281 GLU cc_start: 0.7803 (mp0) cc_final: 0.7416 (mp0) REVERT: B 296 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6671 (mm-30) REVERT: B 336 ARG cc_start: 0.8223 (ptt-90) cc_final: 0.7876 (ptt-90) REVERT: B 530 THR cc_start: 0.7800 (t) cc_final: 0.7456 (p) REVERT: B 584 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7278 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7409 (m-30) cc_final: 0.7131 (m-30) REVERT: B 693 GLN cc_start: 0.8435 (tp40) cc_final: 0.8165 (tm-30) REVERT: B 724 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: B 770 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7883 (mp) REVERT: B 925 MET cc_start: 0.8151 (mmm) cc_final: 0.7835 (mmm) REVERT: B 1006 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: C 18 ASN cc_start: 0.8039 (t0) cc_final: 0.7644 (t0) REVERT: C 77 ASP cc_start: 0.6329 (p0) cc_final: 0.5949 (p0) REVERT: C 102 ASN cc_start: 0.8112 (t0) cc_final: 0.7387 (t0) REVERT: C 170 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8149 (mt-10) REVERT: C 187 MET cc_start: 0.9047 (OUTLIER) cc_final: 0.8649 (ttm) REVERT: C 245 GLN cc_start: 0.7510 (mt0) cc_final: 0.7178 (mt0) REVERT: C 278 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7936 (mm) REVERT: C 280 ASP cc_start: 0.6547 (m-30) cc_final: 0.6249 (m-30) REVERT: C 281 GLU cc_start: 0.7797 (mp0) cc_final: 0.7406 (mp0) REVERT: C 296 GLU cc_start: 0.7196 (mm-30) cc_final: 0.6663 (mm-30) REVERT: C 336 ARG cc_start: 0.8218 (ptt-90) cc_final: 0.7875 (ptt-90) REVERT: C 530 THR cc_start: 0.7681 (t) cc_final: 0.7332 (p) REVERT: C 584 PRO cc_start: 0.7773 (Cg_endo) cc_final: 0.7277 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7403 (m-30) cc_final: 0.7129 (m-30) REVERT: C 693 GLN cc_start: 0.8432 (tp40) cc_final: 0.8159 (tm-30) REVERT: C 724 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7348 (tt0) REVERT: C 770 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.7892 (mp) REVERT: C 925 MET cc_start: 0.8143 (mmm) cc_final: 0.7823 (mmm) REVERT: C 1006 GLU cc_start: 0.7934 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: D 18 ASN cc_start: 0.8035 (t0) cc_final: 0.7648 (t0) REVERT: D 77 ASP cc_start: 0.6317 (p0) cc_final: 0.5929 (p0) REVERT: D 102 ASN cc_start: 0.8118 (t0) cc_final: 0.7395 (t0) REVERT: D 170 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8153 (mt-10) REVERT: D 187 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8654 (ttm) REVERT: D 245 GLN cc_start: 0.7510 (mt0) cc_final: 0.7150 (mt0) REVERT: D 277 GLU cc_start: 0.6915 (mm-30) cc_final: 0.6041 (pp20) REVERT: D 278 ILE cc_start: 0.8152 (OUTLIER) cc_final: 0.7866 (mm) REVERT: D 280 ASP cc_start: 0.6555 (m-30) cc_final: 0.6258 (m-30) REVERT: D 281 GLU cc_start: 0.7801 (mp0) cc_final: 0.7410 (mp0) REVERT: D 296 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6648 (mm-30) REVERT: D 336 ARG cc_start: 0.8221 (ptt-90) cc_final: 0.7879 (ptt-90) REVERT: D 530 THR cc_start: 0.7650 (t) cc_final: 0.7256 (p) REVERT: D 584 PRO cc_start: 0.7771 (Cg_endo) cc_final: 0.7280 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7398 (m-30) cc_final: 0.7127 (m-30) REVERT: D 693 GLN cc_start: 0.8438 (tp40) cc_final: 0.8167 (tm-30) REVERT: D 724 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7365 (tt0) REVERT: D 770 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7887 (mp) REVERT: D 925 MET cc_start: 0.8143 (mmm) cc_final: 0.7822 (mmm) REVERT: D 1006 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7622 (pt0) outliers start: 146 outliers final: 70 residues processed: 610 average time/residue: 1.7351 time to fit residues: 1233.5507 Evaluate side-chains 594 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 500 time to evaluate : 4.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 187 MET 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 632 SER Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 754 LYS 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 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL 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 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 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS 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 838 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 1006 GLU 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 187 MET 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 378 LEU 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 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS 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 838 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 1006 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 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 672 VAL Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 754 LYS 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 838 THR Chi-restraints excluded: chain D residue 855 THR 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 388 optimal weight: 10.0000 chunk 173 optimal weight: 20.0000 chunk 160 optimal weight: 6.9990 chunk 348 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 344 optimal weight: 0.9980 chunk 132 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 241 optimal weight: 10.0000 chunk 251 optimal weight: 7.9990 chunk 279 optimal weight: 2.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 GLN A 221 GLN A 226 HIS A 395 HIS ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 878 HIS A 903 GLN A 945 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 221 GLN B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 945 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 221 GLN C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 878 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 945 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 GLN D 221 GLN D 226 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 878 HIS D 903 GLN D 945 ASN ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.121425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.103340 restraints weight = 39421.321| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.44 r_work: 0.2903 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 33468 Z= 0.235 Angle : 0.613 7.337 45660 Z= 0.322 Chirality : 0.047 0.158 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.280 28.228 4428 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 4.14 % Allowed : 12.96 % Favored : 82.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.13), residues: 4036 helix: -0.44 (0.22), residues: 488 sheet: 0.53 (0.14), residues: 1288 loop : -0.17 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 553 HIS 0.009 0.001 HIS A 395 PHE 0.014 0.002 PHE D 143 TYR 0.022 0.002 TYR B 100 ARG 0.003 0.001 ARG A 699 Details of bonding type rmsd hydrogen bonds : bond 0.04140 ( 1160) hydrogen bonds : angle 5.23859 ( 3180) covalent geometry : bond 0.00545 (33468) covalent geometry : angle 0.61289 (45660) *********************** 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 655 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 512 time to evaluate : 9.612 Fit side-chains REVERT: A 18 ASN cc_start: 0.8055 (t0) cc_final: 0.7603 (t0) REVERT: A 77 ASP cc_start: 0.6292 (p0) cc_final: 0.5868 (p0) REVERT: A 102 ASN cc_start: 0.8178 (t0) cc_final: 0.7442 (t0) REVERT: A 170 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8183 (mt-10) REVERT: A 245 GLN cc_start: 0.7598 (mt0) cc_final: 0.7307 (mt0) REVERT: A 277 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6031 (pp20) REVERT: A 278 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7636 (mp) REVERT: A 280 ASP cc_start: 0.6509 (m-30) cc_final: 0.6223 (m-30) REVERT: A 281 GLU cc_start: 0.7810 (mp0) cc_final: 0.7522 (mp0) REVERT: A 336 ARG cc_start: 0.8285 (ptt-90) cc_final: 0.8006 (ptt-90) REVERT: A 584 PRO cc_start: 0.7825 (Cg_endo) cc_final: 0.7329 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7496 (m-30) cc_final: 0.7180 (m-30) REVERT: A 693 GLN cc_start: 0.8396 (tp40) cc_final: 0.8136 (tm-30) REVERT: A 724 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: A 770 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7928 (mp) REVERT: A 1006 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: B 18 ASN cc_start: 0.8061 (t0) cc_final: 0.7614 (t0) REVERT: B 77 ASP cc_start: 0.6298 (p0) cc_final: 0.5876 (p0) REVERT: B 102 ASN cc_start: 0.8177 (t0) cc_final: 0.7443 (t0) REVERT: B 170 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: B 245 GLN cc_start: 0.7597 (mt0) cc_final: 0.7244 (mt0) REVERT: B 278 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7694 (mp) REVERT: B 280 ASP cc_start: 0.6508 (m-30) cc_final: 0.6215 (m-30) REVERT: B 281 GLU cc_start: 0.7821 (mp0) cc_final: 0.7535 (mp0) REVERT: B 336 ARG cc_start: 0.8269 (ptt-90) cc_final: 0.7993 (ptt-90) REVERT: B 584 PRO cc_start: 0.7825 (Cg_endo) cc_final: 0.7329 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7495 (m-30) cc_final: 0.7177 (m-30) REVERT: B 693 GLN cc_start: 0.8398 (tp40) cc_final: 0.8135 (tm-30) REVERT: B 724 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7446 (tt0) REVERT: B 770 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7929 (mp) REVERT: B 1006 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7616 (pt0) REVERT: C 18 ASN cc_start: 0.8059 (t0) cc_final: 0.7607 (t0) REVERT: C 77 ASP cc_start: 0.6307 (p0) cc_final: 0.5881 (p0) REVERT: C 102 ASN cc_start: 0.8176 (t0) cc_final: 0.7444 (t0) REVERT: C 170 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: C 245 GLN cc_start: 0.7592 (mt0) cc_final: 0.7235 (mt0) REVERT: C 278 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7692 (mp) REVERT: C 280 ASP cc_start: 0.6513 (m-30) cc_final: 0.6218 (m-30) REVERT: C 281 GLU cc_start: 0.7818 (mp0) cc_final: 0.7533 (mp0) REVERT: C 336 ARG cc_start: 0.8267 (ptt-90) cc_final: 0.7996 (ptt-90) REVERT: C 584 PRO cc_start: 0.7828 (Cg_endo) cc_final: 0.7331 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7493 (m-30) cc_final: 0.7182 (m-30) REVERT: C 693 GLN cc_start: 0.8399 (tp40) cc_final: 0.8133 (tm-30) REVERT: C 724 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7444 (tt0) REVERT: C 770 ILE cc_start: 0.8288 (OUTLIER) cc_final: 0.7926 (mp) REVERT: C 1006 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7612 (pt0) REVERT: D 18 ASN cc_start: 0.8065 (t0) cc_final: 0.7617 (t0) REVERT: D 77 ASP cc_start: 0.6288 (p0) cc_final: 0.5860 (p0) REVERT: D 102 ASN cc_start: 0.8180 (t0) cc_final: 0.7443 (t0) REVERT: D 170 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: D 245 GLN cc_start: 0.7588 (mt0) cc_final: 0.7238 (mt0) REVERT: D 277 GLU cc_start: 0.7128 (mm-30) cc_final: 0.6051 (pp20) REVERT: D 278 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7642 (mp) REVERT: D 280 ASP cc_start: 0.6533 (m-30) cc_final: 0.6251 (m-30) REVERT: D 281 GLU cc_start: 0.7822 (mp0) cc_final: 0.7540 (mp0) REVERT: D 336 ARG cc_start: 0.8275 (ptt-90) cc_final: 0.8001 (ptt-90) REVERT: D 530 THR cc_start: 0.7771 (t) cc_final: 0.7368 (p) REVERT: D 584 PRO cc_start: 0.7830 (Cg_endo) cc_final: 0.7338 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7493 (m-30) cc_final: 0.7179 (m-30) REVERT: D 693 GLN cc_start: 0.8404 (tp40) cc_final: 0.8143 (tm-30) REVERT: D 724 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7459 (tt0) REVERT: D 770 ILE cc_start: 0.8289 (OUTLIER) cc_final: 0.7924 (mp) REVERT: D 1006 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7625 (pt0) outliers start: 143 outliers final: 78 residues processed: 584 average time/residue: 2.1057 time to fit residues: 1433.6811 Evaluate side-chains 587 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 489 time to evaluate : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 ASP Chi-restraints excluded: chain A residue 85 VAL 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 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 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 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 754 LYS 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 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 15 ASP Chi-restraints excluded: chain B residue 85 VAL 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 227 VAL 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 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 724 GLU Chi-restraints excluded: chain B residue 754 LYS 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 838 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 1006 GLU Chi-restraints excluded: chain C residue 15 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 278 ILE Chi-restraints excluded: chain C residue 378 LEU 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 724 GLU Chi-restraints excluded: chain C residue 754 LYS 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 838 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 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 85 VAL 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 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 378 LEU 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 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 754 LYS 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 838 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 1006 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 6 optimal weight: 3.9990 chunk 184 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 92 optimal weight: 8.9990 chunk 123 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 309 optimal weight: 4.9990 chunk 280 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- 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 ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 226 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.122172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.104299 restraints weight = 39378.608| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.39 r_work: 0.2923 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33468 Z= 0.192 Angle : 0.581 6.781 45660 Z= 0.305 Chirality : 0.046 0.155 4752 Planarity : 0.005 0.045 6036 Dihedral : 5.185 27.552 4428 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.02 % Allowed : 13.92 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.13), residues: 4036 helix: -0.28 (0.23), residues: 488 sheet: 0.54 (0.14), residues: 1288 loop : -0.15 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 553 HIS 0.008 0.001 HIS B 395 PHE 0.013 0.001 PHE B 143 TYR 0.023 0.002 TYR D 100 ARG 0.003 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 1160) hydrogen bonds : angle 5.14835 ( 3180) covalent geometry : bond 0.00445 (33468) covalent geometry : angle 0.58058 (45660) *********************** 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 650 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 511 time to evaluate : 4.652 Fit side-chains REVERT: A 18 ASN cc_start: 0.8022 (t0) cc_final: 0.7598 (t0) REVERT: A 77 ASP cc_start: 0.6307 (p0) cc_final: 0.5841 (p0) REVERT: A 102 ASN cc_start: 0.8174 (t0) cc_final: 0.7438 (t0) REVERT: A 170 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8166 (mt-10) REVERT: A 187 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8680 (ttm) REVERT: A 245 GLN cc_start: 0.7543 (mt0) cc_final: 0.7241 (mt0) REVERT: A 277 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6022 (pp20) REVERT: A 278 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7612 (mp) REVERT: A 280 ASP cc_start: 0.6419 (m-30) cc_final: 0.6150 (m-30) REVERT: A 281 GLU cc_start: 0.7810 (mp0) cc_final: 0.7519 (mp0) REVERT: A 291 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8157 (mm) REVERT: A 296 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6686 (mm-30) REVERT: A 336 ARG cc_start: 0.8262 (ptt-90) cc_final: 0.8016 (ptt-90) REVERT: A 584 PRO cc_start: 0.7816 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7441 (m-30) cc_final: 0.7148 (m-30) REVERT: A 693 GLN cc_start: 0.8419 (tp40) cc_final: 0.8153 (tm-30) REVERT: A 724 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7432 (tt0) REVERT: A 770 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7907 (mp) REVERT: A 1006 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: B 18 ASN cc_start: 0.8027 (t0) cc_final: 0.7604 (t0) REVERT: B 77 ASP cc_start: 0.6305 (p0) cc_final: 0.5846 (p0) REVERT: B 102 ASN cc_start: 0.8172 (t0) cc_final: 0.7428 (t0) REVERT: B 170 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: B 187 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: B 245 GLN cc_start: 0.7419 (mt0) cc_final: 0.7135 (mt0) REVERT: B 277 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6160 (pp20) REVERT: B 278 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7588 (mp) REVERT: B 281 GLU cc_start: 0.7781 (mp0) cc_final: 0.7514 (mp0) REVERT: B 296 GLU cc_start: 0.7369 (mm-30) cc_final: 0.6682 (mm-30) REVERT: B 336 ARG cc_start: 0.8243 (ptt-90) cc_final: 0.7996 (ptt-90) REVERT: B 584 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7439 (m-30) cc_final: 0.7143 (m-30) REVERT: B 693 GLN cc_start: 0.8414 (tp40) cc_final: 0.8145 (tm-30) REVERT: B 724 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: B 770 ILE cc_start: 0.8337 (OUTLIER) cc_final: 0.7911 (mp) REVERT: B 1006 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: C 18 ASN cc_start: 0.8028 (t0) cc_final: 0.7603 (t0) REVERT: C 77 ASP cc_start: 0.6314 (p0) cc_final: 0.5850 (p0) REVERT: C 102 ASN cc_start: 0.8170 (t0) cc_final: 0.7428 (t0) REVERT: C 170 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: C 187 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: C 245 GLN cc_start: 0.7412 (mt0) cc_final: 0.7128 (mt0) REVERT: C 277 GLU cc_start: 0.7267 (mm-30) cc_final: 0.6149 (pp20) REVERT: C 278 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7581 (mp) REVERT: C 281 GLU cc_start: 0.7774 (mp0) cc_final: 0.7507 (mp0) REVERT: C 296 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6682 (mm-30) REVERT: C 336 ARG cc_start: 0.8234 (ptt-90) cc_final: 0.7991 (ptt-90) REVERT: C 584 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7324 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7443 (m-30) cc_final: 0.7148 (m-30) REVERT: C 693 GLN cc_start: 0.8413 (tp40) cc_final: 0.8140 (tm-30) REVERT: C 724 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7420 (tt0) REVERT: C 770 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7903 (mp) REVERT: C 1006 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: D 18 ASN cc_start: 0.8032 (t0) cc_final: 0.7605 (t0) REVERT: D 77 ASP cc_start: 0.6304 (p0) cc_final: 0.5832 (p0) REVERT: D 102 ASN cc_start: 0.8172 (t0) cc_final: 0.7429 (t0) REVERT: D 170 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: D 187 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8682 (ttm) REVERT: D 245 GLN cc_start: 0.7400 (mt0) cc_final: 0.7111 (mt0) REVERT: D 277 GLU cc_start: 0.7098 (mm-30) cc_final: 0.6032 (pp20) REVERT: D 278 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7587 (mp) REVERT: D 281 GLU cc_start: 0.7780 (mp0) cc_final: 0.7503 (mp0) REVERT: D 291 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8228 (mm) REVERT: D 296 GLU cc_start: 0.7353 (mm-30) cc_final: 0.6666 (mm-30) REVERT: D 336 ARG cc_start: 0.8252 (ptt-90) cc_final: 0.8008 (ptt-90) REVERT: D 584 PRO cc_start: 0.7832 (Cg_endo) cc_final: 0.7338 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7431 (m-30) cc_final: 0.7140 (m-30) REVERT: D 693 GLN cc_start: 0.8422 (tp40) cc_final: 0.8152 (tm-30) REVERT: D 724 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.7437 (tt0) REVERT: D 770 ILE cc_start: 0.8329 (OUTLIER) cc_final: 0.7905 (mp) REVERT: D 1006 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7629 (pt0) outliers start: 139 outliers final: 85 residues processed: 583 average time/residue: 2.0464 time to fit residues: 1384.7750 Evaluate side-chains 617 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 506 time to evaluate : 3.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 187 MET 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 291 LEU 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 499 ILE 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 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 754 LYS 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 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL 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 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS 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 838 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 1006 GLU 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 187 MET 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 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS 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 838 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 1006 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 LEU 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 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 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 754 LYS 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 838 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 1006 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 139 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 221 optimal weight: 10.0000 chunk 251 optimal weight: 2.9990 chunk 352 optimal weight: 6.9990 chunk 224 optimal weight: 10.0000 chunk 380 optimal weight: 6.9990 chunk 253 optimal weight: 2.9990 chunk 101 optimal weight: 10.0000 chunk 330 optimal weight: 20.0000 chunk 132 optimal weight: 7.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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 ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 739 HIS A 903 GLN A 945 ASN ** A 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS ** B 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 903 GLN B 945 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS ** C 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 903 GLN C 945 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 226 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 739 HIS D 903 GLN D 945 ASN ** D 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.122494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.104627 restraints weight = 39119.889| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 1.39 r_work: 0.2926 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33468 Z= 0.185 Angle : 0.575 6.724 45660 Z= 0.302 Chirality : 0.045 0.153 4752 Planarity : 0.005 0.045 6036 Dihedral : 5.154 26.642 4428 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.17 % Allowed : 14.27 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4036 helix: -0.21 (0.23), residues: 488 sheet: 0.47 (0.14), residues: 1296 loop : -0.09 (0.14), residues: 2252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 553 HIS 0.008 0.001 HIS B 395 PHE 0.012 0.001 PHE D 143 TYR 0.022 0.002 TYR A 100 ARG 0.004 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 1160) hydrogen bonds : angle 5.12024 ( 3180) covalent geometry : bond 0.00428 (33468) covalent geometry : angle 0.57502 (45660) *********************** 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 662 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 518 time to evaluate : 3.442 Fit side-chains REVERT: A 18 ASN cc_start: 0.8000 (t0) cc_final: 0.7567 (t0) REVERT: A 77 ASP cc_start: 0.6354 (p0) cc_final: 0.5875 (p0) REVERT: A 102 ASN cc_start: 0.8175 (t0) cc_final: 0.7420 (t0) REVERT: A 170 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8151 (mt-10) REVERT: A 187 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8673 (ttm) REVERT: A 245 GLN cc_start: 0.7644 (mt0) cc_final: 0.7382 (mt0) REVERT: A 277 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6215 (mm-30) REVERT: A 278 ILE cc_start: 0.8205 (OUTLIER) cc_final: 0.7646 (mp) REVERT: A 280 ASP cc_start: 0.6498 (m-30) cc_final: 0.6217 (m-30) REVERT: A 281 GLU cc_start: 0.7799 (mp0) cc_final: 0.7548 (mp0) REVERT: A 291 LEU cc_start: 0.8521 (OUTLIER) cc_final: 0.8210 (mm) REVERT: A 296 GLU cc_start: 0.7313 (mm-30) cc_final: 0.6703 (mm-30) REVERT: A 336 ARG cc_start: 0.8273 (ptt-90) cc_final: 0.8059 (ptt-90) REVERT: A 530 THR cc_start: 0.7745 (t) cc_final: 0.7315 (p) REVERT: A 542 MET cc_start: 0.8633 (ttt) cc_final: 0.8265 (ttt) REVERT: A 584 PRO cc_start: 0.7816 (Cg_endo) cc_final: 0.7317 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7405 (m-30) cc_final: 0.7134 (m-30) REVERT: A 693 GLN cc_start: 0.8414 (tp40) cc_final: 0.8150 (tm-30) REVERT: A 724 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7382 (tt0) REVERT: A 753 ASN cc_start: 0.6951 (t0) cc_final: 0.6590 (m-40) REVERT: A 770 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.7873 (mp) REVERT: A 1006 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7649 (pt0) REVERT: B 18 ASN cc_start: 0.8008 (t0) cc_final: 0.7578 (t0) REVERT: B 77 ASP cc_start: 0.6359 (p0) cc_final: 0.5887 (p0) REVERT: B 102 ASN cc_start: 0.8160 (t0) cc_final: 0.7407 (t0) REVERT: B 170 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: B 187 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8667 (ttm) REVERT: B 245 GLN cc_start: 0.7380 (mt0) cc_final: 0.7120 (mt0) REVERT: B 278 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7640 (mp) REVERT: B 280 ASP cc_start: 0.6416 (m-30) cc_final: 0.6154 (m-30) REVERT: B 281 GLU cc_start: 0.7777 (mp0) cc_final: 0.7334 (mp0) REVERT: B 296 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6735 (mm-30) REVERT: B 336 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.8033 (ptt-90) REVERT: B 530 THR cc_start: 0.7747 (t) cc_final: 0.7278 (p) REVERT: B 542 MET cc_start: 0.8639 (ttt) cc_final: 0.8277 (ttt) REVERT: B 584 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7318 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7404 (m-30) cc_final: 0.7125 (m-30) REVERT: B 693 GLN cc_start: 0.8410 (tp40) cc_final: 0.8140 (tm-30) REVERT: B 724 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7391 (tt0) REVERT: B 753 ASN cc_start: 0.6954 (t0) cc_final: 0.6588 (m-40) REVERT: B 770 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 1006 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7624 (pt0) REVERT: C 18 ASN cc_start: 0.8009 (t0) cc_final: 0.7576 (t0) REVERT: C 77 ASP cc_start: 0.6360 (p0) cc_final: 0.5881 (p0) REVERT: C 102 ASN cc_start: 0.8158 (t0) cc_final: 0.7407 (t0) REVERT: C 170 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: C 187 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8666 (ttm) REVERT: C 245 GLN cc_start: 0.7376 (mt0) cc_final: 0.7116 (mt0) REVERT: C 278 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7639 (mp) REVERT: C 280 ASP cc_start: 0.6419 (m-30) cc_final: 0.6157 (m-30) REVERT: C 281 GLU cc_start: 0.7773 (mp0) cc_final: 0.7335 (mp0) REVERT: C 296 GLU cc_start: 0.7261 (mm-30) cc_final: 0.6601 (mm-30) REVERT: C 336 ARG cc_start: 0.8248 (ptt-90) cc_final: 0.8033 (ptt-90) REVERT: C 530 THR cc_start: 0.7747 (t) cc_final: 0.7280 (p) REVERT: C 542 MET cc_start: 0.8645 (ttt) cc_final: 0.8284 (ttt) REVERT: C 584 PRO cc_start: 0.7819 (Cg_endo) cc_final: 0.7320 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7407 (m-30) cc_final: 0.7133 (m-30) REVERT: C 693 GLN cc_start: 0.8415 (tp40) cc_final: 0.8142 (tm-30) REVERT: C 724 GLU cc_start: 0.7727 (OUTLIER) cc_final: 0.7388 (tt0) REVERT: C 753 ASN cc_start: 0.6950 (t0) cc_final: 0.6592 (m-40) REVERT: C 760 ARG cc_start: 0.7618 (mtp180) cc_final: 0.7232 (mmm-85) REVERT: C 770 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7871 (mp) REVERT: C 1006 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7645 (pt0) REVERT: D 18 ASN cc_start: 0.8012 (t0) cc_final: 0.7580 (t0) REVERT: D 77 ASP cc_start: 0.6349 (p0) cc_final: 0.5865 (p0) REVERT: D 102 ASN cc_start: 0.8175 (t0) cc_final: 0.7421 (t0) REVERT: D 170 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: D 187 MET cc_start: 0.9005 (OUTLIER) cc_final: 0.8674 (ttm) REVERT: D 245 GLN cc_start: 0.7364 (mt0) cc_final: 0.7091 (mt0) REVERT: D 277 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6204 (mm-30) REVERT: D 278 ILE cc_start: 0.8170 (OUTLIER) cc_final: 0.7605 (mp) REVERT: D 280 ASP cc_start: 0.6430 (m-30) cc_final: 0.6165 (m-30) REVERT: D 281 GLU cc_start: 0.7767 (mp0) cc_final: 0.7528 (mp0) REVERT: D 291 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8230 (mm) REVERT: D 296 GLU cc_start: 0.7301 (mm-30) cc_final: 0.6664 (mm-30) REVERT: D 336 ARG cc_start: 0.8263 (ptt-90) cc_final: 0.8047 (ptt-90) REVERT: D 487 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 530 THR cc_start: 0.7734 (t) cc_final: 0.7308 (p) REVERT: D 542 MET cc_start: 0.8639 (ttt) cc_final: 0.8269 (ttt) REVERT: D 584 PRO cc_start: 0.7830 (Cg_endo) cc_final: 0.7331 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7401 (m-30) cc_final: 0.7144 (m-30) REVERT: D 693 GLN cc_start: 0.8418 (tp40) cc_final: 0.8149 (tm-30) REVERT: D 724 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7402 (tt0) REVERT: D 753 ASN cc_start: 0.6953 (t0) cc_final: 0.6593 (m-40) REVERT: D 770 ILE cc_start: 0.8314 (OUTLIER) cc_final: 0.7870 (mp) REVERT: D 1006 GLU cc_start: 0.7963 (OUTLIER) cc_final: 0.7645 (pt0) outliers start: 144 outliers final: 80 residues processed: 598 average time/residue: 1.6634 time to fit residues: 1161.8837 Evaluate side-chains 600 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 494 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 116 THR Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 187 MET 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 291 LEU Chi-restraints excluded: chain A residue 378 LEU 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 672 VAL Chi-restraints excluded: chain A residue 675 GLN Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 754 LYS 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 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL Chi-restraints excluded: chain B residue 116 THR Chi-restraints excluded: chain B residue 170 GLU Chi-restraints excluded: chain B residue 187 MET Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 227 VAL 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 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 745 MET Chi-restraints excluded: chain B residue 754 LYS 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 838 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 969 GLU Chi-restraints excluded: chain B residue 1006 GLU 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 187 MET 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 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 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS 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 838 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 969 GLU Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 85 VAL Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain D residue 170 GLU Chi-restraints excluded: chain D residue 187 MET Chi-restraints excluded: chain D residue 220 THR Chi-restraints excluded: chain D residue 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 378 LEU 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 672 VAL Chi-restraints excluded: chain D residue 675 GLN Chi-restraints excluded: chain D residue 724 GLU Chi-restraints excluded: chain D residue 754 LYS 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 838 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 969 GLU 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 44 optimal weight: 10.0000 chunk 185 optimal weight: 10.0000 chunk 190 optimal weight: 0.9990 chunk 198 optimal weight: 9.9990 chunk 342 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 192 optimal weight: 10.0000 chunk 177 optimal weight: 4.9990 chunk 194 optimal weight: 8.9990 chunk 265 optimal weight: 9.9990 chunk 163 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** 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 ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 878 HIS B 903 GLN B 945 ASN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 903 GLN C 945 ASN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 226 HIS D 395 HIS ** 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** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.120755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.103146 restraints weight = 39349.382| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.35 r_work: 0.2904 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.062 33468 Z= 0.306 Angle : 0.684 8.106 45660 Z= 0.359 Chirality : 0.049 0.161 4752 Planarity : 0.006 0.047 6036 Dihedral : 5.543 29.465 4428 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.14 % Allowed : 14.61 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.13), residues: 4036 helix: -0.62 (0.22), residues: 488 sheet: 0.36 (0.14), residues: 1284 loop : -0.25 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP B 553 HIS 0.009 0.001 HIS C 395 PHE 0.015 0.002 PHE B 143 TYR 0.023 0.003 TYR C 588 ARG 0.005 0.001 ARG B 938 Details of bonding type rmsd hydrogen bonds : bond 0.04518 ( 1160) hydrogen bonds : angle 5.42465 ( 3180) covalent geometry : bond 0.00715 (33468) covalent geometry : angle 0.68367 (45660) *********************** 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 641 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 498 time to evaluate : 3.633 Fit side-chains REVERT: A 18 ASN cc_start: 0.8043 (t0) cc_final: 0.7607 (t0) REVERT: A 77 ASP cc_start: 0.6458 (p0) cc_final: 0.5958 (p0) REVERT: A 102 ASN cc_start: 0.8220 (t0) cc_final: 0.7806 (t0) REVERT: A 170 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8188 (mt-10) REVERT: A 277 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6109 (pp20) REVERT: A 278 ILE cc_start: 0.8151 (OUTLIER) cc_final: 0.7589 (mp) REVERT: A 280 ASP cc_start: 0.6520 (m-30) cc_final: 0.6251 (m-30) REVERT: A 281 GLU cc_start: 0.7774 (mp0) cc_final: 0.7477 (mp0) REVERT: A 291 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8093 (mm) REVERT: A 296 GLU cc_start: 0.7271 (mm-30) cc_final: 0.6672 (mm-30) REVERT: A 542 MET cc_start: 0.8764 (ttt) cc_final: 0.8475 (ttt) REVERT: A 584 PRO cc_start: 0.7830 (Cg_endo) cc_final: 0.7315 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7650 (m-30) cc_final: 0.7349 (m-30) REVERT: A 693 GLN cc_start: 0.8397 (tp40) cc_final: 0.8124 (tm-30) REVERT: A 724 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7516 (tt0) REVERT: A 745 MET cc_start: 0.6591 (OUTLIER) cc_final: 0.5999 (mpp) REVERT: A 753 ASN cc_start: 0.6996 (t0) cc_final: 0.6626 (m-40) REVERT: A 770 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7915 (mp) REVERT: A 1006 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7630 (pt0) REVERT: B 18 ASN cc_start: 0.8039 (t0) cc_final: 0.7607 (t0) REVERT: B 77 ASP cc_start: 0.6467 (p0) cc_final: 0.5976 (p0) REVERT: B 102 ASN cc_start: 0.8214 (t0) cc_final: 0.7794 (t0) REVERT: B 170 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: B 245 GLN cc_start: 0.7558 (mt0) cc_final: 0.7306 (mt0) REVERT: B 277 GLU cc_start: 0.7171 (mm-30) cc_final: 0.6099 (pp20) REVERT: B 278 ILE cc_start: 0.8143 (OUTLIER) cc_final: 0.7579 (mp) REVERT: B 280 ASP cc_start: 0.6501 (m-30) cc_final: 0.6250 (m-30) REVERT: B 281 GLU cc_start: 0.7781 (mp0) cc_final: 0.7493 (mp0) REVERT: B 296 GLU cc_start: 0.7283 (mm-30) cc_final: 0.6684 (mm-30) REVERT: B 542 MET cc_start: 0.8767 (ttt) cc_final: 0.8482 (ttt) REVERT: B 584 PRO cc_start: 0.7829 (Cg_endo) cc_final: 0.7313 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7639 (m-30) cc_final: 0.7337 (m-30) REVERT: B 693 GLN cc_start: 0.8410 (tp40) cc_final: 0.8131 (tm-30) REVERT: B 724 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7494 (tt0) REVERT: B 753 ASN cc_start: 0.6999 (t0) cc_final: 0.6627 (m-40) REVERT: B 770 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7912 (mp) REVERT: B 1006 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7643 (pt0) REVERT: C 18 ASN cc_start: 0.8046 (t0) cc_final: 0.7613 (t0) REVERT: C 77 ASP cc_start: 0.6467 (p0) cc_final: 0.5959 (p0) REVERT: C 102 ASN cc_start: 0.8214 (t0) cc_final: 0.7797 (t0) REVERT: C 245 GLN cc_start: 0.7555 (mt0) cc_final: 0.7302 (mt0) REVERT: C 277 GLU cc_start: 0.7179 (mm-30) cc_final: 0.6099 (pp20) REVERT: C 278 ILE cc_start: 0.8142 (OUTLIER) cc_final: 0.7580 (mp) REVERT: C 280 ASP cc_start: 0.6489 (m-30) cc_final: 0.6239 (m-30) REVERT: C 281 GLU cc_start: 0.7776 (mp0) cc_final: 0.7489 (mp0) REVERT: C 296 GLU cc_start: 0.7276 (mm-30) cc_final: 0.6660 (mm-30) REVERT: C 542 MET cc_start: 0.8773 (ttt) cc_final: 0.8488 (ttt) REVERT: C 584 PRO cc_start: 0.7829 (Cg_endo) cc_final: 0.7323 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7648 (m-30) cc_final: 0.7344 (m-30) REVERT: C 693 GLN cc_start: 0.8397 (tp40) cc_final: 0.8120 (tm-30) REVERT: C 724 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7490 (tt0) REVERT: C 753 ASN cc_start: 0.6999 (t0) cc_final: 0.6627 (m-40) REVERT: C 770 ILE cc_start: 0.8311 (OUTLIER) cc_final: 0.7916 (mp) REVERT: C 1006 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7619 (pt0) REVERT: D 18 ASN cc_start: 0.8044 (t0) cc_final: 0.7610 (t0) REVERT: D 77 ASP cc_start: 0.6463 (p0) cc_final: 0.5953 (p0) REVERT: D 102 ASN cc_start: 0.8217 (t0) cc_final: 0.7799 (t0) REVERT: D 170 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.8199 (mt-10) REVERT: D 245 GLN cc_start: 0.7556 (mt0) cc_final: 0.7278 (mt0) REVERT: D 277 GLU cc_start: 0.7173 (mm-30) cc_final: 0.6135 (pp20) REVERT: D 278 ILE cc_start: 0.8158 (OUTLIER) cc_final: 0.7594 (mp) REVERT: D 280 ASP cc_start: 0.6531 (m-30) cc_final: 0.6270 (m-30) REVERT: D 281 GLU cc_start: 0.7783 (mp0) cc_final: 0.7493 (mp0) REVERT: D 291 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8107 (mm) REVERT: D 296 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6656 (mm-30) REVERT: D 542 MET cc_start: 0.8749 (ttt) cc_final: 0.8456 (ttt) REVERT: D 584 PRO cc_start: 0.7918 (Cg_endo) cc_final: 0.7419 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7647 (m-30) cc_final: 0.7344 (m-30) REVERT: D 693 GLN cc_start: 0.8398 (tp40) cc_final: 0.8124 (tm-30) REVERT: D 724 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7499 (tt0) REVERT: D 745 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5990 (mpp) REVERT: D 753 ASN cc_start: 0.7004 (t0) cc_final: 0.6633 (m-40) REVERT: D 770 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7909 (mp) REVERT: D 1006 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7636 (pt0) outliers start: 143 outliers final: 88 residues processed: 575 average time/residue: 1.7526 time to fit residues: 1164.5263 Evaluate side-chains 596 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 485 time to evaluate : 3.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 373 VAL 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 530 THR 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 754 LYS 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 838 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 996 ASP Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL 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 227 VAL Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 373 VAL 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 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 745 MET Chi-restraints excluded: chain B residue 754 LYS 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 838 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 969 GLU Chi-restraints excluded: chain B residue 996 ASP Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 116 THR 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 373 VAL 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 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 745 MET Chi-restraints excluded: chain C residue 754 LYS 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 838 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 969 GLU Chi-restraints excluded: chain C residue 996 ASP Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 85 VAL 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 227 VAL Chi-restraints excluded: chain D residue 278 ILE Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 373 VAL 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 530 THR 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 754 LYS 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 838 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 969 GLU 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 65 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 266 optimal weight: 5.9990 chunk 202 optimal weight: 4.9990 chunk 104 optimal weight: 0.0070 chunk 23 optimal weight: 20.0000 chunk 124 optimal weight: 20.0000 chunk 235 optimal weight: 4.9990 chunk 357 optimal weight: 0.9990 chunk 80 optimal weight: 10.0000 chunk 105 optimal weight: 0.9980 overall best weight: 1.5802 ------------------------------------------------------------------------------- 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 ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN ** A 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN A 945 ASN A 956 GLN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 739 HIS B 903 GLN B 945 ASN B 956 GLN ** B 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 903 GLN C 945 ASN C 956 GLN ** C 958 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS D 226 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 945 ASN D 956 GLN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.124053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.106460 restraints weight = 38961.674| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.37 r_work: 0.2956 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33468 Z= 0.121 Angle : 0.534 5.511 45660 Z= 0.283 Chirality : 0.044 0.152 4752 Planarity : 0.004 0.042 6036 Dihedral : 5.007 25.909 4428 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.89 % Allowed : 16.09 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.13), residues: 4036 helix: -0.00 (0.23), residues: 496 sheet: 0.38 (0.14), residues: 1376 loop : -0.09 (0.14), residues: 2164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP B 553 HIS 0.007 0.001 HIS A 395 PHE 0.010 0.001 PHE C 143 TYR 0.020 0.002 TYR D 100 ARG 0.005 0.000 ARG A 404 Details of bonding type rmsd hydrogen bonds : bond 0.03220 ( 1160) hydrogen bonds : angle 5.00257 ( 3180) covalent geometry : bond 0.00276 (33468) covalent geometry : angle 0.53446 (45660) *********************** 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 629 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 529 time to evaluate : 3.716 Fit side-chains REVERT: A 77 ASP cc_start: 0.6359 (p0) cc_final: 0.5862 (p0) REVERT: A 102 ASN cc_start: 0.8152 (t0) cc_final: 0.7418 (t0) REVERT: A 170 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 277 GLU cc_start: 0.7124 (mm-30) cc_final: 0.6235 (mm-30) REVERT: A 281 GLU cc_start: 0.7808 (mp0) cc_final: 0.7385 (mp0) REVERT: A 291 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 296 GLU cc_start: 0.7329 (mm-30) cc_final: 0.6771 (mm-30) REVERT: A 542 MET cc_start: 0.8644 (ttt) cc_final: 0.8310 (ttt) REVERT: A 584 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7256 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7372 (m-30) cc_final: 0.7153 (m-30) REVERT: A 693 GLN cc_start: 0.8413 (tp40) cc_final: 0.8108 (tm-30) REVERT: A 724 GLU cc_start: 0.7668 (OUTLIER) cc_final: 0.7312 (tt0) REVERT: A 753 ASN cc_start: 0.6927 (t0) cc_final: 0.6566 (m-40) REVERT: A 770 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7850 (mp) REVERT: A 942 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8336 (mmm-85) REVERT: A 1006 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7597 (pt0) REVERT: B 77 ASP cc_start: 0.6352 (p0) cc_final: 0.5855 (p0) REVERT: B 102 ASN cc_start: 0.8134 (t0) cc_final: 0.7405 (t0) REVERT: B 170 GLU cc_start: 0.8423 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: B 245 GLN cc_start: 0.7312 (mt0) cc_final: 0.7086 (mt0) REVERT: B 277 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6198 (mm-30) REVERT: B 281 GLU cc_start: 0.7853 (mp0) cc_final: 0.7429 (mp0) REVERT: B 296 GLU cc_start: 0.7304 (mm-30) cc_final: 0.6765 (mm-30) REVERT: B 530 THR cc_start: 0.7935 (t) cc_final: 0.7523 (p) REVERT: B 542 MET cc_start: 0.8643 (ttt) cc_final: 0.8311 (ttt) REVERT: B 584 PRO cc_start: 0.7763 (Cg_endo) cc_final: 0.7255 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7367 (m-30) cc_final: 0.7146 (m-30) REVERT: B 693 GLN cc_start: 0.8365 (tp40) cc_final: 0.8064 (tm-30) REVERT: B 724 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7318 (tt0) REVERT: B 745 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5492 (tpp) REVERT: B 753 ASN cc_start: 0.6929 (t0) cc_final: 0.6570 (m-40) REVERT: B 770 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7849 (mp) REVERT: B 942 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8398 (mmm-85) REVERT: B 1006 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7584 (pt0) REVERT: C 77 ASP cc_start: 0.6362 (p0) cc_final: 0.5861 (p0) REVERT: C 102 ASN cc_start: 0.8138 (t0) cc_final: 0.7411 (t0) REVERT: C 245 GLN cc_start: 0.7303 (mt0) cc_final: 0.7066 (mt0) REVERT: C 277 GLU cc_start: 0.7092 (mm-30) cc_final: 0.6212 (mm-30) REVERT: C 281 GLU cc_start: 0.7846 (mp0) cc_final: 0.7419 (mp0) REVERT: C 296 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6745 (mm-30) REVERT: C 530 THR cc_start: 0.7938 (t) cc_final: 0.7524 (p) REVERT: C 542 MET cc_start: 0.8655 (ttt) cc_final: 0.8330 (ttt) REVERT: C 584 PRO cc_start: 0.7765 (Cg_endo) cc_final: 0.7262 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7367 (m-30) cc_final: 0.7149 (m-30) REVERT: C 693 GLN cc_start: 0.8371 (tp40) cc_final: 0.8069 (tm-30) REVERT: C 724 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: C 745 MET cc_start: 0.6377 (OUTLIER) cc_final: 0.5474 (tpp) REVERT: C 753 ASN cc_start: 0.6931 (t0) cc_final: 0.6571 (m-40) REVERT: C 770 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7857 (mp) REVERT: C 942 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8400 (mmm-85) REVERT: C 1006 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7590 (pt0) REVERT: D 77 ASP cc_start: 0.6363 (p0) cc_final: 0.5852 (p0) REVERT: D 102 ASN cc_start: 0.8146 (t0) cc_final: 0.7409 (t0) REVERT: D 170 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8014 (mt-10) REVERT: D 245 GLN cc_start: 0.7186 (mt0) cc_final: 0.6945 (mt0) REVERT: D 277 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6233 (mm-30) REVERT: D 281 GLU cc_start: 0.7814 (mp0) cc_final: 0.7396 (mp0) REVERT: D 291 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8207 (mm) REVERT: D 296 GLU cc_start: 0.7310 (mm-30) cc_final: 0.6746 (mm-30) REVERT: D 530 THR cc_start: 0.7947 (t) cc_final: 0.7530 (p) REVERT: D 542 MET cc_start: 0.8650 (ttt) cc_final: 0.8318 (ttt) REVERT: D 584 PRO cc_start: 0.7768 (Cg_endo) cc_final: 0.7262 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7374 (m-30) cc_final: 0.7150 (m-30) REVERT: D 693 GLN cc_start: 0.8417 (tp40) cc_final: 0.8112 (tm-30) REVERT: D 724 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7325 (tt0) REVERT: D 753 ASN cc_start: 0.6931 (t0) cc_final: 0.6570 (m-40) REVERT: D 770 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7851 (mp) REVERT: D 942 ARG cc_start: 0.8626 (OUTLIER) cc_final: 0.8342 (mmm-85) REVERT: D 1006 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7600 (pt0) outliers start: 100 outliers final: 40 residues processed: 577 average time/residue: 1.7296 time to fit residues: 1159.9430 Evaluate side-chains 579 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 516 time to evaluate : 3.986 ------------------------------------------------------------------------------- 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 291 LEU 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 632 SER Chi-restraints excluded: chain A residue 724 GLU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 969 GLU 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 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 745 MET 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 942 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1006 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 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 745 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 969 GLU 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 291 LEU Chi-restraints excluded: chain D residue 305 ILE 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 773 LYS Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 942 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 130 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 236 optimal weight: 4.9990 chunk 287 optimal weight: 30.0000 chunk 392 optimal weight: 9.9990 chunk 288 optimal weight: 0.0870 chunk 371 optimal weight: 5.9990 chunk 144 optimal weight: 0.0470 chunk 159 optimal weight: 9.9990 overall best weight: 2.6262 ------------------------------------------------------------------------------- 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 ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 675 GLN B 739 HIS B 903 GLN B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 990 HIS C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 675 GLN C 739 HIS C 903 GLN C 945 ASN ** C 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 990 HIS C1022 GLN D 226 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS D1022 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.123686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.105877 restraints weight = 38998.393| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.39 r_work: 0.2943 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2833 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 33468 Z= 0.153 Angle : 0.560 6.278 45660 Z= 0.295 Chirality : 0.044 0.152 4752 Planarity : 0.004 0.044 6036 Dihedral : 5.036 25.354 4428 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.60 % Allowed : 16.38 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.14), residues: 4036 helix: 0.22 (0.23), residues: 472 sheet: 0.35 (0.14), residues: 1388 loop : -0.04 (0.14), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 553 HIS 0.007 0.001 HIS A 395 PHE 0.013 0.001 PHE C 143 TYR 0.021 0.002 TYR A 100 ARG 0.004 0.000 ARG A 237 Details of bonding type rmsd hydrogen bonds : bond 0.03462 ( 1160) hydrogen bonds : angle 5.01960 ( 3180) covalent geometry : bond 0.00355 (33468) covalent geometry : angle 0.55991 (45660) ********************** 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 601 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 511 time to evaluate : 3.779 Fit side-chains REVERT: A 77 ASP cc_start: 0.6362 (p0) cc_final: 0.5835 (p0) REVERT: A 102 ASN cc_start: 0.8166 (t0) cc_final: 0.7438 (t0) REVERT: A 170 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: A 187 MET cc_start: 0.9034 (ttm) cc_final: 0.8643 (ttm) REVERT: A 277 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6247 (mm-30) REVERT: A 280 ASP cc_start: 0.6497 (m-30) cc_final: 0.6253 (m-30) REVERT: A 281 GLU cc_start: 0.7771 (mp0) cc_final: 0.7336 (mp0) REVERT: A 296 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6785 (mm-30) REVERT: A 530 THR cc_start: 0.7925 (t) cc_final: 0.7511 (p) REVERT: A 542 MET cc_start: 0.8666 (ttt) cc_final: 0.8343 (ttt) REVERT: A 584 PRO cc_start: 0.7759 (Cg_endo) cc_final: 0.7247 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7335 (m-30) cc_final: 0.7102 (m-30) REVERT: A 693 GLN cc_start: 0.8414 (tp40) cc_final: 0.8143 (tm-30) REVERT: A 724 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7321 (tt0) REVERT: A 753 ASN cc_start: 0.6913 (t0) cc_final: 0.6571 (m-40) REVERT: A 770 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7822 (mp) REVERT: A 1006 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7650 (pt0) REVERT: B 77 ASP cc_start: 0.6363 (p0) cc_final: 0.5838 (p0) REVERT: B 102 ASN cc_start: 0.8152 (t0) cc_final: 0.7422 (t0) REVERT: B 170 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8124 (mt-10) REVERT: B 187 MET cc_start: 0.9041 (ttm) cc_final: 0.8647 (ttm) REVERT: B 245 GLN cc_start: 0.7376 (mt0) cc_final: 0.7163 (mt0) REVERT: B 277 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6213 (mm-30) REVERT: B 280 ASP cc_start: 0.6489 (m-30) cc_final: 0.6235 (m-30) REVERT: B 281 GLU cc_start: 0.7776 (mp0) cc_final: 0.7337 (mp0) REVERT: B 296 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6791 (mm-30) REVERT: B 530 THR cc_start: 0.7891 (t) cc_final: 0.7506 (p) REVERT: B 542 MET cc_start: 0.8663 (ttt) cc_final: 0.8344 (ttt) REVERT: B 584 PRO cc_start: 0.7758 (Cg_endo) cc_final: 0.7243 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7334 (m-30) cc_final: 0.7095 (m-30) REVERT: B 693 GLN cc_start: 0.8403 (tp40) cc_final: 0.8132 (tm-30) REVERT: B 724 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7324 (tt0) REVERT: B 753 ASN cc_start: 0.6914 (t0) cc_final: 0.6579 (m-40) REVERT: B 760 ARG cc_start: 0.7617 (mtp180) cc_final: 0.7330 (mmm-85) REVERT: B 770 ILE cc_start: 0.8241 (OUTLIER) cc_final: 0.7847 (mp) REVERT: B 1006 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: C 77 ASP cc_start: 0.6357 (p0) cc_final: 0.5818 (p0) REVERT: C 102 ASN cc_start: 0.8152 (t0) cc_final: 0.7420 (t0) REVERT: C 187 MET cc_start: 0.9037 (ttm) cc_final: 0.8648 (ttm) REVERT: C 245 GLN cc_start: 0.7385 (mt0) cc_final: 0.7169 (mt0) REVERT: C 277 GLU cc_start: 0.7105 (mm-30) cc_final: 0.6221 (mm-30) REVERT: C 280 ASP cc_start: 0.6495 (m-30) cc_final: 0.6244 (m-30) REVERT: C 281 GLU cc_start: 0.7775 (mp0) cc_final: 0.7339 (mp0) REVERT: C 296 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6779 (mm-30) REVERT: C 530 THR cc_start: 0.7895 (t) cc_final: 0.7513 (p) REVERT: C 542 MET cc_start: 0.8673 (ttt) cc_final: 0.8354 (ttt) REVERT: C 584 PRO cc_start: 0.7762 (Cg_endo) cc_final: 0.7249 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7340 (m-30) cc_final: 0.7098 (m-30) REVERT: C 693 GLN cc_start: 0.8398 (tp40) cc_final: 0.8122 (tm-30) REVERT: C 724 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7314 (tt0) REVERT: C 753 ASN cc_start: 0.6889 (t0) cc_final: 0.6563 (m-40) REVERT: C 760 ARG cc_start: 0.7625 (mtp180) cc_final: 0.7332 (mmm-85) REVERT: C 770 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7898 (mp) REVERT: C 1006 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7666 (pt0) REVERT: D 77 ASP cc_start: 0.6357 (p0) cc_final: 0.5840 (p0) REVERT: D 102 ASN cc_start: 0.8162 (t0) cc_final: 0.7427 (t0) REVERT: D 170 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: D 187 MET cc_start: 0.9032 (ttm) cc_final: 0.8645 (ttm) REVERT: D 245 GLN cc_start: 0.7371 (mt0) cc_final: 0.7165 (mt0) REVERT: D 277 GLU cc_start: 0.7141 (mm-30) cc_final: 0.6239 (mm-30) REVERT: D 280 ASP cc_start: 0.6496 (m-30) cc_final: 0.6247 (m-30) REVERT: D 281 GLU cc_start: 0.7775 (mp0) cc_final: 0.7348 (mp0) REVERT: D 296 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6749 (mm-30) REVERT: D 530 THR cc_start: 0.7926 (t) cc_final: 0.7518 (p) REVERT: D 542 MET cc_start: 0.8667 (ttt) cc_final: 0.8354 (ttt) REVERT: D 584 PRO cc_start: 0.7768 (Cg_endo) cc_final: 0.7257 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7336 (m-30) cc_final: 0.7095 (m-30) REVERT: D 693 GLN cc_start: 0.8410 (tp40) cc_final: 0.8134 (tm-30) REVERT: D 724 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7333 (tt0) REVERT: D 753 ASN cc_start: 0.6885 (t0) cc_final: 0.6559 (m-40) REVERT: D 770 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 1006 GLU cc_start: 0.7973 (OUTLIER) cc_final: 0.7661 (pt0) outliers start: 90 outliers final: 50 residues processed: 559 average time/residue: 1.8645 time to fit residues: 1208.1861 Evaluate side-chains 566 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 501 time to evaluate : 3.885 ------------------------------------------------------------------------------- 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 773 LYS Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 942 ARG Chi-restraints excluded: chain A residue 969 GLU 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 745 MET 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 942 ARG Chi-restraints excluded: chain B residue 969 GLU Chi-restraints excluded: chain B residue 1006 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 745 MET Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 969 GLU 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 773 LYS Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 942 ARG Chi-restraints excluded: chain D residue 969 GLU Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 57 optimal weight: 6.9990 chunk 365 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 289 optimal weight: 10.0000 chunk 254 optimal weight: 10.0000 chunk 138 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 0.0570 chunk 331 optimal weight: 1.9990 chunk 204 optimal weight: 5.9990 chunk 337 optimal weight: 8.9990 overall best weight: 3.8106 ------------------------------------------------------------------------------- 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 ** A 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 675 GLN A 903 GLN A 945 ASN ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 990 HIS B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** B 990 HIS C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** C 990 HIS D 226 HIS D 395 HIS ** D 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 675 GLN ** D 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 945 ASN ** D 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.122725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.104966 restraints weight = 38971.808| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 1.39 r_work: 0.2932 rms_B_bonded: 1.83 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 3.16 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 33468 Z= 0.198 Angle : 0.599 6.812 45660 Z= 0.315 Chirality : 0.046 0.155 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.225 26.038 4428 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.40 % Allowed : 16.58 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.13), residues: 4036 helix: 0.09 (0.23), residues: 464 sheet: 0.54 (0.14), residues: 1272 loop : -0.17 (0.14), residues: 2300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 553 HIS 0.008 0.001 HIS B 395 PHE 0.014 0.002 PHE A 143 TYR 0.022 0.002 TYR A 100 ARG 0.004 0.001 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03814 ( 1160) hydrogen bonds : angle 5.12203 ( 3180) covalent geometry : bond 0.00459 (33468) covalent geometry : angle 0.59917 (45660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 26257.91 seconds wall clock time: 457 minutes 25.83 seconds (27445.83 seconds total)