Starting phenix.real_space_refine on Thu May 29 17:31:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bk8_16092/05_2025/8bk8_16092.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bk8_16092/05_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_16092/05_2025/8bk8_16092.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bk8_16092/05_2025/8bk8_16092.map" model { file = "/net/cci-nas-00/data/ceres_data/8bk8_16092/05_2025/8bk8_16092.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bk8_16092/05_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-5687/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: 21.41, per 1000 atoms: 0.66 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: 7.64 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: 5.00 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: 14.24 Time building geometry restraints manager: 8.89 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: 0.23 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: 0.940 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: 1.150 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 74.660 Find NCS groups from input model: 0.700 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 88.680 ------------------------------------------------------------------------------- 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 : 3.513 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: 1.7149 time to fit residues: 1346.8178 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 : 3.364 ------------------------------------------------------------------------------- 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 = 53)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.103234 restraints weight = 39073.025| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 1.45 r_work: 0.2902 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 3.365 Fit side-chains REVERT: A 77 ASP cc_start: 0.6316 (p0) cc_final: 0.6080 (p0) REVERT: A 102 ASN cc_start: 0.8221 (t0) cc_final: 0.7528 (t0) REVERT: A 170 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: A 221 GLN cc_start: 0.8345 (mt0) cc_final: 0.8020 (mt0) REVERT: A 280 ASP cc_start: 0.6614 (m-30) cc_final: 0.6290 (m-30) REVERT: A 281 GLU cc_start: 0.7827 (mp0) cc_final: 0.7564 (mp0) REVERT: A 336 ARG cc_start: 0.8340 (ptt-90) cc_final: 0.7976 (ptt-90) REVERT: A 584 PRO cc_start: 0.7858 (Cg_endo) cc_final: 0.7388 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7761 (m-30) cc_final: 0.7282 (m-30) REVERT: A 693 GLN cc_start: 0.8397 (tp40) cc_final: 0.8162 (tm-30) REVERT: A 724 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7352 (tt0) REVERT: A 925 MET cc_start: 0.8187 (mmm) cc_final: 0.7748 (mmm) REVERT: B 77 ASP cc_start: 0.6323 (p0) cc_final: 0.6091 (p0) REVERT: B 102 ASN cc_start: 0.8220 (t0) cc_final: 0.7524 (t0) REVERT: B 170 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: B 245 GLN cc_start: 0.7702 (mt0) cc_final: 0.7294 (mt0) REVERT: B 280 ASP cc_start: 0.6612 (m-30) cc_final: 0.6283 (m-30) REVERT: B 281 GLU cc_start: 0.7830 (mp0) cc_final: 0.7568 (mp0) REVERT: B 336 ARG cc_start: 0.8332 (ptt-90) cc_final: 0.7965 (ptt-90) REVERT: B 584 PRO cc_start: 0.7849 (Cg_endo) cc_final: 0.7378 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7753 (m-30) cc_final: 0.7276 (m-30) REVERT: B 693 GLN cc_start: 0.8397 (tp40) cc_final: 0.8156 (tm-30) REVERT: B 724 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7362 (tt0) REVERT: B 925 MET cc_start: 0.8181 (mmm) cc_final: 0.7745 (mmm) REVERT: C 77 ASP cc_start: 0.6334 (p0) cc_final: 0.6103 (p0) REVERT: C 102 ASN cc_start: 0.8213 (t0) cc_final: 0.7522 (t0) REVERT: C 170 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8204 (mt-10) REVERT: C 245 GLN cc_start: 0.7685 (mt0) cc_final: 0.7281 (mt0) REVERT: C 280 ASP cc_start: 0.6620 (m-30) cc_final: 0.6291 (m-30) REVERT: C 281 GLU cc_start: 0.7827 (mp0) cc_final: 0.7563 (mp0) REVERT: C 336 ARG cc_start: 0.8327 (ptt-90) cc_final: 0.7960 (ptt-90) REVERT: C 584 PRO cc_start: 0.7854 (Cg_endo) cc_final: 0.7380 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7757 (m-30) cc_final: 0.7284 (m-30) REVERT: C 693 GLN cc_start: 0.8393 (tp40) cc_final: 0.8147 (tm-30) REVERT: C 724 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: C 925 MET cc_start: 0.8181 (mmm) cc_final: 0.7744 (mmm) REVERT: D 77 ASP cc_start: 0.6322 (p0) cc_final: 0.6088 (p0) REVERT: D 102 ASN cc_start: 0.8214 (t0) cc_final: 0.7516 (t0) REVERT: D 170 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8208 (mt-10) REVERT: D 245 GLN cc_start: 0.7705 (mt0) cc_final: 0.7309 (mt0) REVERT: D 280 ASP cc_start: 0.6632 (m-30) cc_final: 0.6309 (m-30) REVERT: D 281 GLU cc_start: 0.7832 (mp0) cc_final: 0.7578 (mp0) REVERT: D 336 ARG cc_start: 0.8335 (ptt-90) cc_final: 0.7968 (ptt-90) REVERT: D 584 PRO cc_start: 0.7857 (Cg_endo) cc_final: 0.7388 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7754 (m-30) cc_final: 0.7273 (m-30) REVERT: D 693 GLN cc_start: 0.8395 (tp40) cc_final: 0.8156 (tm-30) REVERT: D 724 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7356 (tt0) REVERT: D 925 MET cc_start: 0.8184 (mmm) cc_final: 0.7748 (mmm) outliers start: 123 outliers final: 44 residues processed: 573 average time/residue: 1.6183 time to fit residues: 1077.4051 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 : 3.579 ------------------------------------------------------------------------------- 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: 9.9990 chunk 123 optimal weight: 5.9990 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: 6.9990 chunk 132 optimal weight: 0.9980 overall best weight: 3.3186 ------------------------------------------------------------------------------- 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 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 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.122216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.104358 restraints weight = 39261.743| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.39 r_work: 0.2930 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 33468 Z= 0.176 Angle : 0.569 6.691 45660 Z= 0.300 Chirality : 0.045 0.160 4752 Planarity : 0.005 0.043 6036 Dihedral : 5.131 29.071 4428 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.84 % Allowed : 12.04 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.44 (0.22), residues: 496 sheet: 0.50 (0.14), residues: 1336 loop : -0.14 (0.14), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP C 553 HIS 0.009 0.001 HIS D 395 PHE 0.012 0.001 PHE B 143 TYR 0.022 0.002 TYR D 100 ARG 0.003 0.000 ARG B 237 Details of bonding type rmsd hydrogen bonds : bond 0.03884 ( 1160) hydrogen bonds : angle 5.15255 ( 3180) covalent geometry : bond 0.00402 (33468) covalent geometry : angle 0.56916 (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 630 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 532 time to evaluate : 3.334 Fit side-chains REVERT: A 18 ASN cc_start: 0.8064 (t0) cc_final: 0.7627 (t0) REVERT: A 77 ASP cc_start: 0.6365 (p0) cc_final: 0.6048 (p0) REVERT: A 102 ASN cc_start: 0.8167 (t0) cc_final: 0.7456 (t0) REVERT: A 170 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (mt-10) REVERT: A 245 GLN cc_start: 0.7394 (mt0) cc_final: 0.7108 (mt0) REVERT: A 278 ILE cc_start: 0.8195 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 280 ASP cc_start: 0.6613 (m-30) cc_final: 0.6308 (m-30) REVERT: A 281 GLU cc_start: 0.7786 (mp0) cc_final: 0.7569 (mp0) REVERT: A 336 ARG cc_start: 0.8202 (ptt-90) cc_final: 0.7868 (ptt-90) REVERT: A 584 PRO cc_start: 0.7766 (Cg_endo) cc_final: 0.7284 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7573 (m-30) cc_final: 0.7218 (m-30) REVERT: A 693 GLN cc_start: 0.8385 (tp40) cc_final: 0.8097 (tm-30) REVERT: A 724 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7330 (tt0) REVERT: A 770 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7859 (mp) REVERT: A 925 MET cc_start: 0.8143 (mmm) cc_final: 0.7738 (mmm) REVERT: A 1006 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7566 (pt0) REVERT: B 18 ASN cc_start: 0.8066 (t0) cc_final: 0.7628 (t0) REVERT: B 77 ASP cc_start: 0.6372 (p0) cc_final: 0.6060 (p0) REVERT: B 102 ASN cc_start: 0.8170 (t0) cc_final: 0.7453 (t0) REVERT: B 170 GLU cc_start: 0.8433 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: B 245 GLN cc_start: 0.7542 (mt0) cc_final: 0.7200 (mt0) REVERT: B 278 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7973 (mm) REVERT: B 280 ASP cc_start: 0.6609 (m-30) cc_final: 0.6305 (m-30) REVERT: B 281 GLU cc_start: 0.7826 (mp0) cc_final: 0.7615 (mp0) REVERT: B 336 ARG cc_start: 0.8179 (ptt-90) cc_final: 0.7834 (ptt-90) REVERT: B 584 PRO cc_start: 0.7767 (Cg_endo) cc_final: 0.7285 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7570 (m-30) cc_final: 0.7211 (m-30) REVERT: B 693 GLN cc_start: 0.8407 (tp40) cc_final: 0.8117 (tm-30) REVERT: B 724 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7331 (tt0) REVERT: B 770 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 925 MET cc_start: 0.8154 (mmm) cc_final: 0.7756 (mmm) REVERT: B 1006 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7560 (pt0) REVERT: C 18 ASN cc_start: 0.8066 (t0) cc_final: 0.7628 (t0) REVERT: C 77 ASP cc_start: 0.6391 (p0) cc_final: 0.6085 (p0) REVERT: C 102 ASN cc_start: 0.8167 (t0) cc_final: 0.7455 (t0) REVERT: C 170 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.8173 (mt-10) REVERT: C 245 GLN cc_start: 0.7533 (mt0) cc_final: 0.7186 (mt0) REVERT: C 278 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7963 (mm) REVERT: C 280 ASP cc_start: 0.6611 (m-30) cc_final: 0.6302 (m-30) REVERT: C 281 GLU cc_start: 0.7821 (mp0) cc_final: 0.7606 (mp0) REVERT: C 336 ARG cc_start: 0.8178 (ptt-90) cc_final: 0.7838 (ptt-90) REVERT: C 584 PRO cc_start: 0.7769 (Cg_endo) cc_final: 0.7287 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7571 (m-30) cc_final: 0.7216 (m-30) REVERT: C 693 GLN cc_start: 0.8407 (tp40) cc_final: 0.8115 (tm-30) REVERT: C 724 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7322 (tt0) REVERT: C 770 ILE cc_start: 0.8270 (OUTLIER) cc_final: 0.7866 (mp) REVERT: C 925 MET cc_start: 0.8149 (mmm) cc_final: 0.7747 (mmm) REVERT: C 1006 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7558 (pt0) REVERT: D 18 ASN cc_start: 0.8070 (t0) cc_final: 0.7632 (t0) REVERT: D 77 ASP cc_start: 0.6365 (p0) cc_final: 0.6044 (p0) REVERT: D 102 ASN cc_start: 0.8165 (t0) cc_final: 0.7449 (t0) REVERT: D 170 GLU cc_start: 0.8436 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: D 245 GLN cc_start: 0.7576 (mt0) cc_final: 0.7185 (mt0) REVERT: D 278 ILE cc_start: 0.8186 (OUTLIER) cc_final: 0.7965 (mm) REVERT: D 280 ASP cc_start: 0.6619 (m-30) cc_final: 0.6316 (m-30) REVERT: D 336 ARG cc_start: 0.8195 (ptt-90) cc_final: 0.7856 (ptt-90) REVERT: D 584 PRO cc_start: 0.7766 (Cg_endo) cc_final: 0.7281 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7561 (m-30) cc_final: 0.7204 (m-30) REVERT: D 693 GLN cc_start: 0.8392 (tp40) cc_final: 0.8102 (tm-30) REVERT: D 724 GLU cc_start: 0.7699 (OUTLIER) cc_final: 0.7326 (tt0) REVERT: D 770 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7859 (mp) REVERT: D 925 MET cc_start: 0.8152 (mmm) cc_final: 0.7753 (mmm) REVERT: D 1006 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.7565 (pt0) outliers start: 98 outliers final: 52 residues processed: 578 average time/residue: 1.6263 time to fit residues: 1107.2246 Evaluate side-chains 572 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 500 time to evaluate : 3.482 ------------------------------------------------------------------------------- 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 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 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 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 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 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 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 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 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 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 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 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 1006 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 324 optimal weight: 3.9990 chunk 195 optimal weight: 7.9990 chunk 187 optimal weight: 5.9990 chunk 228 optimal weight: 10.0000 chunk 387 optimal weight: 9.9990 chunk 216 optimal weight: 20.0000 chunk 341 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 283 optimal weight: 9.9990 chunk 188 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 50 GLN B 221 GLN B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 878 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 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 903 GLN 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: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.120581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.102848 restraints weight = 39500.257| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.37 r_work: 0.2900 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.2792 rms_B_bonded: 3.13 restraints_weight: 0.2500 r_work (final): 0.2792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 33468 Z= 0.282 Angle : 0.658 7.854 45660 Z= 0.346 Chirality : 0.049 0.160 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.464 30.633 4428 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 4.95 % Allowed : 11.78 % Favored : 83.28 % 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: -0.18 (0.13), residues: 4036 helix: -0.70 (0.22), residues: 488 sheet: 0.50 (0.14), residues: 1276 loop : -0.27 (0.14), residues: 2272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 553 HIS 0.009 0.001 HIS A 395 PHE 0.015 0.002 PHE C 143 TYR 0.022 0.003 TYR A 100 ARG 0.004 0.001 ARG A 699 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 1160) hydrogen bonds : angle 5.39406 ( 3180) covalent geometry : bond 0.00656 (33468) covalent geometry : angle 0.65782 (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 695 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 524 time to evaluate : 3.925 Fit side-chains REVERT: A 77 ASP cc_start: 0.6388 (p0) cc_final: 0.6023 (p0) REVERT: A 102 ASN cc_start: 0.8172 (t0) cc_final: 0.7454 (t0) REVERT: A 170 GLU cc_start: 0.8399 (OUTLIER) cc_final: 0.8180 (mt-10) REVERT: A 245 GLN cc_start: 0.7535 (mt0) cc_final: 0.7247 (mt0) REVERT: A 278 ILE cc_start: 0.8167 (OUTLIER) cc_final: 0.7915 (mm) REVERT: A 280 ASP cc_start: 0.6642 (m-30) cc_final: 0.6328 (m-30) REVERT: A 281 GLU cc_start: 0.7852 (mp0) cc_final: 0.7573 (mp0) REVERT: A 336 ARG cc_start: 0.8272 (ptt-90) cc_final: 0.7981 (ptt-90) REVERT: A 584 PRO cc_start: 0.7830 (Cg_endo) cc_final: 0.7341 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7672 (m-30) cc_final: 0.7298 (m-30) REVERT: A 693 GLN cc_start: 0.8410 (tp40) cc_final: 0.8125 (tm-30) REVERT: A 724 GLU cc_start: 0.7756 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: A 770 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.7903 (mp) REVERT: A 854 LYS cc_start: 0.8641 (mttp) cc_final: 0.8416 (mtmm) REVERT: A 1006 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7646 (pt0) REVERT: B 71 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7077 (mt-10) REVERT: B 77 ASP cc_start: 0.6394 (p0) cc_final: 0.6037 (p0) REVERT: B 102 ASN cc_start: 0.8172 (t0) cc_final: 0.7452 (t0) REVERT: B 170 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: B 245 GLN cc_start: 0.7679 (mt0) cc_final: 0.7247 (mt0) REVERT: B 278 ILE cc_start: 0.8134 (OUTLIER) cc_final: 0.7637 (mp) REVERT: B 280 ASP cc_start: 0.6637 (m-30) cc_final: 0.6320 (m-30) REVERT: B 281 GLU cc_start: 0.7857 (mp0) cc_final: 0.7576 (mp0) REVERT: B 336 ARG cc_start: 0.8254 (ptt-90) cc_final: 0.7959 (ptt-90) REVERT: B 584 PRO cc_start: 0.7831 (Cg_endo) cc_final: 0.7339 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7672 (m-30) cc_final: 0.7293 (m-30) REVERT: B 693 GLN cc_start: 0.8396 (tp40) cc_final: 0.8115 (tm-30) REVERT: B 724 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7377 (tt0) REVERT: B 770 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7906 (mp) REVERT: B 854 LYS cc_start: 0.8642 (mttp) cc_final: 0.8415 (mtmm) REVERT: B 1006 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7633 (pt0) REVERT: C 71 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7081 (mt-10) REVERT: C 77 ASP cc_start: 0.6392 (p0) cc_final: 0.6029 (p0) REVERT: C 102 ASN cc_start: 0.8177 (t0) cc_final: 0.7461 (t0) REVERT: C 170 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8192 (mt-10) REVERT: C 245 GLN cc_start: 0.7674 (mt0) cc_final: 0.7243 (mt0) REVERT: C 278 ILE cc_start: 0.8124 (OUTLIER) cc_final: 0.7633 (mp) REVERT: C 280 ASP cc_start: 0.6637 (m-30) cc_final: 0.6317 (m-30) REVERT: C 281 GLU cc_start: 0.7816 (mp0) cc_final: 0.7542 (mp0) REVERT: C 336 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.7966 (ptt-90) REVERT: C 584 PRO cc_start: 0.7832 (Cg_endo) cc_final: 0.7341 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7675 (m-30) cc_final: 0.7299 (m-30) REVERT: C 693 GLN cc_start: 0.8398 (tp40) cc_final: 0.8112 (tm-30) REVERT: C 724 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7366 (tt0) REVERT: C 770 ILE cc_start: 0.8268 (OUTLIER) cc_final: 0.7903 (mp) REVERT: C 854 LYS cc_start: 0.8637 (mttp) cc_final: 0.8413 (mtmm) REVERT: C 1006 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: D 71 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.7076 (mt-10) REVERT: D 77 ASP cc_start: 0.6386 (p0) cc_final: 0.6021 (p0) REVERT: D 102 ASN cc_start: 0.8174 (t0) cc_final: 0.7458 (t0) REVERT: D 170 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.8196 (mt-10) REVERT: D 245 GLN cc_start: 0.7671 (mt0) cc_final: 0.7247 (mt0) REVERT: D 278 ILE cc_start: 0.8137 (OUTLIER) cc_final: 0.7617 (mp) REVERT: D 280 ASP cc_start: 0.6521 (m-30) cc_final: 0.6295 (m-30) REVERT: D 336 ARG cc_start: 0.8259 (ptt-90) cc_final: 0.7964 (ptt-90) REVERT: D 584 PRO cc_start: 0.7836 (Cg_endo) cc_final: 0.7345 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7674 (m-30) cc_final: 0.7298 (m-30) REVERT: D 693 GLN cc_start: 0.8412 (tp40) cc_final: 0.8123 (tm-30) REVERT: D 724 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: D 770 ILE cc_start: 0.8267 (OUTLIER) cc_final: 0.7901 (mp) REVERT: D 854 LYS cc_start: 0.8631 (mttp) cc_final: 0.8405 (mtmm) REVERT: D 1006 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7641 (pt0) outliers start: 171 outliers final: 84 residues processed: 604 average time/residue: 1.6176 time to fit residues: 1135.9279 Evaluate side-chains 615 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 508 time to evaluate : 3.555 ------------------------------------------------------------------------------- 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 230 ARG Chi-restraints excluded: chain A residue 278 ILE 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 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 71 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 484 VAL Chi-restraints excluded: chain B residue 499 ILE 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 1006 GLU Chi-restraints excluded: chain C residue 15 ASP Chi-restraints excluded: chain C residue 71 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 484 VAL Chi-restraints excluded: chain C residue 499 ILE 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 1006 GLU Chi-restraints excluded: chain D residue 15 ASP Chi-restraints excluded: chain D residue 71 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 388 optimal weight: 9.9990 chunk 173 optimal weight: 20.0000 chunk 160 optimal weight: 10.0000 chunk 348 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 33 optimal weight: 0.7980 chunk 241 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- 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 226 HIS 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: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.121256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.103541 restraints weight = 39288.272| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.36 r_work: 0.2906 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 33468 Z= 0.247 Angle : 0.628 7.529 45660 Z= 0.330 Chirality : 0.047 0.159 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.424 30.129 4428 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 4.14 % Allowed : 13.69 % Favored : 82.18 % 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: -0.19 (0.13), residues: 4036 helix: -0.66 (0.22), residues: 488 sheet: 0.44 (0.14), residues: 1288 loop : -0.26 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 553 HIS 0.009 0.001 HIS D 395 PHE 0.015 0.002 PHE B 143 TYR 0.023 0.002 TYR A 100 ARG 0.004 0.001 ARG D 699 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 1160) hydrogen bonds : angle 5.33778 ( 3180) covalent geometry : bond 0.00573 (33468) covalent geometry : angle 0.62754 (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 : 3.373 Fit side-chains REVERT: A 18 ASN cc_start: 0.8036 (t0) cc_final: 0.7606 (t0) REVERT: A 77 ASP cc_start: 0.6396 (p0) cc_final: 0.5997 (p0) REVERT: A 102 ASN cc_start: 0.8187 (t0) cc_final: 0.7481 (t0) REVERT: A 170 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: A 245 GLN cc_start: 0.7596 (mt0) cc_final: 0.7294 (mt0) REVERT: A 277 GLU cc_start: 0.6993 (mm-30) cc_final: 0.5965 (pp20) REVERT: A 278 ILE cc_start: 0.8185 (OUTLIER) cc_final: 0.7597 (mp) REVERT: A 280 ASP cc_start: 0.6651 (m-30) cc_final: 0.6338 (m-30) REVERT: A 281 GLU cc_start: 0.7837 (mp0) cc_final: 0.7555 (mp0) REVERT: A 291 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8176 (mm) REVERT: A 336 ARG cc_start: 0.8293 (ptt-90) cc_final: 0.8055 (ptt-90) REVERT: A 584 PRO cc_start: 0.7838 (Cg_endo) cc_final: 0.7341 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7644 (m-30) cc_final: 0.7283 (m-30) REVERT: A 693 GLN cc_start: 0.8353 (tp40) cc_final: 0.8057 (tm-30) REVERT: A 724 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: A 753 ASN cc_start: 0.7056 (t0) cc_final: 0.6656 (m-40) REVERT: A 770 ILE cc_start: 0.8294 (OUTLIER) cc_final: 0.7914 (mp) REVERT: A 1006 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: B 18 ASN cc_start: 0.8045 (t0) cc_final: 0.7617 (t0) REVERT: B 77 ASP cc_start: 0.6399 (p0) cc_final: 0.6002 (p0) REVERT: B 102 ASN cc_start: 0.8186 (t0) cc_final: 0.7479 (t0) REVERT: B 170 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: B 245 GLN cc_start: 0.7525 (mt0) cc_final: 0.7201 (mt0) REVERT: B 277 GLU cc_start: 0.7135 (mm-30) cc_final: 0.6074 (pp20) REVERT: B 278 ILE cc_start: 0.8163 (OUTLIER) cc_final: 0.7557 (mp) REVERT: B 280 ASP cc_start: 0.6513 (m-30) cc_final: 0.6236 (m-30) REVERT: B 281 GLU cc_start: 0.7815 (mp0) cc_final: 0.7533 (mp0) REVERT: B 291 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8175 (mm) REVERT: B 336 ARG cc_start: 0.8263 (ptt-90) cc_final: 0.8017 (ptt-90) REVERT: B 584 PRO cc_start: 0.7838 (Cg_endo) cc_final: 0.7340 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7646 (m-30) cc_final: 0.7284 (m-30) REVERT: B 693 GLN cc_start: 0.8355 (tp40) cc_final: 0.8062 (tm-30) REVERT: B 724 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: B 753 ASN cc_start: 0.7053 (t0) cc_final: 0.6653 (m-40) REVERT: B 770 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7915 (mp) REVERT: B 1006 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7631 (pt0) REVERT: C 18 ASN cc_start: 0.8044 (t0) cc_final: 0.7613 (t0) REVERT: C 77 ASP cc_start: 0.6402 (p0) cc_final: 0.5991 (p0) REVERT: C 102 ASN cc_start: 0.8185 (t0) cc_final: 0.7485 (t0) REVERT: C 170 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: C 245 GLN cc_start: 0.7520 (mt0) cc_final: 0.7191 (mt0) REVERT: C 277 GLU cc_start: 0.7140 (mm-30) cc_final: 0.6083 (pp20) REVERT: C 278 ILE cc_start: 0.8164 (OUTLIER) cc_final: 0.7563 (mp) REVERT: C 280 ASP cc_start: 0.6516 (m-30) cc_final: 0.6218 (m-30) REVERT: C 281 GLU cc_start: 0.7810 (mp0) cc_final: 0.7528 (mp0) REVERT: C 291 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8178 (mm) REVERT: C 336 ARG cc_start: 0.8262 (ptt-90) cc_final: 0.8020 (ptt-90) REVERT: C 584 PRO cc_start: 0.7840 (Cg_endo) cc_final: 0.7345 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7648 (m-30) cc_final: 0.7286 (m-30) REVERT: C 693 GLN cc_start: 0.8355 (tp40) cc_final: 0.8061 (tm-30) REVERT: C 724 GLU cc_start: 0.7808 (OUTLIER) cc_final: 0.7463 (tt0) REVERT: C 770 ILE cc_start: 0.8296 (OUTLIER) cc_final: 0.7935 (mp) REVERT: C 1006 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7617 (pt0) REVERT: D 18 ASN cc_start: 0.8047 (t0) cc_final: 0.7621 (t0) REVERT: D 77 ASP cc_start: 0.6392 (p0) cc_final: 0.5988 (p0) REVERT: D 102 ASN cc_start: 0.8186 (t0) cc_final: 0.7481 (t0) REVERT: D 170 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: D 245 GLN cc_start: 0.7612 (mt0) cc_final: 0.7240 (mt0) REVERT: D 277 GLU cc_start: 0.6982 (mm-30) cc_final: 0.5980 (pp20) REVERT: D 278 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7602 (mp) REVERT: D 280 ASP cc_start: 0.6463 (m-30) cc_final: 0.6249 (m-30) REVERT: D 291 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8176 (mm) REVERT: D 336 ARG cc_start: 0.8282 (ptt-90) cc_final: 0.8043 (ptt-90) REVERT: D 584 PRO cc_start: 0.7843 (Cg_endo) cc_final: 0.7347 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7643 (m-30) cc_final: 0.7282 (m-30) REVERT: D 693 GLN cc_start: 0.8363 (tp40) cc_final: 0.8068 (tm-30) REVERT: D 724 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: D 770 ILE cc_start: 0.8292 (OUTLIER) cc_final: 0.7930 (mp) REVERT: D 1006 GLU cc_start: 0.7954 (OUTLIER) cc_final: 0.7627 (pt0) outliers start: 143 outliers final: 88 residues processed: 584 average time/residue: 1.6511 time to fit residues: 1119.8137 Evaluate side-chains 612 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 500 time to evaluate : 3.476 ------------------------------------------------------------------------------- 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 230 ARG 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 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 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 230 ARG Chi-restraints excluded: chain B residue 278 ILE Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 484 VAL Chi-restraints excluded: chain B residue 499 ILE Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 672 VAL Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 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 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 230 ARG Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 291 LEU Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 499 ILE Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 672 VAL Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 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 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 230 ARG 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 6 optimal weight: 6.9990 chunk 184 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 92 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 309 optimal weight: 0.8980 chunk 280 optimal weight: 0.7980 chunk 112 optimal weight: 20.0000 chunk 71 optimal weight: 9.9990 chunk 289 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 956 GLN ** 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 956 GLN ** 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 956 GLN ** 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 885 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 903 GLN D 945 ASN D 956 GLN ** 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: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.123930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.106324 restraints weight = 39275.974| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.39 r_work: 0.2957 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 3.18 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 33468 Z= 0.113 Angle : 0.510 5.582 45660 Z= 0.269 Chirality : 0.043 0.153 4752 Planarity : 0.004 0.043 6036 Dihedral : 4.862 26.000 4428 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.95 % Allowed : 15.34 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.16 (0.14), residues: 4036 helix: 0.18 (0.23), residues: 472 sheet: 0.48 (0.14), residues: 1376 loop : -0.05 (0.14), residues: 2188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP C 553 HIS 0.007 0.001 HIS B 395 PHE 0.009 0.001 PHE D 143 TYR 0.020 0.001 TYR C 100 ARG 0.004 0.000 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 1160) hydrogen bonds : angle 4.92873 ( 3180) covalent geometry : bond 0.00259 (33468) covalent geometry : angle 0.50956 (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 656 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 554 time to evaluate : 3.533 Fit side-chains REVERT: A 77 ASP cc_start: 0.6255 (p0) cc_final: 0.5786 (p0) REVERT: A 102 ASN cc_start: 0.8126 (t0) cc_final: 0.7424 (t0) REVERT: A 170 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: A 187 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8568 (ttm) REVERT: A 245 GLN cc_start: 0.7463 (mt0) cc_final: 0.7249 (mt0) REVERT: A 281 GLU cc_start: 0.7767 (mp0) cc_final: 0.7336 (mp0) REVERT: A 291 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8196 (mm) REVERT: A 336 ARG cc_start: 0.8230 (ptt-90) cc_final: 0.7995 (ptt-90) REVERT: A 530 THR cc_start: 0.7686 (t) cc_final: 0.7309 (p) REVERT: A 584 PRO cc_start: 0.7722 (Cg_endo) cc_final: 0.7209 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7314 (m-30) cc_final: 0.7070 (m-30) REVERT: A 693 GLN cc_start: 0.8318 (tp40) cc_final: 0.7997 (tm-30) REVERT: A 724 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7243 (tt0) REVERT: A 753 ASN cc_start: 0.6938 (t0) cc_final: 0.6570 (m-40) REVERT: A 770 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7846 (mp) REVERT: A 1006 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7600 (pt0) REVERT: B 77 ASP cc_start: 0.6261 (p0) cc_final: 0.5795 (p0) REVERT: B 102 ASN cc_start: 0.8121 (t0) cc_final: 0.7417 (t0) REVERT: B 170 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8005 (mt-10) REVERT: B 187 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8574 (ttm) REVERT: B 245 GLN cc_start: 0.7212 (mt0) cc_final: 0.6988 (mt0) REVERT: B 281 GLU cc_start: 0.7804 (mp0) cc_final: 0.7372 (mp0) REVERT: B 291 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8147 (mm) REVERT: B 336 ARG cc_start: 0.8243 (ptt-90) cc_final: 0.8006 (ptt-90) REVERT: B 530 THR cc_start: 0.7727 (t) cc_final: 0.7368 (p) REVERT: B 584 PRO cc_start: 0.7720 (Cg_endo) cc_final: 0.7207 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7310 (m-30) cc_final: 0.7066 (m-30) REVERT: B 693 GLN cc_start: 0.8336 (tp40) cc_final: 0.8025 (tm-30) REVERT: B 724 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: B 745 MET cc_start: 0.6384 (OUTLIER) cc_final: 0.5526 (tpp) REVERT: B 753 ASN cc_start: 0.6938 (t0) cc_final: 0.6575 (m-40) REVERT: B 760 ARG cc_start: 0.7571 (mtp180) cc_final: 0.7227 (mmm-85) REVERT: B 770 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.7852 (mp) REVERT: B 1006 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: C 77 ASP cc_start: 0.6268 (p0) cc_final: 0.5797 (p0) REVERT: C 102 ASN cc_start: 0.8124 (t0) cc_final: 0.7418 (t0) REVERT: C 170 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8020 (mt-10) REVERT: C 187 MET cc_start: 0.8981 (OUTLIER) cc_final: 0.8550 (ttm) REVERT: C 245 GLN cc_start: 0.7198 (mt0) cc_final: 0.6964 (mt0) REVERT: C 281 GLU cc_start: 0.7793 (mp0) cc_final: 0.7354 (mp0) REVERT: C 291 LEU cc_start: 0.8480 (OUTLIER) cc_final: 0.8189 (mm) REVERT: C 336 ARG cc_start: 0.8227 (ptt-90) cc_final: 0.7992 (ptt-90) REVERT: C 530 THR cc_start: 0.7729 (t) cc_final: 0.7371 (p) REVERT: C 584 PRO cc_start: 0.7720 (Cg_endo) cc_final: 0.7211 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7302 (m-30) cc_final: 0.7059 (m-30) REVERT: C 693 GLN cc_start: 0.8320 (tp40) cc_final: 0.8003 (tm-30) REVERT: C 724 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7250 (tt0) REVERT: C 745 MET cc_start: 0.6383 (OUTLIER) cc_final: 0.5537 (tpp) REVERT: C 760 ARG cc_start: 0.7579 (mtp180) cc_final: 0.7239 (mmm-85) REVERT: C 770 ILE cc_start: 0.8230 (OUTLIER) cc_final: 0.7870 (mp) REVERT: C 1006 GLU cc_start: 0.7938 (OUTLIER) cc_final: 0.7598 (pt0) REVERT: D 77 ASP cc_start: 0.6264 (p0) cc_final: 0.5792 (p0) REVERT: D 102 ASN cc_start: 0.8125 (t0) cc_final: 0.7419 (t0) REVERT: D 170 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: D 187 MET cc_start: 0.8994 (OUTLIER) cc_final: 0.8568 (ttm) REVERT: D 245 GLN cc_start: 0.7218 (mt0) cc_final: 0.6986 (mt0) REVERT: D 280 ASP cc_start: 0.6424 (m-30) cc_final: 0.6164 (m-30) REVERT: D 281 GLU cc_start: 0.7818 (mp0) cc_final: 0.7496 (mp0) REVERT: D 291 LEU cc_start: 0.8466 (OUTLIER) cc_final: 0.8176 (mm) REVERT: D 336 ARG cc_start: 0.8219 (ptt-90) cc_final: 0.7980 (ptt-90) REVERT: D 530 THR cc_start: 0.7826 (t) cc_final: 0.7455 (p) REVERT: D 584 PRO cc_start: 0.7720 (Cg_endo) cc_final: 0.7210 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7311 (m-30) cc_final: 0.7060 (m-30) REVERT: D 693 GLN cc_start: 0.8330 (tp40) cc_final: 0.8010 (tm-30) REVERT: D 724 GLU cc_start: 0.7637 (OUTLIER) cc_final: 0.7265 (tt0) REVERT: D 760 ARG cc_start: 0.7595 (mtp180) cc_final: 0.7222 (mmm-85) REVERT: D 770 ILE cc_start: 0.8217 (OUTLIER) cc_final: 0.7857 (mp) REVERT: D 1006 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7609 (pt0) outliers start: 102 outliers final: 45 residues processed: 602 average time/residue: 1.5503 time to fit residues: 1086.8853 Evaluate side-chains 570 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 499 time to evaluate : 3.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL 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 291 LEU 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 969 GLU Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL 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 291 LEU 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 1006 GLU Chi-restraints excluded: chain C residue 85 VAL 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 291 LEU 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 1006 GLU Chi-restraints excluded: chain D residue 85 VAL 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 291 LEU 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 1006 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 139 optimal weight: 0.9990 chunk 306 optimal weight: 4.9990 chunk 221 optimal weight: 0.6980 chunk 251 optimal weight: 3.9990 chunk 352 optimal weight: 8.9990 chunk 224 optimal weight: 10.0000 chunk 380 optimal weight: 10.0000 chunk 253 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 132 optimal weight: 20.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- 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** A 990 HIS B 226 HIS B 395 HIS ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 739 HIS B 903 GLN B 945 ASN ** B 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS C 395 HIS ** C 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 739 HIS C 903 GLN C 945 ASN ** 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 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 = 0.3249 r_free = 0.3249 target = 0.122410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.104423 restraints weight = 39139.769| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.43 r_work: 0.2917 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 33468 Z= 0.193 Angle : 0.581 6.821 45660 Z= 0.305 Chirality : 0.045 0.155 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.108 26.421 4428 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.85 % Allowed : 15.10 % Favored : 81.05 % 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: 0.06 (0.13), residues: 4036 helix: -0.25 (0.22), residues: 496 sheet: 0.58 (0.14), residues: 1276 loop : -0.12 (0.14), residues: 2264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 553 HIS 0.008 0.001 HIS B 395 PHE 0.012 0.002 PHE B 143 TYR 0.021 0.002 TYR B 100 ARG 0.004 0.001 ARG D 237 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 1160) hydrogen bonds : angle 5.08214 ( 3180) covalent geometry : bond 0.00449 (33468) covalent geometry : angle 0.58119 (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 640 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 133 poor density : 507 time to evaluate : 3.566 Fit side-chains REVERT: A 18 ASN cc_start: 0.7990 (t0) cc_final: 0.7567 (t0) REVERT: A 77 ASP cc_start: 0.6345 (p0) cc_final: 0.5866 (p0) REVERT: A 102 ASN cc_start: 0.8176 (t0) cc_final: 0.7451 (t0) REVERT: A 170 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: A 245 GLN cc_start: 0.7588 (mt0) cc_final: 0.7361 (mt0) REVERT: A 277 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6014 (pp20) REVERT: A 278 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7874 (mm) REVERT: A 280 ASP cc_start: 0.6433 (m-30) cc_final: 0.6181 (m-30) REVERT: A 281 GLU cc_start: 0.7838 (mp0) cc_final: 0.7385 (mp0) REVERT: A 296 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6731 (mm-30) REVERT: A 336 ARG cc_start: 0.8262 (ptt-90) cc_final: 0.8045 (ptt-90) REVERT: A 530 THR cc_start: 0.7892 (t) cc_final: 0.7490 (p) REVERT: A 584 PRO cc_start: 0.7809 (Cg_endo) cc_final: 0.7304 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7385 (m-30) cc_final: 0.7129 (m-30) REVERT: A 693 GLN cc_start: 0.8422 (tp40) cc_final: 0.8144 (tm-30) REVERT: A 724 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7338 (tt0) REVERT: A 753 ASN cc_start: 0.6939 (t0) cc_final: 0.6626 (m-40) REVERT: A 760 ARG cc_start: 0.7657 (mtp180) cc_final: 0.7321 (mmm-85) REVERT: A 770 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7864 (mp) REVERT: A 942 ARG cc_start: 0.8631 (mmt90) cc_final: 0.8410 (mmm-85) REVERT: A 1006 GLU cc_start: 0.7858 (OUTLIER) cc_final: 0.7533 (pt0) REVERT: B 18 ASN cc_start: 0.7991 (t0) cc_final: 0.7567 (t0) REVERT: B 77 ASP cc_start: 0.6353 (p0) cc_final: 0.5880 (p0) REVERT: B 102 ASN cc_start: 0.8179 (t0) cc_final: 0.7470 (t0) REVERT: B 170 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8148 (mt-10) REVERT: B 245 GLN cc_start: 0.7340 (mt0) cc_final: 0.7071 (mt0) REVERT: B 277 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6030 (pp20) REVERT: B 278 ILE cc_start: 0.8189 (OUTLIER) cc_final: 0.7873 (mm) REVERT: B 280 ASP cc_start: 0.6430 (m-30) cc_final: 0.6173 (m-30) REVERT: B 281 GLU cc_start: 0.7802 (mp0) cc_final: 0.7358 (mp0) REVERT: B 296 GLU cc_start: 0.7361 (mm-30) cc_final: 0.6741 (mm-30) REVERT: B 336 ARG cc_start: 0.8263 (ptt-90) cc_final: 0.8050 (ptt-90) REVERT: B 530 THR cc_start: 0.7780 (OUTLIER) cc_final: 0.7388 (p) REVERT: B 584 PRO cc_start: 0.7811 (Cg_endo) cc_final: 0.7300 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7377 (m-30) cc_final: 0.7119 (m-30) REVERT: B 693 GLN cc_start: 0.8425 (tp40) cc_final: 0.8164 (tm-30) REVERT: B 724 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7346 (tt0) REVERT: B 753 ASN cc_start: 0.6944 (t0) cc_final: 0.6632 (m-40) REVERT: B 770 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7860 (mp) REVERT: B 1006 GLU cc_start: 0.7871 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: C 18 ASN cc_start: 0.7997 (t0) cc_final: 0.7566 (t0) REVERT: C 77 ASP cc_start: 0.6357 (p0) cc_final: 0.5874 (p0) REVERT: C 102 ASN cc_start: 0.8173 (t0) cc_final: 0.7466 (t0) REVERT: C 170 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: C 245 GLN cc_start: 0.7330 (mt0) cc_final: 0.7061 (mt0) REVERT: C 277 GLU cc_start: 0.7122 (mm-30) cc_final: 0.6043 (pp20) REVERT: C 278 ILE cc_start: 0.8191 (OUTLIER) cc_final: 0.7876 (mm) REVERT: C 280 ASP cc_start: 0.6439 (m-30) cc_final: 0.6185 (m-30) REVERT: C 281 GLU cc_start: 0.7844 (mp0) cc_final: 0.7389 (mp0) REVERT: C 296 GLU cc_start: 0.7355 (mm-30) cc_final: 0.6925 (mm-30) REVERT: C 336 ARG cc_start: 0.8251 (ptt-90) cc_final: 0.8038 (ptt-90) REVERT: C 530 THR cc_start: 0.7782 (OUTLIER) cc_final: 0.7394 (p) REVERT: C 584 PRO cc_start: 0.7812 (Cg_endo) cc_final: 0.7308 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7381 (m-30) cc_final: 0.7123 (m-30) REVERT: C 693 GLN cc_start: 0.8425 (tp40) cc_final: 0.8162 (tm-30) REVERT: C 724 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7347 (tt0) REVERT: C 770 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7876 (mp) REVERT: C 1006 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7539 (pt0) REVERT: D 18 ASN cc_start: 0.7988 (t0) cc_final: 0.7562 (t0) REVERT: D 77 ASP cc_start: 0.6341 (p0) cc_final: 0.5849 (p0) REVERT: D 102 ASN cc_start: 0.8179 (t0) cc_final: 0.7469 (t0) REVERT: D 170 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: D 245 GLN cc_start: 0.7326 (mt0) cc_final: 0.7069 (mt0) REVERT: D 277 GLU cc_start: 0.7109 (mm-30) cc_final: 0.6026 (pp20) REVERT: D 278 ILE cc_start: 0.8181 (OUTLIER) cc_final: 0.7871 (mm) REVERT: D 280 ASP cc_start: 0.6460 (m-30) cc_final: 0.6195 (m-30) REVERT: D 281 GLU cc_start: 0.7942 (mp0) cc_final: 0.7646 (mp0) REVERT: D 296 GLU cc_start: 0.7349 (mm-30) cc_final: 0.6723 (mm-30) REVERT: D 336 ARG cc_start: 0.8261 (ptt-90) cc_final: 0.8043 (ptt-90) REVERT: D 530 THR cc_start: 0.7887 (t) cc_final: 0.7485 (p) REVERT: D 584 PRO cc_start: 0.7812 (Cg_endo) cc_final: 0.7304 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7382 (m-30) cc_final: 0.7118 (m-30) REVERT: D 693 GLN cc_start: 0.8432 (tp40) cc_final: 0.8167 (tm-30) REVERT: D 724 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7360 (tt0) REVERT: D 770 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7876 (mp) REVERT: D 1006 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7528 (pt0) outliers start: 133 outliers final: 59 residues processed: 577 average time/residue: 1.6359 time to fit residues: 1099.4057 Evaluate side-chains 575 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 494 time to evaluate : 3.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 484 VAL Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 632 SER Chi-restraints excluded: chain A residue 675 GLN 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 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 969 GLU Chi-restraints excluded: chain A residue 1006 GLU Chi-restraints excluded: chain B residue 85 VAL 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 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 530 THR Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 675 GLN Chi-restraints excluded: chain B residue 724 GLU Chi-restraints excluded: chain B residue 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 1006 GLU Chi-restraints excluded: chain C residue 85 VAL Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 227 VAL Chi-restraints excluded: chain C residue 278 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 530 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 632 SER Chi-restraints excluded: chain C residue 675 GLN Chi-restraints excluded: chain C residue 724 GLU Chi-restraints excluded: chain C residue 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 1006 GLU Chi-restraints excluded: chain D residue 85 VAL 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 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 675 GLN 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 799 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 404 random chunks: chunk 44 optimal weight: 8.9990 chunk 185 optimal weight: 6.9990 chunk 190 optimal weight: 0.9990 chunk 198 optimal weight: 10.0000 chunk 342 optimal weight: 10.0000 chunk 295 optimal weight: 7.9990 chunk 192 optimal weight: 9.9990 chunk 177 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 265 optimal weight: 0.9980 chunk 163 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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 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 903 GLN B 945 ASN ** 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 903 GLN C 945 ASN ** 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 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 990 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.121888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.103753 restraints weight = 39119.393| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.45 r_work: 0.2922 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 33468 Z= 0.227 Angle : 0.617 7.199 45660 Z= 0.325 Chirality : 0.047 0.157 4752 Planarity : 0.005 0.046 6036 Dihedral : 5.295 27.589 4428 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.44 % Allowed : 15.48 % Favored : 81.08 % 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: -0.05 (0.13), residues: 4036 helix: -0.36 (0.22), residues: 488 sheet: 0.52 (0.14), residues: 1268 loop : -0.20 (0.14), residues: 2280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP C 553 HIS 0.009 0.001 HIS D 395 PHE 0.014 0.002 PHE B 143 TYR 0.023 0.002 TYR B 100 ARG 0.004 0.001 ARG A 599 Details of bonding type rmsd hydrogen bonds : bond 0.04021 ( 1160) hydrogen bonds : angle 5.21199 ( 3180) covalent geometry : bond 0.00527 (33468) covalent geometry : angle 0.61689 (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 626 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 507 time to evaluate : 3.377 Fit side-chains REVERT: A 77 ASP cc_start: 0.6403 (p0) cc_final: 0.5914 (p0) REVERT: A 102 ASN cc_start: 0.8206 (t0) cc_final: 0.7491 (t0) REVERT: A 170 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8186 (mt-10) REVERT: A 277 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6010 (pp20) REVERT: A 278 ILE cc_start: 0.8194 (OUTLIER) cc_final: 0.7878 (mm) REVERT: A 281 GLU cc_start: 0.7769 (mp0) cc_final: 0.7523 (mp0) REVERT: A 296 GLU cc_start: 0.7327 (mm-30) cc_final: 0.6656 (mm-30) REVERT: A 530 THR cc_start: 0.7890 (t) cc_final: 0.7450 (p) REVERT: A 584 PRO cc_start: 0.7841 (Cg_endo) cc_final: 0.7341 (Cg_exo) REVERT: A 598 ASP cc_start: 0.7481 (m-30) cc_final: 0.7196 (m-30) REVERT: A 693 GLN cc_start: 0.8403 (tp40) cc_final: 0.8118 (tm-30) REVERT: A 724 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7426 (tt0) REVERT: A 753 ASN cc_start: 0.6929 (t0) cc_final: 0.6611 (m-40) REVERT: A 760 ARG cc_start: 0.7660 (mtp180) cc_final: 0.7273 (mmm-85) REVERT: A 770 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7875 (mp) REVERT: A 942 ARG cc_start: 0.8669 (mmt90) cc_final: 0.8445 (mmm-85) REVERT: A 1006 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7652 (pt0) REVERT: B 77 ASP cc_start: 0.6417 (p0) cc_final: 0.5926 (p0) REVERT: B 102 ASN cc_start: 0.8210 (t0) cc_final: 0.7496 (t0) REVERT: B 170 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: B 245 GLN cc_start: 0.7480 (mt0) cc_final: 0.7201 (mt0) REVERT: B 277 GLU cc_start: 0.7112 (mm-30) cc_final: 0.6025 (pp20) REVERT: B 278 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7879 (mm) REVERT: B 281 GLU cc_start: 0.7816 (mp0) cc_final: 0.7573 (mp0) REVERT: B 296 GLU cc_start: 0.7341 (mm-30) cc_final: 0.6667 (mm-30) REVERT: B 584 PRO cc_start: 0.7841 (Cg_endo) cc_final: 0.7337 (Cg_exo) REVERT: B 598 ASP cc_start: 0.7484 (m-30) cc_final: 0.7194 (m-30) REVERT: B 693 GLN cc_start: 0.8393 (tp40) cc_final: 0.8119 (tm-30) REVERT: B 724 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7431 (tt0) REVERT: B 753 ASN cc_start: 0.6918 (t0) cc_final: 0.6599 (m-40) REVERT: B 770 ILE cc_start: 0.8323 (OUTLIER) cc_final: 0.7873 (mp) REVERT: B 1006 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7648 (pt0) REVERT: C 77 ASP cc_start: 0.6419 (p0) cc_final: 0.5921 (p0) REVERT: C 102 ASN cc_start: 0.8206 (t0) cc_final: 0.7490 (t0) REVERT: C 170 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: C 245 GLN cc_start: 0.7470 (mt0) cc_final: 0.7194 (mt0) REVERT: C 277 GLU cc_start: 0.7126 (mm-30) cc_final: 0.6039 (pp20) REVERT: C 278 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7882 (mm) REVERT: C 281 GLU cc_start: 0.7803 (mp0) cc_final: 0.7558 (mp0) REVERT: C 296 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6651 (mm-30) REVERT: C 584 PRO cc_start: 0.7847 (Cg_endo) cc_final: 0.7347 (Cg_exo) REVERT: C 598 ASP cc_start: 0.7481 (m-30) cc_final: 0.7191 (m-30) REVERT: C 693 GLN cc_start: 0.8403 (tp40) cc_final: 0.8128 (tm-30) REVERT: C 724 GLU cc_start: 0.7754 (OUTLIER) cc_final: 0.7421 (tt0) REVERT: C 753 ASN cc_start: 0.6951 (t0) cc_final: 0.6594 (m-40) REVERT: C 770 ILE cc_start: 0.8334 (OUTLIER) cc_final: 0.7880 (mp) REVERT: C 1006 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7642 (pt0) REVERT: D 77 ASP cc_start: 0.6401 (p0) cc_final: 0.5899 (p0) REVERT: D 102 ASN cc_start: 0.8207 (t0) cc_final: 0.7492 (t0) REVERT: D 170 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8190 (mt-10) REVERT: D 245 GLN cc_start: 0.7479 (mt0) cc_final: 0.7207 (mt0) REVERT: D 277 GLU cc_start: 0.7118 (mm-30) cc_final: 0.6038 (pp20) REVERT: D 278 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7878 (mm) REVERT: D 280 ASP cc_start: 0.6547 (m-30) cc_final: 0.6273 (m-30) REVERT: D 281 GLU cc_start: 0.8009 (mp0) cc_final: 0.7665 (mp0) REVERT: D 296 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6643 (mm-30) REVERT: D 530 THR cc_start: 0.7880 (t) cc_final: 0.7441 (p) REVERT: D 584 PRO cc_start: 0.7848 (Cg_endo) cc_final: 0.7348 (Cg_exo) REVERT: D 598 ASP cc_start: 0.7478 (m-30) cc_final: 0.7190 (m-30) REVERT: D 693 GLN cc_start: 0.8406 (tp40) cc_final: 0.8129 (tm-30) REVERT: D 724 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: D 753 ASN cc_start: 0.6956 (t0) cc_final: 0.6601 (m-40) REVERT: D 770 ILE cc_start: 0.8324 (OUTLIER) cc_final: 0.7871 (mp) REVERT: D 1006 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7650 (pt0) outliers start: 119 outliers final: 73 residues processed: 571 average time/residue: 1.6864 time to fit residues: 1114.0613 Evaluate side-chains 596 residues out of total 3456 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 503 time to evaluate : 3.649 ------------------------------------------------------------------------------- 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 305 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 770 ILE Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 799 THR Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 861 SER Chi-restraints excluded: chain A residue 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 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 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 770 ILE Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 799 THR Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain B residue 861 SER Chi-restraints excluded: chain B residue 942 ARG Chi-restraints excluded: chain B residue 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 278 ILE Chi-restraints excluded: chain C residue 305 ILE Chi-restraints excluded: chain C residue 378 LEU Chi-restraints excluded: chain C residue 484 VAL Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 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 770 ILE Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 799 THR Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 861 SER Chi-restraints excluded: chain C residue 942 ARG Chi-restraints excluded: chain C residue 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 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 770 ILE Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 799 THR Chi-restraints excluded: chain D residue 855 THR Chi-restraints excluded: chain D residue 861 SER Chi-restraints excluded: chain D residue 1006 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 73.2162 > 50: distance: 133 - 154: 26.888 distance: 137 - 166: 34.777 distance: 147 - 180: 32.648 distance: 150 - 154: 28.049 distance: 151 - 189: 32.943 distance: 154 - 155: 44.960 distance: 155 - 158: 41.419 distance: 156 - 157: 41.570 distance: 156 - 166: 69.052 distance: 157 - 194: 13.869 distance: 158 - 159: 46.116 distance: 159 - 160: 53.188 distance: 159 - 161: 4.703 distance: 160 - 162: 35.850 distance: 162 - 164: 47.716 distance: 163 - 164: 41.805 distance: 164 - 165: 49.548 distance: 166 - 167: 38.695 distance: 167 - 168: 47.994 distance: 167 - 170: 43.855 distance: 168 - 169: 14.290 distance: 168 - 180: 12.566 distance: 169 - 205: 59.437 distance: 170 - 171: 41.542 distance: 171 - 172: 23.854 distance: 171 - 173: 10.975 distance: 172 - 174: 34.099 distance: 173 - 175: 4.383 distance: 173 - 176: 39.106 distance: 174 - 175: 3.565 distance: 175 - 177: 49.110 distance: 177 - 179: 7.268 distance: 178 - 179: 39.965 distance: 181 - 182: 5.206 distance: 181 - 184: 40.104 distance: 182 - 183: 3.549 distance: 182 - 189: 5.613 distance: 183 - 216: 8.313 distance: 185 - 186: 40.275 distance: 186 - 188: 15.267 distance: 189 - 190: 27.575 distance: 190 - 191: 42.935 distance: 190 - 193: 42.518 distance: 191 - 192: 39.917 distance: 191 - 194: 40.036 distance: 192 - 225: 55.158 distance: 194 - 195: 32.130 distance: 195 - 196: 32.970 distance: 195 - 198: 9.523 distance: 196 - 197: 56.344 distance: 196 - 205: 38.666 distance: 198 - 199: 16.433 distance: 199 - 200: 42.453 distance: 199 - 201: 52.193 distance: 200 - 202: 70.289 distance: 201 - 203: 40.545 distance: 202 - 204: 55.835 distance: 203 - 204: 54.674 distance: 206 - 207: 39.572 distance: 207 - 208: 56.099 distance: 207 - 216: 32.868 distance: 209 - 210: 45.325 distance: 210 - 211: 22.276 distance: 212 - 213: 55.736 distance: 213 - 214: 56.219 distance: 213 - 215: 56.549 distance: 216 - 217: 40.682 distance: 217 - 220: 57.704 distance: 218 - 225: 55.335 distance: 220 - 221: 32.859 distance: 221 - 222: 8.668 distance: 222 - 223: 29.444 distance: 222 - 224: 41.175 distance: 225 - 226: 40.604 distance: 226 - 229: 42.065 distance: 227 - 228: 40.648 distance: 227 - 237: 40.385 distance: 229 - 230: 14.573 distance: 230 - 231: 39.274 distance: 231 - 233: 40.526 distance: 232 - 234: 40.482 distance: 233 - 235: 40.251 distance: 235 - 236: 34.260 distance: 237 - 238: 55.880 distance: 237 - 243: 40.229 distance: 238 - 241: 40.523 distance: 239 - 240: 39.932 distance: 242 - 243: 55.150 distance: 245 - 246: 38.875 distance: 245 - 248: 40.286 distance: 246 - 255: 34.590 distance: 248 - 249: 40.440 distance: 250 - 251: 40.910 distance: 252 - 253: 56.277 distance: 252 - 254: 39.553