Starting phenix.real_space_refine on Sat Feb 7 22:15:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hki_52230/02_2026/9hki_52230.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hki_52230/02_2026/9hki_52230.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9hki_52230/02_2026/9hki_52230.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hki_52230/02_2026/9hki_52230.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9hki_52230/02_2026/9hki_52230.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hki_52230/02_2026/9hki_52230.map" } resolution = 1.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.017 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: 6 Type Number sf(0) Gaussians Mg 4 5.21 5 S 156 5.16 5 Na 8 4.78 5 C 20736 2.51 5 N 5800 2.21 5 O 10048 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36752 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1021, 8197 Classifications: {'peptide': 1021} Link IDs: {'CIS': 3, 'PCIS': 5, 'PTRANS': 57, 'TRANS': 955} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 1, ' NA': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 988 Classifications: {'water': 988} Link IDs: {None: 987} Chain: "B" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 988 Classifications: {'water': 988} Link IDs: {None: 987} Chain: "C" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 988 Classifications: {'water': 988} Link IDs: {None: 987} Chain: "D" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 988 Classifications: {'water': 988} Link IDs: {None: 987} Restraints were copied for chains: B, C, D Time building chain proxies: 8.46, per 1000 atoms: 0.23 Number of scatterers: 36752 At special positions: 0 Unit cell: (193.842, 100.914, 150.282, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 156 16.00 Mg 4 11.99 Na 8 11.00 O 10048 8.00 N 5800 7.00 C 20736 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7600 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 56 sheets defined 18.7% alpha, 35.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 Processing helix chain 'A' and resid 6 through 11 Processing helix chain 'A' and resid 12 through 18 removed outlier: 6.147A pdb=" N ASP A 15 " --> pdb=" O GLN A 12 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP A 16 " --> pdb=" O ARG A 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN A 18 " --> pdb=" O ASP A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 45 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 94 Processing helix chain 'A' and resid 130 through 136 removed outlier: 3.779A pdb=" N LEU A 134 " --> pdb=" O ASP A 130 " (cutoff:3.500A) removed outlier: 3.807A 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: 4.208A pdb=" N TYR A 399 " --> pdb=" O HIS A 395 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.777A pdb=" N MET A 443 " --> pdb=" O ARG A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.535A pdb=" N ASP A 469 " --> pdb=" O GLY A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 525 removed outlier: 4.052A pdb=" N SER A 525 " --> pdb=" O LYS A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 559 removed outlier: 3.618A pdb=" N TYR A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 removed outlier: 3.969A pdb=" N CYS A 602 " --> pdb=" O ARG A 599 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 624 removed outlier: 3.956A 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 814 Processing helix 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 2 through 5 Processing helix chain 'B' and resid 6 through 11 Processing helix chain 'B' and resid 12 through 18 removed outlier: 6.147A pdb=" N ASP B 15 " --> pdb=" O GLN B 12 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP B 16 " --> pdb=" O ARG B 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN B 18 " --> pdb=" O ASP B 15 " (cutoff:3.500A) Processing helix chain 'B' and resid 38 through 45 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 94 Processing helix chain 'B' and resid 130 through 136 removed outlier: 3.779A pdb=" N LEU B 134 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 3.807A 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: 4.208A pdb=" N TYR B 399 " --> pdb=" O HIS B 395 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.777A pdb=" N MET B 443 " --> pdb=" O ARG B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 465 through 479 removed outlier: 3.535A pdb=" N ASP B 469 " --> pdb=" O GLY B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 525 removed outlier: 4.052A pdb=" N SER B 525 " --> pdb=" O LYS B 521 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 559 removed outlier: 3.618A pdb=" N TYR B 552 " --> pdb=" O GLY B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 598 through 603 removed outlier: 3.969A pdb=" N CYS B 602 " --> pdb=" O ARG B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 624 removed outlier: 3.956A 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 814 Processing helix 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 2 through 5 Processing helix chain 'C' and resid 6 through 11 Processing helix chain 'C' and resid 12 through 18 removed outlier: 6.147A pdb=" N ASP C 15 " --> pdb=" O GLN C 12 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP C 16 " --> pdb=" O ARG C 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN C 18 " --> pdb=" O ASP C 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 45 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 94 Processing helix chain 'C' and resid 130 through 136 removed outlier: 3.779A pdb=" N LEU C 134 " --> pdb=" O ASP C 130 " (cutoff:3.500A) removed outlier: 3.807A 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: 4.208A pdb=" N TYR C 399 " --> pdb=" O HIS C 395 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.777A pdb=" N MET C 443 " --> pdb=" O ARG C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 465 through 479 removed outlier: 3.535A pdb=" N ASP C 469 " --> pdb=" O GLY C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 519 through 525 removed outlier: 4.052A pdb=" N SER C 525 " --> pdb=" O LYS C 521 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 559 removed outlier: 3.618A pdb=" N TYR C 552 " --> pdb=" O GLY C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 598 through 603 removed outlier: 3.969A pdb=" N CYS C 602 " --> pdb=" O ARG C 599 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 624 removed outlier: 3.956A 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 814 Processing helix 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 2 through 5 Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 18 removed outlier: 6.147A pdb=" N ASP D 15 " --> pdb=" O GLN D 12 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TRP D 16 " --> pdb=" O ARG D 13 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASN D 18 " --> pdb=" O ASP D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 45 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 94 Processing helix chain 'D' and resid 130 through 136 removed outlier: 3.779A pdb=" N LEU D 134 " --> pdb=" O ASP D 130 " (cutoff:3.500A) removed outlier: 3.807A 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: 4.208A pdb=" N TYR D 399 " --> pdb=" O HIS D 395 " (cutoff:3.500A) removed outlier: 3.703A 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: 3.777A pdb=" N MET D 443 " --> pdb=" O ARG D 439 " (cutoff:3.500A) Processing helix chain 'D' and resid 465 through 479 removed outlier: 3.535A pdb=" N ASP D 469 " --> pdb=" O GLY D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 525 removed outlier: 4.052A pdb=" N SER D 525 " --> pdb=" O LYS D 521 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 559 removed outlier: 3.618A pdb=" N TYR D 552 " --> pdb=" O GLY D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 598 through 603 removed outlier: 3.969A pdb=" N CYS D 602 " --> pdb=" O ARG D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 624 removed outlier: 3.956A 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 814 Processing helix 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: 6.684A pdb=" N LEU A 152 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR A 161 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE A 150 " --> pdb=" O TYR A 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY A 180 " --> pdb=" O VAL A 129 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR A 126 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 8.856A 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: 4.404A pdb=" N THR A 101 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET A 202 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 147 Processing sheet with id=AA5, first strand: chain 'A' and resid 221 through 231 removed outlier: 5.612A pdb=" N ILE A 222 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS A 247 " --> pdb=" O ILE A 222 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 265 through 272 removed outlier: 6.678A pdb=" N LEU A 260 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 269 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL A 258 " --> pdb=" O SER A 269 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR A 271 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL A 256 " --> pdb=" O THR A 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR A 317 " --> pdb=" O LEU A 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU A 322 " --> pdb=" O THR A 317 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 338 Processing sheet with id=AA8, first strand: chain 'A' and resid 484 through 485 removed outlier: 8.196A pdb=" N GLN A 485 " --> pdb=" O ILE A 454 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP A 456 " --> pdb=" O GLN A 485 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL A 409 " --> pdb=" O ILE A 455 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER A 457 " --> pdb=" O VAL A 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP A 411 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG A 352 " --> pdb=" O ALA A 386 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG A 388 " --> pdb=" O ARG A 352 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL A 354 " --> pdb=" O ARG A 388 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU A 533 " --> pdb=" O GLY A 564 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N PHE A 566 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU A 535 " --> pdb=" O PHE A 566 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 575 through 578 Processing sheet with id=AB1, first strand: chain 'A' and resid 627 through 632 Processing sheet with id=AB2, first strand: chain 'A' and resid 661 through 669 removed outlier: 6.717A pdb=" N VAL A 656 " --> pdb=" O LEU A 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER A 665 " --> pdb=" O TRP A 654 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP A 654 " --> pdb=" O SER A 665 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU A 667 " --> pdb=" O LEU A 652 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU A 652 " --> pdb=" O GLU A 667 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY A 692 " --> pdb=" O GLU A 724 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU A 724 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU A 694 " --> pdb=" O LEU A 722 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA A 716 " --> pdb=" O VAL A 700 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN A 702 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE A 714 " --> pdb=" O GLN A 702 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 739 through 742 removed outlier: 6.246A pdb=" N ASN A 759 " --> pdb=" O LEU A 765 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU A 765 " --> pdb=" O ASN A 759 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP A 954 " --> pdb=" O GLN A1017 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN A1017 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N GLN A 956 " --> pdb=" O HIS A1015 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N HIS A1015 " --> pdb=" O GLN A 956 " (cutoff:3.500A) removed outlier: 20.500A pdb=" N ASN A 958 " --> pdb=" O ARG A1013 " (cutoff:3.500A) removed outlier: 23.519A pdb=" N ARG A1013 " --> pdb=" O ASN A 958 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR A 848 " --> pdb=" O HIS A 844 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS A 844 " --> pdb=" O THR A 848 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA A 841 " --> pdb=" O LEU A 822 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU A 822 " --> pdb=" O ALA A 841 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN A 843 " --> pdb=" O ALA A 820 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA A 820 " --> pdb=" O GLN A 843 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN A 887 " --> pdb=" O LEU A 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN A 885 " --> pdb=" O PRO A 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG A 781 " --> pdb=" O GLY A 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY A 883 " --> pdb=" O ARG A 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN A 783 " --> pdb=" O ARG A 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG A 881 " --> pdb=" O GLN A 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE A 882 " --> pdb=" O GLY A 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE A 989 " --> pdb=" O ASP A 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP A 954 " --> pdb=" O PHE A 989 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG A 942 " --> pdb=" O GLY A 953 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE A 955 " --> pdb=" O GLY A 940 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY A 940 " --> pdb=" O PHE A 955 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR A 941 " --> pdb=" O LEU A 900 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU A 900 " --> pdb=" O THR A 941 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU A 943 " --> pdb=" O LEU A 898 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 23 through 24 removed outlier: 6.684A pdb=" N LEU B 152 " --> pdb=" O VAL B 159 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR B 161 " --> pdb=" O PHE B 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE B 150 " --> pdb=" O TYR B 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY B 180 " --> pdb=" O VAL B 129 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR B 126 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLU B 57 " --> pdb=" O THR B 126 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 53 Processing sheet with id=AB8, first strand: chain 'B' and resid 99 through 101 removed outlier: 4.404A pdb=" N THR B 101 " --> pdb=" O MET B 202 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET B 202 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AC1, first strand: chain 'B' and resid 221 through 231 removed outlier: 5.612A pdb=" N ILE B 222 " --> pdb=" O CYS B 247 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS B 247 " --> pdb=" O ILE B 222 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 265 through 272 removed outlier: 6.678A pdb=" N LEU B 260 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER B 269 " --> pdb=" O VAL B 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL B 258 " --> pdb=" O SER B 269 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR B 271 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL B 256 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR B 317 " --> pdb=" O LEU B 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU B 322 " --> pdb=" O THR B 317 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 335 through 338 Processing sheet with id=AC4, first strand: chain 'B' and resid 484 through 485 removed outlier: 8.196A pdb=" N GLN B 485 " --> pdb=" O ILE B 454 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP B 456 " --> pdb=" O GLN B 485 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL B 409 " --> pdb=" O ILE B 455 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER B 457 " --> pdb=" O VAL B 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP B 411 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG B 352 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG B 388 " --> pdb=" O ARG B 352 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL B 354 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU B 533 " --> pdb=" O GLY B 564 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N PHE B 566 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU B 535 " --> pdb=" O PHE B 566 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 575 through 578 Processing sheet with id=AC6, first strand: chain 'B' and resid 627 through 632 Processing sheet with id=AC7, first strand: chain 'B' and resid 661 through 669 removed outlier: 6.717A pdb=" N VAL B 656 " --> pdb=" O LEU B 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER B 665 " --> pdb=" O TRP B 654 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP B 654 " --> pdb=" O SER B 665 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU B 667 " --> pdb=" O LEU B 652 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU B 652 " --> pdb=" O GLU B 667 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY B 692 " --> pdb=" O GLU B 724 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU B 724 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 694 " --> pdb=" O LEU B 722 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA B 716 " --> pdb=" O VAL B 700 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN B 702 " --> pdb=" O ILE B 714 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE B 714 " --> pdb=" O GLN B 702 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 739 through 742 removed outlier: 6.246A pdb=" N ASN B 759 " --> pdb=" O LEU B 765 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU B 765 " --> pdb=" O ASN B 759 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP B 954 " --> pdb=" O GLN B1017 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN B1017 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N GLN B 956 " --> pdb=" O HIS B1015 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N HIS B1015 " --> pdb=" O GLN B 956 " (cutoff:3.500A) removed outlier: 20.500A pdb=" N ASN B 958 " --> pdb=" O ARG B1013 " (cutoff:3.500A) removed outlier: 23.519A pdb=" N ARG B1013 " --> pdb=" O ASN B 958 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR B 848 " --> pdb=" O HIS B 844 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS B 844 " --> pdb=" O THR B 848 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA B 841 " --> pdb=" O LEU B 822 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU B 822 " --> pdb=" O ALA B 841 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN B 843 " --> pdb=" O ALA B 820 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA B 820 " --> pdb=" O GLN B 843 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN B 887 " --> pdb=" O LEU B 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN B 885 " --> pdb=" O PRO B 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG B 781 " --> pdb=" O GLY B 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY B 883 " --> pdb=" O ARG B 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN B 783 " --> pdb=" O ARG B 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG B 881 " --> pdb=" O GLN B 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE B 882 " --> pdb=" O GLY B 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE B 989 " --> pdb=" O ASP B 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP B 954 " --> pdb=" O PHE B 989 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG B 942 " --> pdb=" O GLY B 953 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE B 955 " --> pdb=" O GLY B 940 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY B 940 " --> pdb=" O PHE B 955 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR B 941 " --> pdb=" O LEU B 900 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU B 900 " --> pdb=" O THR B 941 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU B 943 " --> pdb=" O LEU B 898 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 23 through 24 removed outlier: 6.684A pdb=" N LEU C 152 " --> pdb=" O VAL C 159 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR C 161 " --> pdb=" O PHE C 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE C 150 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY C 180 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR C 126 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLU C 57 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 51 through 53 Processing sheet with id=AD4, first strand: chain 'C' and resid 99 through 101 removed outlier: 4.404A pdb=" N THR C 101 " --> pdb=" O MET C 202 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET C 202 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 146 through 147 Processing sheet with id=AD6, first strand: chain 'C' and resid 221 through 231 removed outlier: 5.612A pdb=" N ILE C 222 " --> pdb=" O CYS C 247 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS C 247 " --> pdb=" O ILE C 222 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 265 through 272 removed outlier: 6.678A pdb=" N LEU C 260 " --> pdb=" O VAL C 267 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER C 269 " --> pdb=" O VAL C 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL C 258 " --> pdb=" O SER C 269 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR C 271 " --> pdb=" O VAL C 256 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL C 256 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR C 317 " --> pdb=" O LEU C 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU C 322 " --> pdb=" O THR C 317 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 335 through 338 Processing sheet with id=AD9, first strand: chain 'C' and resid 484 through 485 removed outlier: 8.196A pdb=" N GLN C 485 " --> pdb=" O ILE C 454 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP C 456 " --> pdb=" O GLN C 485 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL C 409 " --> pdb=" O ILE C 455 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER C 457 " --> pdb=" O VAL C 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP C 411 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG C 352 " --> pdb=" O ALA C 386 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG C 388 " --> pdb=" O ARG C 352 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL C 354 " --> pdb=" O ARG C 388 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU C 533 " --> pdb=" O GLY C 564 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N PHE C 566 " --> pdb=" O LEU C 533 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU C 535 " --> pdb=" O PHE C 566 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 575 through 578 Processing sheet with id=AE2, first strand: chain 'C' and resid 627 through 632 Processing sheet with id=AE3, first strand: chain 'C' and resid 661 through 669 removed outlier: 6.717A pdb=" N VAL C 656 " --> pdb=" O LEU C 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER C 665 " --> pdb=" O TRP C 654 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP C 654 " --> pdb=" O SER C 665 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU C 667 " --> pdb=" O LEU C 652 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU C 652 " --> pdb=" O GLU C 667 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY C 692 " --> pdb=" O GLU C 724 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU C 724 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU C 694 " --> pdb=" O LEU C 722 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA C 716 " --> pdb=" O VAL C 700 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN C 702 " --> pdb=" O ILE C 714 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE C 714 " --> pdb=" O GLN C 702 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 739 through 742 removed outlier: 6.246A pdb=" N ASN C 759 " --> pdb=" O LEU C 765 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU C 765 " --> pdb=" O ASN C 759 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP C 954 " --> pdb=" O GLN C1017 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN C1017 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N GLN C 956 " --> pdb=" O HIS C1015 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N HIS C1015 " --> pdb=" O GLN C 956 " (cutoff:3.500A) removed outlier: 20.500A pdb=" N ASN C 958 " --> pdb=" O ARG C1013 " (cutoff:3.500A) removed outlier: 23.519A pdb=" N ARG C1013 " --> pdb=" O ASN C 958 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR C 848 " --> pdb=" O HIS C 844 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS C 844 " --> pdb=" O THR C 848 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA C 841 " --> pdb=" O LEU C 822 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU C 822 " --> pdb=" O ALA C 841 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN C 843 " --> pdb=" O ALA C 820 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA C 820 " --> pdb=" O GLN C 843 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN C 887 " --> pdb=" O LEU C 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN C 885 " --> pdb=" O PRO C 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG C 781 " --> pdb=" O GLY C 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY C 883 " --> pdb=" O ARG C 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C 783 " --> pdb=" O ARG C 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG C 881 " --> pdb=" O GLN C 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE C 882 " --> pdb=" O GLY C 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE C 989 " --> pdb=" O ASP C 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP C 954 " --> pdb=" O PHE C 989 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG C 942 " --> pdb=" O GLY C 953 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE C 955 " --> pdb=" O GLY C 940 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY C 940 " --> pdb=" O PHE C 955 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 941 " --> pdb=" O LEU C 900 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU C 900 " --> pdb=" O THR C 941 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU C 943 " --> pdb=" O LEU C 898 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 23 through 24 removed outlier: 6.684A pdb=" N LEU D 152 " --> pdb=" O VAL D 159 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR D 161 " --> pdb=" O PHE D 150 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N PHE D 150 " --> pdb=" O TYR D 161 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLY D 180 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR D 126 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 8.856A pdb=" N GLU D 57 " --> pdb=" O THR D 126 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 51 through 53 Processing sheet with id=AE9, first strand: chain 'D' and resid 99 through 101 removed outlier: 4.404A pdb=" N THR D 101 " --> pdb=" O MET D 202 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N MET D 202 " --> pdb=" O THR D 101 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 146 through 147 Processing sheet with id=AF2, first strand: chain 'D' and resid 221 through 231 removed outlier: 5.612A pdb=" N ILE D 222 " --> pdb=" O CYS D 247 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N CYS D 247 " --> pdb=" O ILE D 222 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 265 through 272 removed outlier: 6.678A pdb=" N LEU D 260 " --> pdb=" O VAL D 267 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER D 269 " --> pdb=" O VAL D 258 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N VAL D 258 " --> pdb=" O SER D 269 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR D 271 " --> pdb=" O VAL D 256 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL D 256 " --> pdb=" O THR D 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR D 317 " --> pdb=" O LEU D 322 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N LEU D 322 " --> pdb=" O THR D 317 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 335 through 338 Processing sheet with id=AF5, first strand: chain 'D' and resid 484 through 485 removed outlier: 8.196A pdb=" N GLN D 485 " --> pdb=" O ILE D 454 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N TRP D 456 " --> pdb=" O GLN D 485 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N VAL D 409 " --> pdb=" O ILE D 455 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER D 457 " --> pdb=" O VAL D 409 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ASP D 411 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N ARG D 352 " --> pdb=" O ALA D 386 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ARG D 388 " --> pdb=" O ARG D 352 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL D 354 " --> pdb=" O ARG D 388 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N LEU D 533 " --> pdb=" O GLY D 564 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N PHE D 566 " --> pdb=" O LEU D 533 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LEU D 535 " --> pdb=" O PHE D 566 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'D' and resid 575 through 578 Processing sheet with id=AF7, first strand: chain 'D' and resid 627 through 632 Processing sheet with id=AF8, first strand: chain 'D' and resid 661 through 669 removed outlier: 6.717A pdb=" N VAL D 656 " --> pdb=" O LEU D 663 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N SER D 665 " --> pdb=" O TRP D 654 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP D 654 " --> pdb=" O SER D 665 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU D 667 " --> pdb=" O LEU D 652 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 652 " --> pdb=" O GLU D 667 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N GLY D 692 " --> pdb=" O GLU D 724 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N GLU D 724 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU D 694 " --> pdb=" O LEU D 722 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N ALA D 716 " --> pdb=" O VAL D 700 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN D 702 " --> pdb=" O ILE D 714 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE D 714 " --> pdb=" O GLN D 702 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 739 through 742 removed outlier: 6.246A pdb=" N ASN D 759 " --> pdb=" O LEU D 765 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LEU D 765 " --> pdb=" O ASN D 759 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ASP D 954 " --> pdb=" O GLN D1017 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N GLN D1017 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 10.438A pdb=" N GLN D 956 " --> pdb=" O HIS D1015 " (cutoff:3.500A) removed outlier: 13.403A pdb=" N HIS D1015 " --> pdb=" O GLN D 956 " (cutoff:3.500A) removed outlier: 20.500A pdb=" N ASN D 958 " --> pdb=" O ARG D1013 " (cutoff:3.500A) removed outlier: 23.519A pdb=" N ARG D1013 " --> pdb=" O ASN D 958 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N THR D 848 " --> pdb=" O HIS D 844 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N HIS D 844 " --> pdb=" O THR D 848 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ALA D 841 " --> pdb=" O LEU D 822 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N LEU D 822 " --> pdb=" O ALA D 841 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLN D 843 " --> pdb=" O ALA D 820 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N ALA D 820 " --> pdb=" O GLN D 843 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 776 through 783 removed outlier: 6.282A pdb=" N GLN D 887 " --> pdb=" O LEU D 777 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N ASN D 885 " --> pdb=" O PRO D 779 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ARG D 781 " --> pdb=" O GLY D 883 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLY D 883 " --> pdb=" O ARG D 781 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN D 783 " --> pdb=" O ARG D 881 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N ARG D 881 " --> pdb=" O GLN D 783 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ILE D 882 " --> pdb=" O GLY D 988 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N PHE D 989 " --> pdb=" O ASP D 954 " (cutoff:3.500A) removed outlier: 11.981A pdb=" N ASP D 954 " --> pdb=" O PHE D 989 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ARG D 942 " --> pdb=" O GLY D 953 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N PHE D 955 " --> pdb=" O GLY D 940 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLY D 940 " --> pdb=" O PHE D 955 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR D 941 " --> pdb=" O LEU D 900 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LEU D 900 " --> pdb=" O THR D 941 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLU D 943 " --> pdb=" O LEU D 898 " (cutoff:3.500A) 1272 hydrogen bonds defined for protein. 3240 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: 10.91 Time building geometry restraints manager: 3.79 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: 10244 1.33 - 1.46: 6308 1.46 - 1.58: 16956 1.58 - 1.70: 0 1.70 - 1.82: 248 Bond restraints: 33756 Sorted by residual: bond pdb=" N GLN C 817 " pdb=" CA GLN C 817 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.65e+00 bond pdb=" N GLN A 817 " pdb=" CA GLN A 817 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.65e+00 bond pdb=" N GLN D 817 " pdb=" CA GLN D 817 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.65e+00 bond pdb=" N GLN B 817 " pdb=" CA GLN B 817 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.33e-02 5.65e+03 7.65e+00 bond pdb=" N VAL C 870 " pdb=" CA VAL C 870 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.14e-02 7.69e+03 7.25e+00 ... (remaining 33751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 44684 1.63 - 3.25: 1196 3.25 - 4.88: 140 4.88 - 6.51: 24 6.51 - 8.13: 16 Bond angle restraints: 46060 Sorted by residual: angle pdb=" CA TRP A 553 " pdb=" CB TRP A 553 " pdb=" CG TRP A 553 " ideal model delta sigma weight residual 113.60 106.31 7.29 1.90e+00 2.77e-01 1.47e+01 angle pdb=" CA TRP C 553 " pdb=" CB TRP C 553 " pdb=" CG TRP C 553 " ideal model delta sigma weight residual 113.60 106.31 7.29 1.90e+00 2.77e-01 1.47e+01 angle pdb=" CA TRP D 553 " pdb=" CB TRP D 553 " pdb=" CG TRP D 553 " ideal model delta sigma weight residual 113.60 106.31 7.29 1.90e+00 2.77e-01 1.47e+01 angle pdb=" CA TRP B 553 " pdb=" CB TRP B 553 " pdb=" CG TRP B 553 " ideal model delta sigma weight residual 113.60 106.31 7.29 1.90e+00 2.77e-01 1.47e+01 angle pdb=" CA VAL A 335 " pdb=" C VAL A 335 " pdb=" O VAL A 335 " ideal model delta sigma weight residual 120.39 116.54 3.85 1.05e+00 9.07e-01 1.34e+01 ... (remaining 46055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 18360 17.88 - 35.77: 1056 35.77 - 53.65: 212 53.65 - 71.53: 96 71.53 - 89.41: 48 Dihedral angle restraints: 19772 sinusoidal: 7968 harmonic: 11804 Sorted by residual: dihedral pdb=" CD ARG C 251 " pdb=" NE ARG C 251 " pdb=" CZ ARG C 251 " pdb=" NH1 ARG C 251 " ideal model delta sinusoidal sigma weight residual 0.00 42.10 -42.10 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CD ARG D 251 " pdb=" NE ARG D 251 " pdb=" CZ ARG D 251 " pdb=" NH1 ARG D 251 " ideal model delta sinusoidal sigma weight residual 0.00 42.10 -42.10 1 1.00e+01 1.00e-02 2.48e+01 dihedral pdb=" CD ARG A 251 " pdb=" NE ARG A 251 " pdb=" CZ ARG A 251 " pdb=" NH1 ARG A 251 " ideal model delta sinusoidal sigma weight residual 0.00 42.10 -42.10 1 1.00e+01 1.00e-02 2.48e+01 ... (remaining 19769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3648 0.050 - 0.100: 864 0.100 - 0.150: 280 0.150 - 0.200: 20 0.200 - 0.250: 4 Chirality restraints: 4816 Sorted by residual: chirality pdb=" CA VAL D 335 " pdb=" N VAL D 335 " pdb=" C VAL D 335 " pdb=" CB VAL D 335 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL C 335 " pdb=" N VAL C 335 " pdb=" C VAL C 335 " pdb=" CB VAL C 335 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL A 335 " pdb=" N VAL A 335 " pdb=" C VAL A 335 " pdb=" CB VAL A 335 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 4813 not shown) Planarity restraints: 6084 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 251 " -0.733 9.50e-02 1.11e+02 3.28e-01 6.56e+01 pdb=" NE ARG D 251 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG D 251 " 0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG D 251 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG D 251 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 251 " 0.733 9.50e-02 1.11e+02 3.28e-01 6.56e+01 pdb=" NE ARG B 251 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG B 251 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG B 251 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG B 251 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 251 " 0.733 9.50e-02 1.11e+02 3.28e-01 6.56e+01 pdb=" NE ARG C 251 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG C 251 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG C 251 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG C 251 " 0.023 2.00e-02 2.50e+03 ... (remaining 6081 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.03: 10 2.03 - 2.75: 5208 2.75 - 3.46: 57214 3.46 - 4.18: 113612 4.18 - 4.90: 182250 Nonbonded interactions: 358294 Sorted by model distance: nonbonded pdb=" O HOH C1296 " pdb=" O HOH D1296 " model vdw 1.312 3.040 nonbonded pdb=" O HOH A1296 " pdb=" O HOH B1296 " model vdw 1.312 3.040 nonbonded pdb=" O HOH B1382 " pdb=" O HOH B1733 " model vdw 2.009 3.040 nonbonded pdb=" O HOH C1382 " pdb=" O HOH C1733 " model vdw 2.009 3.040 nonbonded pdb=" O HOH D1382 " pdb=" O HOH D1733 " model vdw 2.009 3.040 ... (remaining 358289 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: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 20.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 35.240 Find NCS groups from input model: 0.340 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: 0.010 Load rotamer database and sin/cos tables:8.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 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 0.037 33756 Z= 0.193 Angle : 0.655 8.132 46060 Z= 0.381 Chirality : 0.048 0.250 4816 Planarity : 0.012 0.328 6084 Dihedral : 13.551 89.414 12172 Min Nonbonded Distance : 1.312 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.34 % Allowed : 5.27 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.13), residues: 4076 helix: -0.10 (0.22), residues: 532 sheet: 0.65 (0.14), residues: 1284 loop : 0.14 (0.14), residues: 2260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C1013 TYR 0.018 0.002 TYR A 100 PHE 0.013 0.002 PHE C 989 TRP 0.037 0.002 TRP B 553 HIS 0.008 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00314 (33756) covalent geometry : angle 0.65531 (46060) hydrogen bonds : bond 0.17101 ( 1216) hydrogen bonds : angle 7.44264 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 376 time to evaluate : 1.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 333 ARG cc_start: 0.8611 (OUTLIER) cc_final: 0.6968 (ppt90) REVERT: B 333 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.6972 (ppt90) REVERT: C 333 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.6926 (ppt90) REVERT: D 333 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.6926 (ppt90) outliers start: 12 outliers final: 4 residues processed: 384 average time/residue: 0.9881 time to fit residues: 434.9896 Evaluate side-chains 332 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 324 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 333 ARG Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain B residue 333 ARG Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain D residue 333 ARG Chi-restraints excluded: chain D residue 546 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.5980 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 1.9990 chunk 401 optimal weight: 0.6980 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN A 49 GLN A 102 ASN A 135 GLN A 262 GLN A 510 GLN A 718 GLN A 890 GLN A 965 GLN B 25 ASN B 49 GLN B 102 ASN B 135 GLN B 262 GLN B 510 GLN B 718 GLN B 890 GLN B 965 GLN C 25 ASN C 49 GLN C 102 ASN C 262 GLN C 510 GLN C 718 GLN C 890 GLN C 965 GLN D 25 ASN D 49 GLN D 102 ASN D 262 GLN D 510 GLN D 718 GLN D 890 GLN D 965 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.085101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.065722 restraints weight = 42464.250| |-----------------------------------------------------------------------------| r_work (start): 0.2724 rms_B_bonded: 1.38 r_work: 0.2626 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9160 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 33756 Z= 0.128 Angle : 0.575 7.822 46060 Z= 0.306 Chirality : 0.046 0.150 4816 Planarity : 0.004 0.041 6084 Dihedral : 5.317 57.568 4492 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.97 % Allowed : 5.96 % Favored : 93.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.13), residues: 4076 helix: 0.14 (0.22), residues: 532 sheet: 0.79 (0.14), residues: 1316 loop : 0.07 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.019 0.001 TYR A 100 PHE 0.012 0.001 PHE C 758 TRP 0.032 0.002 TRP D 553 HIS 0.005 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00262 (33756) covalent geometry : angle 0.57539 (46060) hydrogen bonds : bond 0.04655 ( 1216) hydrogen bonds : angle 5.73809 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 362 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 328 time to evaluate : 1.490 Fit side-chains REVERT: A 131 GLU cc_start: 0.7734 (tm-30) cc_final: 0.7375 (tm-30) REVERT: A 135 GLN cc_start: 0.8322 (mt0) cc_final: 0.8112 (mt0) REVERT: A 768 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.7951 (tmt) REVERT: B 131 GLU cc_start: 0.7729 (tm-30) cc_final: 0.7368 (tm-30) REVERT: B 135 GLN cc_start: 0.8322 (mt0) cc_final: 0.8110 (mt0) REVERT: B 768 MET cc_start: 0.8809 (OUTLIER) cc_final: 0.7946 (tmt) REVERT: C 768 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.7954 (tmt) REVERT: D 768 MET cc_start: 0.8807 (OUTLIER) cc_final: 0.7941 (tmt) outliers start: 34 outliers final: 10 residues processed: 348 average time/residue: 0.9219 time to fit residues: 370.9121 Evaluate side-chains 334 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 320 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 768 MET Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 438 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 768 MET Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 768 MET Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 768 MET Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 52 optimal weight: 0.9980 chunk 390 optimal weight: 2.9990 chunk 230 optimal weight: 0.6980 chunk 372 optimal weight: 5.9990 chunk 387 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 303 optimal weight: 0.0970 chunk 222 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 965 GLN B 102 ASN B 965 GLN C 102 ASN C 262 GLN C 965 GLN D 102 ASN D 262 GLN D 965 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.081819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.062310 restraints weight = 42712.179| |-----------------------------------------------------------------------------| r_work (start): 0.2661 rms_B_bonded: 1.39 r_work: 0.2559 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2439 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9206 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 33756 Z= 0.184 Angle : 0.620 8.339 46060 Z= 0.331 Chirality : 0.048 0.156 4816 Planarity : 0.004 0.033 6084 Dihedral : 5.389 58.937 4476 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.97 % Allowed : 6.07 % Favored : 92.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.13), residues: 4076 helix: 0.04 (0.22), residues: 532 sheet: 0.79 (0.14), residues: 1316 loop : 0.07 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 630 TYR 0.021 0.002 TYR B 100 PHE 0.011 0.002 PHE D 989 TRP 0.032 0.002 TRP A 553 HIS 0.007 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00401 (33756) covalent geometry : angle 0.62030 (46060) hydrogen bonds : bond 0.05380 ( 1216) hydrogen bonds : angle 5.68931 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 324 time to evaluate : 1.535 Fit side-chains REVERT: A 75 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7973 (mm-30) REVERT: A 661 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8499 (pttm) REVERT: A 773 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8209 (ttmt) REVERT: B 75 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7974 (mm-30) REVERT: B 661 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8500 (pttm) REVERT: B 773 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8214 (ttmt) REVERT: C 661 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8506 (pttm) REVERT: C 773 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.8221 (ttmt) REVERT: D 661 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8502 (pttm) REVERT: D 773 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8220 (ttmt) outliers start: 34 outliers final: 8 residues processed: 338 average time/residue: 0.9364 time to fit residues: 367.6107 Evaluate side-chains 334 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 316 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 67 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 190 optimal weight: 0.8980 chunk 333 optimal weight: 0.9980 chunk 325 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 144 optimal weight: 4.9990 chunk 343 optimal weight: 0.7980 chunk 81 optimal weight: 7.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 581 ASN A 965 GLN B 102 ASN B 581 ASN B 965 GLN C 102 ASN C 262 GLN C 581 ASN C 965 GLN D 102 ASN D 262 GLN D 581 ASN D 965 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.082250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.062945 restraints weight = 42523.398| |-----------------------------------------------------------------------------| r_work (start): 0.2678 rms_B_bonded: 1.38 r_work: 0.2578 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2460 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9197 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 33756 Z= 0.144 Angle : 0.577 7.315 46060 Z= 0.307 Chirality : 0.046 0.153 4816 Planarity : 0.004 0.033 6084 Dihedral : 5.248 57.569 4476 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.03 % Allowed : 6.50 % Favored : 92.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.13), residues: 4076 helix: 0.11 (0.22), residues: 532 sheet: 0.87 (0.14), residues: 1308 loop : 0.11 (0.13), residues: 2236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 237 TYR 0.020 0.002 TYR C 100 PHE 0.009 0.001 PHE C 989 TRP 0.033 0.002 TRP B 553 HIS 0.006 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00311 (33756) covalent geometry : angle 0.57727 (46060) hydrogen bonds : bond 0.04776 ( 1216) hydrogen bonds : angle 5.51873 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 320 time to evaluate : 1.362 Fit side-chains REVERT: A 131 GLU cc_start: 0.7723 (tm-30) cc_final: 0.7522 (tm-30) REVERT: A 135 GLN cc_start: 0.8412 (mt0) cc_final: 0.8202 (mt0) REVERT: A 237 ARG cc_start: 0.8759 (mtp85) cc_final: 0.7972 (mtp85) REVERT: A 251 ARG cc_start: 0.8098 (mpp-170) cc_final: 0.7730 (mpp-170) REVERT: A 661 LYS cc_start: 0.8829 (OUTLIER) cc_final: 0.8548 (pttm) REVERT: A 745 MET cc_start: 0.8667 (tpp) cc_final: 0.8324 (mmp) REVERT: A 773 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8072 (ttmp) REVERT: B 131 GLU cc_start: 0.7714 (tm-30) cc_final: 0.7512 (tm-30) REVERT: B 135 GLN cc_start: 0.8404 (mt0) cc_final: 0.8195 (mt0) REVERT: B 237 ARG cc_start: 0.8753 (mtp85) cc_final: 0.7963 (mtp85) REVERT: B 251 ARG cc_start: 0.8099 (mpp-170) cc_final: 0.7728 (mpp-170) REVERT: B 661 LYS cc_start: 0.8830 (OUTLIER) cc_final: 0.8550 (pttm) REVERT: B 745 MET cc_start: 0.8662 (tpp) cc_final: 0.8317 (mmp) REVERT: B 773 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8076 (ttmp) REVERT: C 251 ARG cc_start: 0.8079 (mpp-170) cc_final: 0.7680 (mpp-170) REVERT: C 661 LYS cc_start: 0.8832 (OUTLIER) cc_final: 0.8552 (pttm) REVERT: C 773 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8078 (ttmp) REVERT: D 251 ARG cc_start: 0.8075 (mpp-170) cc_final: 0.7676 (mpp-170) REVERT: D 661 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8555 (pttm) REVERT: D 773 LYS cc_start: 0.8484 (OUTLIER) cc_final: 0.8076 (ttmp) outliers start: 36 outliers final: 12 residues processed: 342 average time/residue: 0.9225 time to fit residues: 366.7326 Evaluate side-chains 336 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 316 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 515 VAL Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 515 VAL Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 515 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 515 VAL Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 383 optimal weight: 0.4980 chunk 57 optimal weight: 5.9990 chunk 244 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 289 optimal weight: 0.8980 chunk 398 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 221 optimal weight: 3.9990 chunk 400 optimal weight: 4.9990 chunk 374 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 581 ASN B 102 ASN B 581 ASN C 102 ASN C 262 GLN C 581 ASN C 965 GLN D 102 ASN D 262 GLN D 581 ASN D 965 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.082811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.063579 restraints weight = 42683.758| |-----------------------------------------------------------------------------| r_work (start): 0.2698 rms_B_bonded: 1.38 r_work: 0.2600 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2482 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2482 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9190 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 33756 Z= 0.124 Angle : 0.551 7.269 46060 Z= 0.294 Chirality : 0.045 0.149 4816 Planarity : 0.004 0.032 6084 Dihedral : 5.125 56.715 4476 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.97 % Allowed : 6.53 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.13), residues: 4076 helix: 0.23 (0.22), residues: 532 sheet: 0.94 (0.14), residues: 1304 loop : 0.12 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 292 TYR 0.019 0.001 TYR C 100 PHE 0.009 0.001 PHE A 758 TRP 0.032 0.001 TRP D 553 HIS 0.005 0.001 HIS B 395 Details of bonding type rmsd covalent geometry : bond 0.00267 (33756) covalent geometry : angle 0.55067 (46060) hydrogen bonds : bond 0.04448 ( 1216) hydrogen bonds : angle 5.39733 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 322 time to evaluate : 0.986 Fit side-chains REVERT: A 75 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.7948 (mm-30) REVERT: A 237 ARG cc_start: 0.8803 (mtp85) cc_final: 0.8578 (mtp85) REVERT: A 661 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8561 (pttm) REVERT: A 745 MET cc_start: 0.8655 (tpp) cc_final: 0.8303 (mmp) REVERT: A 773 LYS cc_start: 0.8469 (OUTLIER) cc_final: 0.8059 (ttmp) REVERT: B 75 GLU cc_start: 0.8291 (OUTLIER) cc_final: 0.7950 (mm-30) REVERT: B 237 ARG cc_start: 0.8800 (mtp85) cc_final: 0.8574 (mtp85) REVERT: B 661 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8562 (pttm) REVERT: B 745 MET cc_start: 0.8660 (tpp) cc_final: 0.8306 (mmp) REVERT: B 773 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8067 (ttmp) REVERT: C 319 ASP cc_start: 0.8390 (p0) cc_final: 0.8158 (p0) REVERT: C 661 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8561 (pttm) REVERT: C 745 MET cc_start: 0.8665 (tpp) cc_final: 0.8317 (mmp) REVERT: C 773 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8069 (ttmp) REVERT: D 319 ASP cc_start: 0.8395 (p0) cc_final: 0.8163 (p0) REVERT: D 661 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8562 (pttm) REVERT: D 745 MET cc_start: 0.8657 (tpp) cc_final: 0.8310 (mmp) REVERT: D 773 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.8071 (ttmp) outliers start: 34 outliers final: 8 residues processed: 340 average time/residue: 0.9121 time to fit residues: 359.7162 Evaluate side-chains 334 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 316 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 214 optimal weight: 0.0470 chunk 70 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 219 optimal weight: 2.9990 chunk 387 optimal weight: 5.9990 chunk 78 optimal weight: 0.9980 chunk 182 optimal weight: 2.9990 chunk 217 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 353 optimal weight: 0.5980 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 581 ASN B 102 ASN B 581 ASN C 102 ASN C 262 GLN C 581 ASN D 102 ASN D 262 GLN D 581 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.082134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.062890 restraints weight = 42571.259| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 1.37 r_work: 0.2581 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2464 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9200 moved from start: 0.1523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 33756 Z= 0.143 Angle : 0.570 7.451 46060 Z= 0.305 Chirality : 0.046 0.152 4816 Planarity : 0.004 0.033 6084 Dihedral : 5.221 57.299 4476 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 1.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.80 % Allowed : 6.76 % Favored : 92.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.13), residues: 4076 helix: 0.16 (0.22), residues: 532 sheet: 0.95 (0.14), residues: 1304 loop : 0.11 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 237 TYR 0.020 0.002 TYR C 100 PHE 0.009 0.001 PHE D 225 TRP 0.030 0.002 TRP A 553 HIS 0.006 0.001 HIS A 395 Details of bonding type rmsd covalent geometry : bond 0.00312 (33756) covalent geometry : angle 0.57028 (46060) hydrogen bonds : bond 0.04718 ( 1216) hydrogen bonds : angle 5.44968 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 314 time to evaluate : 1.115 Fit side-chains REVERT: A 75 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7927 (mm-30) REVERT: A 251 ARG cc_start: 0.8079 (mpp-170) cc_final: 0.7678 (mpp-170) REVERT: A 661 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8598 (pttm) REVERT: A 745 MET cc_start: 0.8655 (tpp) cc_final: 0.8294 (mmp) REVERT: A 773 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8075 (ttmp) REVERT: B 75 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: B 251 ARG cc_start: 0.8081 (mpp-170) cc_final: 0.7679 (mpp-170) REVERT: B 661 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8591 (pttm) REVERT: B 745 MET cc_start: 0.8665 (tpp) cc_final: 0.8306 (mmp) REVERT: B 773 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.8081 (ttmp) REVERT: C 251 ARG cc_start: 0.8075 (mpp-170) cc_final: 0.7680 (mpp-170) REVERT: C 319 ASP cc_start: 0.8403 (p0) cc_final: 0.8175 (p0) REVERT: C 661 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8597 (pttm) REVERT: C 745 MET cc_start: 0.8674 (tpp) cc_final: 0.8433 (mmt) REVERT: C 773 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8077 (ttmp) REVERT: D 251 ARG cc_start: 0.8079 (mpp-170) cc_final: 0.7684 (mpp-170) REVERT: D 319 ASP cc_start: 0.8410 (p0) cc_final: 0.8180 (p0) REVERT: D 661 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8598 (pttm) REVERT: D 745 MET cc_start: 0.8662 (tpp) cc_final: 0.8420 (mmt) REVERT: D 773 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8073 (ttmp) outliers start: 28 outliers final: 8 residues processed: 322 average time/residue: 0.9446 time to fit residues: 352.8235 Evaluate side-chains 328 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 5 optimal weight: 0.8980 chunk 341 optimal weight: 8.9990 chunk 343 optimal weight: 1.9990 chunk 316 optimal weight: 0.7980 chunk 251 optimal weight: 1.9990 chunk 159 optimal weight: 6.9990 chunk 312 optimal weight: 0.0970 chunk 337 optimal weight: 7.9990 chunk 125 optimal weight: 0.5980 chunk 119 optimal weight: 2.9990 chunk 396 optimal weight: 0.3980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 581 ASN B 102 ASN B 581 ASN C 102 ASN C 262 GLN C 581 ASN D 102 ASN D 262 GLN D 581 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.083888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.064801 restraints weight = 42675.383| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 1.38 r_work: 0.2627 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9174 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 33756 Z= 0.103 Angle : 0.522 7.198 46060 Z= 0.278 Chirality : 0.044 0.141 4816 Planarity : 0.004 0.032 6084 Dihedral : 4.954 55.028 4476 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 1.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 0.86 % Allowed : 6.99 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.13), residues: 4076 helix: 0.34 (0.23), residues: 532 sheet: 1.03 (0.14), residues: 1348 loop : 0.13 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 237 TYR 0.018 0.001 TYR A 100 PHE 0.008 0.001 PHE B 758 TRP 0.033 0.001 TRP C 553 HIS 0.004 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00218 (33756) covalent geometry : angle 0.52219 (46060) hydrogen bonds : bond 0.04007 ( 1216) hydrogen bonds : angle 5.26738 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 314 time to evaluate : 1.469 Fit side-chains REVERT: A 75 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: A 251 ARG cc_start: 0.8049 (mpp-170) cc_final: 0.7628 (mpp-170) REVERT: A 661 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8612 (pttm) REVERT: A 773 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8062 (ttmp) REVERT: B 75 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.7937 (mm-30) REVERT: B 251 ARG cc_start: 0.8050 (mpp-170) cc_final: 0.7628 (mpp-170) REVERT: B 661 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8613 (pttm) REVERT: B 773 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8075 (ttmp) REVERT: C 237 ARG cc_start: 0.8777 (mtp85) cc_final: 0.7951 (mtp85) REVERT: C 251 ARG cc_start: 0.8061 (mpp-170) cc_final: 0.7635 (mpp-170) REVERT: C 661 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8611 (pttm) REVERT: C 773 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8067 (ttmp) REVERT: D 237 ARG cc_start: 0.8792 (mtp85) cc_final: 0.7962 (mtp85) REVERT: D 251 ARG cc_start: 0.8065 (mpp-170) cc_final: 0.7638 (mpp-170) REVERT: D 661 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8610 (pttm) REVERT: D 773 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8067 (ttmp) outliers start: 30 outliers final: 8 residues processed: 328 average time/residue: 0.8778 time to fit residues: 335.5690 Evaluate side-chains 330 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 312 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 354 optimal weight: 4.9990 chunk 194 optimal weight: 0.1980 chunk 405 optimal weight: 6.9990 chunk 226 optimal weight: 1.9990 chunk 189 optimal weight: 0.4980 chunk 270 optimal weight: 5.9990 chunk 280 optimal weight: 3.9990 chunk 294 optimal weight: 0.0070 chunk 7 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 183 optimal weight: 4.9990 overall best weight: 0.9402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 102 ASN C 102 ASN ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 102 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.082572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.063351 restraints weight = 42546.740| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 1.38 r_work: 0.2596 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2478 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9194 moved from start: 0.1597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 33756 Z= 0.131 Angle : 0.556 7.471 46060 Z= 0.296 Chirality : 0.046 0.149 4816 Planarity : 0.004 0.033 6084 Dihedral : 5.100 56.301 4476 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 2.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.74 % Allowed : 6.93 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.13), residues: 4076 helix: 0.28 (0.22), residues: 532 sheet: 0.99 (0.14), residues: 1304 loop : 0.13 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 237 TYR 0.019 0.002 TYR D 100 PHE 0.009 0.001 PHE D 225 TRP 0.029 0.001 TRP C 553 HIS 0.006 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00283 (33756) covalent geometry : angle 0.55624 (46060) hydrogen bonds : bond 0.04496 ( 1216) hydrogen bonds : angle 5.35055 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 1.476 Fit side-chains REVERT: A 75 GLU cc_start: 0.8295 (OUTLIER) cc_final: 0.7931 (mm-30) REVERT: A 251 ARG cc_start: 0.8083 (mpp-170) cc_final: 0.7661 (mpp-170) REVERT: A 661 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8603 (pttm) REVERT: A 773 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8064 (ttmp) REVERT: B 75 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.7940 (mm-30) REVERT: B 251 ARG cc_start: 0.8084 (mpp-170) cc_final: 0.7660 (mpp-170) REVERT: B 661 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8602 (pttm) REVERT: B 773 LYS cc_start: 0.8486 (OUTLIER) cc_final: 0.8072 (ttmp) REVERT: C 251 ARG cc_start: 0.8091 (mpp-170) cc_final: 0.7678 (mpp-170) REVERT: C 661 LYS cc_start: 0.8834 (OUTLIER) cc_final: 0.8597 (pttm) REVERT: C 773 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8062 (ttmp) REVERT: D 251 ARG cc_start: 0.8096 (mpp-170) cc_final: 0.7682 (mpp-170) REVERT: D 661 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8601 (pttm) REVERT: D 773 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8061 (ttmp) outliers start: 26 outliers final: 11 residues processed: 320 average time/residue: 0.9328 time to fit residues: 346.7726 Evaluate side-chains 329 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 308 time to evaluate : 1.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 319 ASP Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 319 ASP Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 221 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 399 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 254 optimal weight: 0.0770 chunk 36 optimal weight: 4.9990 chunk 354 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN B 102 ASN C 102 ASN C 262 GLN D 102 ASN D 262 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.081502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2666 r_free = 0.2666 target = 0.062234 restraints weight = 42676.114| |-----------------------------------------------------------------------------| r_work (start): 0.2669 rms_B_bonded: 1.38 r_work: 0.2569 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2450 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 33756 Z= 0.170 Angle : 0.597 8.282 46060 Z= 0.318 Chirality : 0.047 0.153 4816 Planarity : 0.004 0.034 6084 Dihedral : 5.303 57.918 4476 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.69 % Allowed : 7.07 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.13), residues: 4076 helix: 0.13 (0.22), residues: 532 sheet: 0.89 (0.14), residues: 1316 loop : 0.11 (0.13), residues: 2228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 237 TYR 0.021 0.002 TYR D 100 PHE 0.010 0.002 PHE C 225 TRP 0.028 0.002 TRP C 553 HIS 0.007 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00375 (33756) covalent geometry : angle 0.59711 (46060) hydrogen bonds : bond 0.04983 ( 1216) hydrogen bonds : angle 5.51244 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 310 time to evaluate : 1.330 Fit side-chains REVERT: A 75 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7934 (mm-30) REVERT: A 251 ARG cc_start: 0.8103 (mpp-170) cc_final: 0.7717 (mpp-170) REVERT: A 661 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8604 (pttm) REVERT: A 745 MET cc_start: 0.8673 (tpp) cc_final: 0.8440 (mmp) REVERT: A 773 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8066 (ttmp) REVERT: B 75 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7943 (mm-30) REVERT: B 251 ARG cc_start: 0.8106 (mpp-170) cc_final: 0.7721 (mpp-170) REVERT: B 661 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8598 (pttm) REVERT: B 745 MET cc_start: 0.8681 (tpp) cc_final: 0.8448 (mmp) REVERT: B 773 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8076 (ttmp) REVERT: C 237 ARG cc_start: 0.8791 (mtp85) cc_final: 0.8562 (mtp85) REVERT: C 251 ARG cc_start: 0.8116 (mpp-170) cc_final: 0.7736 (mpp-170) REVERT: C 661 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8601 (pttm) REVERT: C 745 MET cc_start: 0.8651 (tpp) cc_final: 0.8416 (mmp) REVERT: C 773 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8072 (ttmp) REVERT: D 237 ARG cc_start: 0.8794 (mtp85) cc_final: 0.8565 (mtp85) REVERT: D 251 ARG cc_start: 0.8115 (mpp-170) cc_final: 0.7732 (mpp-170) REVERT: D 661 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8599 (pttm) REVERT: D 745 MET cc_start: 0.8640 (tpp) cc_final: 0.8404 (mmp) REVERT: D 773 LYS cc_start: 0.8491 (OUTLIER) cc_final: 0.8069 (ttmp) outliers start: 24 outliers final: 8 residues processed: 320 average time/residue: 0.9567 time to fit residues: 355.5906 Evaluate side-chains 328 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 310 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 364 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 220 optimal weight: 0.8980 chunk 255 optimal weight: 0.8980 chunk 357 optimal weight: 0.9980 chunk 204 optimal weight: 7.9990 chunk 105 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 311 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 262 GLN B 102 ASN B 262 GLN C 102 ASN C 262 GLN D 102 ASN D 262 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.082592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.063401 restraints weight = 42670.893| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 1.38 r_work: 0.2598 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2480 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 33756 Z= 0.125 Angle : 0.556 8.872 46060 Z= 0.295 Chirality : 0.045 0.147 4816 Planarity : 0.004 0.033 6084 Dihedral : 5.126 56.474 4476 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.52 % Allowed : 7.59 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.13), residues: 4076 helix: 0.25 (0.22), residues: 532 sheet: 0.95 (0.14), residues: 1304 loop : 0.12 (0.13), residues: 2240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 292 TYR 0.019 0.001 TYR A 100 PHE 0.008 0.001 PHE B 225 TRP 0.032 0.001 TRP D 553 HIS 0.005 0.001 HIS D 395 Details of bonding type rmsd covalent geometry : bond 0.00271 (33756) covalent geometry : angle 0.55575 (46060) hydrogen bonds : bond 0.04417 ( 1216) hydrogen bonds : angle 5.37264 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8152 Ramachandran restraints generated. 4076 Oldfield, 0 Emsley, 4076 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 308 time to evaluate : 1.263 Fit side-chains REVERT: A 75 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7929 (mm-30) REVERT: A 251 ARG cc_start: 0.8081 (mpp-170) cc_final: 0.7659 (mpp-170) REVERT: A 299 LYS cc_start: 0.9167 (mttm) cc_final: 0.8910 (mttm) REVERT: A 661 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8610 (pttm) REVERT: A 745 MET cc_start: 0.8657 (tpp) cc_final: 0.8445 (mmp) REVERT: A 773 LYS cc_start: 0.8472 (OUTLIER) cc_final: 0.8058 (ttmp) REVERT: B 75 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7945 (mm-30) REVERT: B 251 ARG cc_start: 0.8086 (mpp-170) cc_final: 0.7665 (mpp-170) REVERT: B 661 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8608 (pttm) REVERT: B 745 MET cc_start: 0.8658 (tpp) cc_final: 0.8444 (mmp) REVERT: B 773 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8071 (ttmp) REVERT: C 251 ARG cc_start: 0.8088 (mpp-170) cc_final: 0.7669 (mpp-170) REVERT: C 661 LYS cc_start: 0.8839 (OUTLIER) cc_final: 0.8605 (pttm) REVERT: C 745 MET cc_start: 0.8675 (tpp) cc_final: 0.8461 (mmp) REVERT: C 773 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.8061 (ttmp) REVERT: D 251 ARG cc_start: 0.8086 (mpp-170) cc_final: 0.7666 (mpp-170) REVERT: D 299 LYS cc_start: 0.9053 (mtpp) cc_final: 0.8804 (mtpt) REVERT: D 661 LYS cc_start: 0.8840 (OUTLIER) cc_final: 0.8605 (pttm) REVERT: D 745 MET cc_start: 0.8668 (tpp) cc_final: 0.8453 (mmp) REVERT: D 773 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.8057 (ttmp) outliers start: 18 outliers final: 8 residues processed: 316 average time/residue: 0.9601 time to fit residues: 351.9391 Evaluate side-chains 326 residues out of total 3492 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 308 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 661 LYS Chi-restraints excluded: chain A residue 773 LYS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain B residue 75 GLU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 661 LYS Chi-restraints excluded: chain B residue 773 LYS Chi-restraints excluded: chain B residue 855 THR Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 661 LYS Chi-restraints excluded: chain C residue 773 LYS Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain D residue 546 LEU Chi-restraints excluded: chain D residue 661 LYS Chi-restraints excluded: chain D residue 773 LYS Chi-restraints excluded: chain D residue 855 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 71 optimal weight: 0.3980 chunk 150 optimal weight: 4.9990 chunk 293 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 224 optimal weight: 3.9990 chunk 188 optimal weight: 2.9990 chunk 365 optimal weight: 1.9990 chunk 358 optimal weight: 0.5980 chunk 196 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 228 optimal weight: 1.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 ASN A 262 GLN A 581 ASN B 102 ASN B 262 GLN B 581 ASN C 102 ASN C 581 ASN D 102 ASN D 581 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.083202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.064094 restraints weight = 42546.090| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 1.37 r_work: 0.2613 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2496 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9186 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 33756 Z= 0.117 Angle : 0.544 9.168 46060 Z= 0.289 Chirality : 0.045 0.147 4816 Planarity : 0.004 0.033 6084 Dihedral : 5.033 55.722 4476 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.57 % Allowed : 7.62 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.06 % Cis-general : 0.31 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.13), residues: 4076 helix: 0.29 (0.22), residues: 532 sheet: 1.03 (0.14), residues: 1348 loop : 0.13 (0.13), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 292 TYR 0.018 0.001 TYR B 100 PHE 0.008 0.001 PHE B 225 TRP 0.032 0.001 TRP A 553 HIS 0.005 0.001 HIS C 395 Details of bonding type rmsd covalent geometry : bond 0.00251 (33756) covalent geometry : angle 0.54376 (46060) hydrogen bonds : bond 0.04254 ( 1216) hydrogen bonds : angle 5.30838 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16666.18 seconds wall clock time: 283 minutes 26.75 seconds (17006.75 seconds total)