Starting phenix.real_space_refine on Wed Feb 21 13:03:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw8_10034/02_2024/6rw8_10034.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw8_10034/02_2024/6rw8_10034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.84 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw8_10034/02_2024/6rw8_10034.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw8_10034/02_2024/6rw8_10034.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw8_10034/02_2024/6rw8_10034.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rw8_10034/02_2024/6rw8_10034.pdb" } resolution = 2.84 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 335 5.16 5 C 59470 2.51 5 N 15660 2.21 5 O 18035 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 102": "NH1" <-> "NH2" Residue "A PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 332": "NH1" <-> "NH2" Residue "A ARG 334": "NH1" <-> "NH2" Residue "A TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 562": "NH1" <-> "NH2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 695": "NH1" <-> "NH2" Residue "A ARG 1014": "NH1" <-> "NH2" Residue "A TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1614": "NH1" <-> "NH2" Residue "A ARG 1662": "NH1" <-> "NH2" Residue "A ARG 1677": "NH1" <-> "NH2" Residue "A PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1925": "NH1" <-> "NH2" Residue "A ARG 2062": "NH1" <-> "NH2" Residue "A ARG 2189": "NH1" <-> "NH2" Residue "A ARG 2343": "NH1" <-> "NH2" Residue "A ARG 2452": "NH1" <-> "NH2" Residue "B ARG 102": "NH1" <-> "NH2" Residue "B PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 332": "NH1" <-> "NH2" Residue "B ARG 334": "NH1" <-> "NH2" Residue "B TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 562": "NH1" <-> "NH2" Residue "B ARG 595": "NH1" <-> "NH2" Residue "B TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 695": "NH1" <-> "NH2" Residue "B ARG 1014": "NH1" <-> "NH2" Residue "B TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1614": "NH1" <-> "NH2" Residue "B ARG 1662": "NH1" <-> "NH2" Residue "B ARG 1677": "NH1" <-> "NH2" Residue "B PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1925": "NH1" <-> "NH2" Residue "B ARG 2062": "NH1" <-> "NH2" Residue "B ARG 2189": "NH1" <-> "NH2" Residue "B ARG 2343": "NH1" <-> "NH2" Residue "B ARG 2452": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 332": "NH1" <-> "NH2" Residue "C ARG 334": "NH1" <-> "NH2" Residue "C TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 562": "NH1" <-> "NH2" Residue "C ARG 595": "NH1" <-> "NH2" Residue "C TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 695": "NH1" <-> "NH2" Residue "C ARG 1014": "NH1" <-> "NH2" Residue "C TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1614": "NH1" <-> "NH2" Residue "C ARG 1662": "NH1" <-> "NH2" Residue "C ARG 1677": "NH1" <-> "NH2" Residue "C PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 1925": "NH1" <-> "NH2" Residue "C ARG 2062": "NH1" <-> "NH2" Residue "C ARG 2189": "NH1" <-> "NH2" Residue "C ARG 2343": "NH1" <-> "NH2" Residue "C ARG 2452": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 332": "NH1" <-> "NH2" Residue "D ARG 334": "NH1" <-> "NH2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 562": "NH1" <-> "NH2" Residue "D ARG 595": "NH1" <-> "NH2" Residue "D TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 695": "NH1" <-> "NH2" Residue "D ARG 1014": "NH1" <-> "NH2" Residue "D TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1614": "NH1" <-> "NH2" Residue "D ARG 1662": "NH1" <-> "NH2" Residue "D ARG 1677": "NH1" <-> "NH2" Residue "D PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 1925": "NH1" <-> "NH2" Residue "D ARG 2062": "NH1" <-> "NH2" Residue "D ARG 2189": "NH1" <-> "NH2" Residue "D ARG 2343": "NH1" <-> "NH2" Residue "D ARG 2452": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 222": "NH1" <-> "NH2" Residue "E TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 332": "NH1" <-> "NH2" Residue "E ARG 334": "NH1" <-> "NH2" Residue "E TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 562": "NH1" <-> "NH2" Residue "E ARG 595": "NH1" <-> "NH2" Residue "E TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 695": "NH1" <-> "NH2" Residue "E ARG 1014": "NH1" <-> "NH2" Residue "E TYR 1110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 1318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1614": "NH1" <-> "NH2" Residue "E ARG 1662": "NH1" <-> "NH2" Residue "E ARG 1677": "NH1" <-> "NH2" Residue "E PHE 1727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1728": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 1779": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 1925": "NH1" <-> "NH2" Residue "E ARG 2062": "NH1" <-> "NH2" Residue "E ARG 2189": "NH1" <-> "NH2" Residue "E ARG 2343": "NH1" <-> "NH2" Residue "E ARG 2452": "NH1" <-> "NH2" Time to flip residues: 0.27s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 93500 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 18700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2337, 18700 Classifications: {'peptide': 2337} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 2253} Chain breaks: 2 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 36.45, per 1000 atoms: 0.39 Number of scatterers: 93500 At special positions: 0 Unit cell: (189.24, 185.82, 262.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 335 16.00 O 18035 8.00 N 15660 7.00 C 59470 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 - 3.50 Amino acid : False - 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: 29.71 Conformation dependent library (CDL) restraints added in 12.7 seconds 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 22280 Finding SS restraints... Secondary structure from input PDB file: 440 helices and 85 sheets defined 50.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.90 Creating SS restraints... Processing helix chain 'A' and resid 21 through 28 removed outlier: 4.081A pdb=" N SER A 26 " --> pdb=" O LEU A 22 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE A 27 " --> pdb=" O THR A 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET A 28 " --> pdb=" O ASN A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 37 Processing helix chain 'A' and resid 43 through 69 Processing helix chain 'A' and resid 72 through 76 Processing helix chain 'A' and resid 88 through 96 Processing helix chain 'A' and resid 98 through 102 Processing helix chain 'A' and resid 114 through 127 Processing helix chain 'A' and resid 137 through 142 Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.327A pdb=" N ALA A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER A 147 " --> pdb=" O PRO A 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 142 through 147' Processing helix chain 'A' and resid 151 through 157 Processing helix chain 'A' and resid 162 through 178 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 217 through 223 removed outlier: 3.501A pdb=" N SER A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 228 Processing helix chain 'A' and resid 231 through 240 Processing helix chain 'A' and resid 243 through 252 removed outlier: 3.711A pdb=" N GLU A 252 " --> pdb=" O GLN A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 267 removed outlier: 3.758A pdb=" N LYS A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 286 removed outlier: 3.563A pdb=" N LEU A 281 " --> pdb=" O SER A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 293 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.659A pdb=" N HIS A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 341' Processing helix chain 'A' and resid 402 through 408 Processing helix chain 'A' and resid 437 through 456 Processing helix chain 'A' and resid 458 through 470 removed outlier: 3.527A pdb=" N ILE A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 493 removed outlier: 3.520A pdb=" N GLN A 487 " --> pdb=" O LEU A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 504 removed outlier: 3.630A pdb=" N LEU A 503 " --> pdb=" O ASP A 499 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 550 through 562 removed outlier: 3.514A pdb=" N LEU A 554 " --> pdb=" O ASN A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 575 removed outlier: 3.697A pdb=" N ALA A 575 " --> pdb=" O LEU A 571 " (cutoff:3.500A) Processing helix chain 'A' and resid 586 through 602 removed outlier: 4.936A pdb=" N LEU A 592 " --> pdb=" O GLU A 588 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL A 596 " --> pdb=" O LEU A 592 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARG A 597 " --> pdb=" O LEU A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 616 Processing helix chain 'A' and resid 623 through 627 Processing helix chain 'A' and resid 628 through 650 Processing helix chain 'A' and resid 652 through 661 Processing helix chain 'A' and resid 669 through 683 removed outlier: 3.789A pdb=" N LEU A 683 " --> pdb=" O LEU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 705 removed outlier: 5.169A pdb=" N ILE A 694 " --> pdb=" O ASP A 690 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG A 695 " --> pdb=" O ASP A 691 " (cutoff:3.500A) Proline residue: A 699 - end of helix Processing helix chain 'A' and resid 709 through 722 Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 743 through 766 Processing helix chain 'A' and resid 773 through 780 removed outlier: 4.052A pdb=" N LEU A 777 " --> pdb=" O GLU A 773 " (cutoff:3.500A) Processing helix chain 'A' and resid 781 through 784 Processing helix chain 'A' and resid 794 through 812 removed outlier: 3.618A pdb=" N GLY A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 824 removed outlier: 3.578A pdb=" N LEU A 824 " --> pdb=" O THR A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 836 Processing helix chain 'A' and resid 839 through 851 Processing helix chain 'A' and resid 860 through 876 Processing helix chain 'A' and resid 879 through 888 Processing helix chain 'A' and resid 901 through 914 Processing helix chain 'A' and resid 917 through 943 removed outlier: 4.140A pdb=" N THR A 934 " --> pdb=" O GLU A 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA A 938 " --> pdb=" O THR A 934 " (cutoff:3.500A) Processing helix chain 'A' and resid 951 through 960 Processing helix chain 'A' and resid 972 through 990 removed outlier: 3.705A pdb=" N ASN A 990 " --> pdb=" O ASN A 986 " (cutoff:3.500A) Processing helix chain 'A' and resid 999 through 1002 removed outlier: 3.586A pdb=" N THR A1002 " --> pdb=" O PRO A 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 999 through 1002' Processing helix chain 'A' and resid 1003 through 1008 Processing helix chain 'A' and resid 1015 through 1028 Processing helix chain 'A' and resid 1029 through 1032 Processing helix chain 'A' and resid 1042 through 1052 Processing helix chain 'A' and resid 1058 through 1078 removed outlier: 3.536A pdb=" N ALA A1072 " --> pdb=" O ASN A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1210 removed outlier: 3.807A pdb=" N LYS A1210 " --> pdb=" O ASN A1206 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1271 Processing helix chain 'A' and resid 1272 through 1276 Processing helix chain 'A' and resid 1582 through 1586 Processing helix chain 'A' and resid 1612 through 1623 removed outlier: 4.136A pdb=" N ALA A1617 " --> pdb=" O SER A1613 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU A1618 " --> pdb=" O ARG A1614 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG A1619 " --> pdb=" O LYS A1615 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE A1622 " --> pdb=" O GLU A1618 " (cutoff:3.500A) Processing helix chain 'A' and resid 1623 through 1628 removed outlier: 3.690A pdb=" N VAL A1627 " --> pdb=" O GLY A1623 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU A1628 " --> pdb=" O ILE A1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1623 through 1628' Processing helix chain 'A' and resid 1629 through 1634 removed outlier: 3.531A pdb=" N GLN A1633 " --> pdb=" O SER A1629 " (cutoff:3.500A) Processing helix chain 'A' and resid 1783 through 1792 Processing helix chain 'A' and resid 1792 through 1805 Processing helix chain 'A' and resid 1807 through 1817 removed outlier: 3.861A pdb=" N ARG A1813 " --> pdb=" O THR A1809 " (cutoff:3.500A) Processing helix chain 'A' and resid 1837 through 1842 Processing helix chain 'A' and resid 1855 through 1863 Processing helix chain 'A' and resid 1864 through 1888 Processing helix chain 'A' and resid 1891 through 1910 removed outlier: 3.521A pdb=" N ASN A1896 " --> pdb=" O ARG A1892 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU A1897 " --> pdb=" O ASP A1893 " (cutoff:3.500A) Processing helix chain 'A' and resid 1925 through 1930 Processing helix chain 'A' and resid 1931 through 1947 Processing helix chain 'A' and resid 1969 through 1987 removed outlier: 3.658A pdb=" N GLN A1973 " --> pdb=" O ASN A1969 " (cutoff:3.500A) Processing helix chain 'A' and resid 2034 through 2121 removed outlier: 3.720A pdb=" N LYS A2089 " --> pdb=" O LYS A2085 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY A2107 " --> pdb=" O GLU A2103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A2121 " --> pdb=" O THR A2117 " (cutoff:3.500A) Processing helix chain 'A' and resid 2124 through 2143 removed outlier: 4.026A pdb=" N THR A2142 " --> pdb=" O SER A2138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER A2143 " --> pdb=" O VAL A2139 " (cutoff:3.500A) Processing helix chain 'A' and resid 2144 through 2155 Processing helix chain 'A' and resid 2171 through 2260 Processing helix chain 'A' and resid 2263 through 2300 removed outlier: 3.505A pdb=" N TYR A2267 " --> pdb=" O ASN A2263 " (cutoff:3.500A) Processing helix chain 'A' and resid 2314 through 2318 Processing helix chain 'A' and resid 2321 through 2341 Processing helix chain 'A' and resid 2353 through 2359 Processing helix chain 'A' and resid 2366 through 2377 removed outlier: 3.818A pdb=" N THR A2372 " --> pdb=" O LYS A2368 " (cutoff:3.500A) Processing helix chain 'A' and resid 2401 through 2405 Processing helix chain 'A' and resid 2406 through 2410 removed outlier: 3.537A pdb=" N THR A2409 " --> pdb=" O ASN A2406 " (cutoff:3.500A) Processing helix chain 'A' and resid 2412 through 2416 removed outlier: 3.647A pdb=" N LEU A2415 " --> pdb=" O PRO A2412 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A2416 " --> pdb=" O ASP A2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 2412 through 2416' Processing helix chain 'A' and resid 2452 through 2454 No H-bonds generated for 'chain 'A' and resid 2452 through 2454' Processing helix chain 'A' and resid 2503 through 2509 removed outlier: 3.798A pdb=" N LEU A2507 " --> pdb=" O GLN A2503 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 28 removed outlier: 4.081A pdb=" N SER B 26 " --> pdb=" O LEU B 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE B 27 " --> pdb=" O THR B 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 43 through 69 Processing helix chain 'B' and resid 72 through 76 Processing helix chain 'B' and resid 88 through 96 Processing helix chain 'B' and resid 98 through 102 Processing helix chain 'B' and resid 114 through 127 Processing helix chain 'B' and resid 137 through 142 Processing helix chain 'B' and resid 142 through 147 removed outlier: 4.327A pdb=" N ALA B 146 " --> pdb=" O ARG B 142 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER B 147 " --> pdb=" O PRO B 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 142 through 147' Processing helix chain 'B' and resid 151 through 157 Processing helix chain 'B' and resid 162 through 178 Processing helix chain 'B' and resid 180 through 189 Processing helix chain 'B' and resid 200 through 214 Processing helix chain 'B' and resid 217 through 223 removed outlier: 3.501A pdb=" N SER B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 228 Processing helix chain 'B' and resid 231 through 240 Processing helix chain 'B' and resid 243 through 252 removed outlier: 3.712A pdb=" N GLU B 252 " --> pdb=" O GLN B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 3.757A pdb=" N LYS B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 286 removed outlier: 3.563A pdb=" N LEU B 281 " --> pdb=" O SER B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 288 through 293 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.658A pdb=" N HIS B 341 " --> pdb=" O PHE B 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 337 through 341' Processing helix chain 'B' and resid 402 through 408 Processing helix chain 'B' and resid 437 through 456 Processing helix chain 'B' and resid 458 through 470 removed outlier: 3.526A pdb=" N ILE B 469 " --> pdb=" O VAL B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 493 removed outlier: 3.519A pdb=" N GLN B 487 " --> pdb=" O LEU B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 504 removed outlier: 3.630A pdb=" N LEU B 503 " --> pdb=" O ASP B 499 " (cutoff:3.500A) Processing helix chain 'B' and resid 518 through 525 Processing helix chain 'B' and resid 550 through 562 removed outlier: 3.514A pdb=" N LEU B 554 " --> pdb=" O ASN B 550 " (cutoff:3.500A) Processing helix chain 'B' and resid 564 through 575 removed outlier: 3.697A pdb=" N ALA B 575 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 586 through 602 removed outlier: 4.937A pdb=" N LEU B 592 " --> pdb=" O GLU B 588 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ARG B 595 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL B 596 " --> pdb=" O LEU B 592 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) Processing helix chain 'B' and resid 606 through 616 Processing helix chain 'B' and resid 623 through 627 Processing helix chain 'B' and resid 628 through 650 Processing helix chain 'B' and resid 652 through 661 Processing helix chain 'B' and resid 669 through 683 removed outlier: 3.788A pdb=" N LEU B 683 " --> pdb=" O LEU B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 688 through 705 removed outlier: 5.169A pdb=" N ILE B 694 " --> pdb=" O ASP B 690 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N ARG B 695 " --> pdb=" O ASP B 691 " (cutoff:3.500A) Proline residue: B 699 - end of helix Processing helix chain 'B' and resid 709 through 722 Processing helix chain 'B' and resid 724 through 728 Processing helix chain 'B' and resid 743 through 766 Processing helix chain 'B' and resid 773 through 780 removed outlier: 4.052A pdb=" N LEU B 777 " --> pdb=" O GLU B 773 " (cutoff:3.500A) Processing helix chain 'B' and resid 781 through 784 Processing helix chain 'B' and resid 794 through 812 removed outlier: 3.618A pdb=" N GLY B 812 " --> pdb=" O ILE B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 814 through 824 removed outlier: 3.577A pdb=" N LEU B 824 " --> pdb=" O THR B 820 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 836 Processing helix chain 'B' and resid 839 through 851 Processing helix chain 'B' and resid 860 through 876 Processing helix chain 'B' and resid 879 through 888 Processing helix chain 'B' and resid 901 through 914 Processing helix chain 'B' and resid 917 through 943 removed outlier: 4.140A pdb=" N THR B 934 " --> pdb=" O GLU B 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA B 938 " --> pdb=" O THR B 934 " (cutoff:3.500A) Processing helix chain 'B' and resid 951 through 960 Processing helix chain 'B' and resid 972 through 990 removed outlier: 3.705A pdb=" N ASN B 990 " --> pdb=" O ASN B 986 " (cutoff:3.500A) Processing helix chain 'B' and resid 999 through 1002 removed outlier: 3.586A pdb=" N THR B1002 " --> pdb=" O PRO B 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 999 through 1002' Processing helix chain 'B' and resid 1003 through 1008 Processing helix chain 'B' and resid 1015 through 1028 Processing helix chain 'B' and resid 1029 through 1032 Processing helix chain 'B' and resid 1042 through 1052 Processing helix chain 'B' and resid 1058 through 1078 removed outlier: 3.536A pdb=" N ALA B1072 " --> pdb=" O ASN B1068 " (cutoff:3.500A) Processing helix chain 'B' and resid 1200 through 1210 removed outlier: 3.807A pdb=" N LYS B1210 " --> pdb=" O ASN B1206 " (cutoff:3.500A) Processing helix chain 'B' and resid 1261 through 1271 Processing helix chain 'B' and resid 1272 through 1276 Processing helix chain 'B' and resid 1582 through 1586 Processing helix chain 'B' and resid 1612 through 1623 removed outlier: 4.137A pdb=" N ALA B1617 " --> pdb=" O SER B1613 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU B1618 " --> pdb=" O ARG B1614 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG B1619 " --> pdb=" O LYS B1615 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE B1622 " --> pdb=" O GLU B1618 " (cutoff:3.500A) Processing helix chain 'B' and resid 1623 through 1628 removed outlier: 3.690A pdb=" N VAL B1627 " --> pdb=" O GLY B1623 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU B1628 " --> pdb=" O ILE B1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1623 through 1628' Processing helix chain 'B' and resid 1629 through 1634 removed outlier: 3.532A pdb=" N GLN B1633 " --> pdb=" O SER B1629 " (cutoff:3.500A) Processing helix chain 'B' and resid 1783 through 1792 Processing helix chain 'B' and resid 1792 through 1805 Processing helix chain 'B' and resid 1807 through 1817 removed outlier: 3.860A pdb=" N ARG B1813 " --> pdb=" O THR B1809 " (cutoff:3.500A) Processing helix chain 'B' and resid 1837 through 1842 Processing helix chain 'B' and resid 1855 through 1863 Processing helix chain 'B' and resid 1864 through 1888 Processing helix chain 'B' and resid 1891 through 1910 removed outlier: 3.521A pdb=" N ASN B1896 " --> pdb=" O ARG B1892 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU B1897 " --> pdb=" O ASP B1893 " (cutoff:3.500A) Processing helix chain 'B' and resid 1925 through 1930 Processing helix chain 'B' and resid 1931 through 1947 Processing helix chain 'B' and resid 1969 through 1987 removed outlier: 3.659A pdb=" N GLN B1973 " --> pdb=" O ASN B1969 " (cutoff:3.500A) Processing helix chain 'B' and resid 2034 through 2121 removed outlier: 3.720A pdb=" N LYS B2089 " --> pdb=" O LYS B2085 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY B2107 " --> pdb=" O GLU B2103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU B2121 " --> pdb=" O THR B2117 " (cutoff:3.500A) Processing helix chain 'B' and resid 2124 through 2143 removed outlier: 4.026A pdb=" N THR B2142 " --> pdb=" O SER B2138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER B2143 " --> pdb=" O VAL B2139 " (cutoff:3.500A) Processing helix chain 'B' and resid 2144 through 2155 Processing helix chain 'B' and resid 2171 through 2260 Processing helix chain 'B' and resid 2263 through 2300 removed outlier: 3.505A pdb=" N TYR B2267 " --> pdb=" O ASN B2263 " (cutoff:3.500A) Processing helix chain 'B' and resid 2314 through 2318 Processing helix chain 'B' and resid 2321 through 2341 Processing helix chain 'B' and resid 2353 through 2359 Processing helix chain 'B' and resid 2366 through 2377 removed outlier: 3.818A pdb=" N THR B2372 " --> pdb=" O LYS B2368 " (cutoff:3.500A) Processing helix chain 'B' and resid 2401 through 2405 Processing helix chain 'B' and resid 2406 through 2410 removed outlier: 3.537A pdb=" N THR B2409 " --> pdb=" O ASN B2406 " (cutoff:3.500A) Processing helix chain 'B' and resid 2412 through 2416 removed outlier: 3.647A pdb=" N LEU B2415 " --> pdb=" O PRO B2412 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY B2416 " --> pdb=" O ASP B2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 2412 through 2416' Processing helix chain 'B' and resid 2452 through 2454 No H-bonds generated for 'chain 'B' and resid 2452 through 2454' Processing helix chain 'B' and resid 2503 through 2509 removed outlier: 3.799A pdb=" N LEU B2507 " --> pdb=" O GLN B2503 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 28 removed outlier: 4.081A pdb=" N SER C 26 " --> pdb=" O LEU C 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE C 27 " --> pdb=" O THR C 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 37 Processing helix chain 'C' and resid 43 through 69 Processing helix chain 'C' and resid 72 through 76 Processing helix chain 'C' and resid 88 through 96 Processing helix chain 'C' and resid 98 through 102 Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 137 through 142 Processing helix chain 'C' and resid 142 through 147 removed outlier: 4.326A pdb=" N ALA C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER C 147 " --> pdb=" O PRO C 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 142 through 147' Processing helix chain 'C' and resid 151 through 157 Processing helix chain 'C' and resid 162 through 178 Processing helix chain 'C' and resid 180 through 189 Processing helix chain 'C' and resid 200 through 214 Processing helix chain 'C' and resid 217 through 223 removed outlier: 3.500A pdb=" N SER C 221 " --> pdb=" O LEU C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 223 through 228 Processing helix chain 'C' and resid 231 through 240 Processing helix chain 'C' and resid 243 through 252 removed outlier: 3.712A pdb=" N GLU C 252 " --> pdb=" O GLN C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 267 removed outlier: 3.757A pdb=" N LYS C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 286 removed outlier: 3.564A pdb=" N LEU C 281 " --> pdb=" O SER C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 293 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.659A pdb=" N HIS C 341 " --> pdb=" O PHE C 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 337 through 341' Processing helix chain 'C' and resid 402 through 408 Processing helix chain 'C' and resid 437 through 456 Processing helix chain 'C' and resid 458 through 470 removed outlier: 3.526A pdb=" N ILE C 469 " --> pdb=" O VAL C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 476 through 493 removed outlier: 3.519A pdb=" N GLN C 487 " --> pdb=" O LEU C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 504 removed outlier: 3.629A pdb=" N LEU C 503 " --> pdb=" O ASP C 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 525 Processing helix chain 'C' and resid 550 through 562 removed outlier: 3.514A pdb=" N LEU C 554 " --> pdb=" O ASN C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 564 through 575 removed outlier: 3.697A pdb=" N ALA C 575 " --> pdb=" O LEU C 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 586 through 602 removed outlier: 4.937A pdb=" N LEU C 592 " --> pdb=" O GLU C 588 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG C 595 " --> pdb=" O SER C 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL C 596 " --> pdb=" O LEU C 592 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG C 597 " --> pdb=" O LEU C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 606 through 616 Processing helix chain 'C' and resid 623 through 627 Processing helix chain 'C' and resid 628 through 650 Processing helix chain 'C' and resid 652 through 661 Processing helix chain 'C' and resid 669 through 683 removed outlier: 3.789A pdb=" N LEU C 683 " --> pdb=" O LEU C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 688 through 705 removed outlier: 5.169A pdb=" N ILE C 694 " --> pdb=" O ASP C 690 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG C 695 " --> pdb=" O ASP C 691 " (cutoff:3.500A) Proline residue: C 699 - end of helix Processing helix chain 'C' and resid 709 through 722 Processing helix chain 'C' and resid 724 through 728 Processing helix chain 'C' and resid 743 through 766 Processing helix chain 'C' and resid 773 through 780 removed outlier: 4.053A pdb=" N LEU C 777 " --> pdb=" O GLU C 773 " (cutoff:3.500A) Processing helix chain 'C' and resid 781 through 784 Processing helix chain 'C' and resid 794 through 812 removed outlier: 3.618A pdb=" N GLY C 812 " --> pdb=" O ILE C 808 " (cutoff:3.500A) Processing helix chain 'C' and resid 814 through 824 removed outlier: 3.578A pdb=" N LEU C 824 " --> pdb=" O THR C 820 " (cutoff:3.500A) Processing helix chain 'C' and resid 831 through 836 Processing helix chain 'C' and resid 839 through 851 Processing helix chain 'C' and resid 860 through 876 Processing helix chain 'C' and resid 879 through 888 Processing helix chain 'C' and resid 901 through 914 Processing helix chain 'C' and resid 917 through 943 removed outlier: 4.140A pdb=" N THR C 934 " --> pdb=" O GLU C 930 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA C 938 " --> pdb=" O THR C 934 " (cutoff:3.500A) Processing helix chain 'C' and resid 951 through 960 Processing helix chain 'C' and resid 972 through 990 removed outlier: 3.705A pdb=" N ASN C 990 " --> pdb=" O ASN C 986 " (cutoff:3.500A) Processing helix chain 'C' and resid 999 through 1002 removed outlier: 3.585A pdb=" N THR C1002 " --> pdb=" O PRO C 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 999 through 1002' Processing helix chain 'C' and resid 1003 through 1008 Processing helix chain 'C' and resid 1015 through 1028 Processing helix chain 'C' and resid 1029 through 1032 Processing helix chain 'C' and resid 1042 through 1052 Processing helix chain 'C' and resid 1058 through 1078 removed outlier: 3.536A pdb=" N ALA C1072 " --> pdb=" O ASN C1068 " (cutoff:3.500A) Processing helix chain 'C' and resid 1200 through 1210 removed outlier: 3.807A pdb=" N LYS C1210 " --> pdb=" O ASN C1206 " (cutoff:3.500A) Processing helix chain 'C' and resid 1261 through 1271 Processing helix chain 'C' and resid 1272 through 1276 Processing helix chain 'C' and resid 1582 through 1586 Processing helix chain 'C' and resid 1612 through 1623 removed outlier: 4.137A pdb=" N ALA C1617 " --> pdb=" O SER C1613 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU C1618 " --> pdb=" O ARG C1614 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG C1619 " --> pdb=" O LYS C1615 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE C1622 " --> pdb=" O GLU C1618 " (cutoff:3.500A) Processing helix chain 'C' and resid 1623 through 1628 removed outlier: 3.690A pdb=" N VAL C1627 " --> pdb=" O GLY C1623 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU C1628 " --> pdb=" O ILE C1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1623 through 1628' Processing helix chain 'C' and resid 1629 through 1634 removed outlier: 3.531A pdb=" N GLN C1633 " --> pdb=" O SER C1629 " (cutoff:3.500A) Processing helix chain 'C' and resid 1783 through 1792 Processing helix chain 'C' and resid 1792 through 1805 Processing helix chain 'C' and resid 1807 through 1817 removed outlier: 3.860A pdb=" N ARG C1813 " --> pdb=" O THR C1809 " (cutoff:3.500A) Processing helix chain 'C' and resid 1837 through 1842 Processing helix chain 'C' and resid 1855 through 1863 Processing helix chain 'C' and resid 1864 through 1888 Processing helix chain 'C' and resid 1891 through 1910 removed outlier: 3.522A pdb=" N ASN C1896 " --> pdb=" O ARG C1892 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C1897 " --> pdb=" O ASP C1893 " (cutoff:3.500A) Processing helix chain 'C' and resid 1925 through 1930 Processing helix chain 'C' and resid 1931 through 1947 Processing helix chain 'C' and resid 1969 through 1987 removed outlier: 3.660A pdb=" N GLN C1973 " --> pdb=" O ASN C1969 " (cutoff:3.500A) Processing helix chain 'C' and resid 2034 through 2121 removed outlier: 3.720A pdb=" N LYS C2089 " --> pdb=" O LYS C2085 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLY C2107 " --> pdb=" O GLU C2103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU C2121 " --> pdb=" O THR C2117 " (cutoff:3.500A) Processing helix chain 'C' and resid 2124 through 2143 removed outlier: 4.026A pdb=" N THR C2142 " --> pdb=" O SER C2138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER C2143 " --> pdb=" O VAL C2139 " (cutoff:3.500A) Processing helix chain 'C' and resid 2144 through 2155 Processing helix chain 'C' and resid 2171 through 2260 Processing helix chain 'C' and resid 2263 through 2300 removed outlier: 3.505A pdb=" N TYR C2267 " --> pdb=" O ASN C2263 " (cutoff:3.500A) Processing helix chain 'C' and resid 2314 through 2318 Processing helix chain 'C' and resid 2321 through 2341 Processing helix chain 'C' and resid 2353 through 2359 Processing helix chain 'C' and resid 2366 through 2377 removed outlier: 3.818A pdb=" N THR C2372 " --> pdb=" O LYS C2368 " (cutoff:3.500A) Processing helix chain 'C' and resid 2401 through 2405 Processing helix chain 'C' and resid 2406 through 2410 removed outlier: 3.538A pdb=" N THR C2409 " --> pdb=" O ASN C2406 " (cutoff:3.500A) Processing helix chain 'C' and resid 2412 through 2416 removed outlier: 3.647A pdb=" N LEU C2415 " --> pdb=" O PRO C2412 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY C2416 " --> pdb=" O ASP C2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 2412 through 2416' Processing helix chain 'C' and resid 2452 through 2454 No H-bonds generated for 'chain 'C' and resid 2452 through 2454' Processing helix chain 'C' and resid 2503 through 2509 removed outlier: 3.799A pdb=" N LEU C2507 " --> pdb=" O GLN C2503 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 28 removed outlier: 4.082A pdb=" N SER D 26 " --> pdb=" O LEU D 22 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N PHE D 27 " --> pdb=" O THR D 23 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N MET D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 37 Processing helix chain 'D' and resid 43 through 69 Processing helix chain 'D' and resid 72 through 76 Processing helix chain 'D' and resid 88 through 96 Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 114 through 127 Processing helix chain 'D' and resid 137 through 142 Processing helix chain 'D' and resid 142 through 147 removed outlier: 4.326A pdb=" N ALA D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N SER D 147 " --> pdb=" O PRO D 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 142 through 147' Processing helix chain 'D' and resid 151 through 157 Processing helix chain 'D' and resid 162 through 178 Processing helix chain 'D' and resid 180 through 189 Processing helix chain 'D' and resid 200 through 214 Processing helix chain 'D' and resid 217 through 223 removed outlier: 3.501A pdb=" N SER D 221 " --> pdb=" O LEU D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 228 Processing helix chain 'D' and resid 231 through 240 Processing helix chain 'D' and resid 243 through 252 removed outlier: 3.712A pdb=" N GLU D 252 " --> pdb=" O GLN D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 267 removed outlier: 3.758A pdb=" N LYS D 264 " --> pdb=" O THR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 277 through 286 removed outlier: 3.564A pdb=" N LEU D 281 " --> pdb=" O SER D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 293 Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.658A pdb=" N HIS D 341 " --> pdb=" O PHE D 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 337 through 341' Processing helix chain 'D' and resid 402 through 408 Processing helix chain 'D' and resid 437 through 456 Processing helix chain 'D' and resid 458 through 470 removed outlier: 3.526A pdb=" N ILE D 469 " --> pdb=" O VAL D 465 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 493 removed outlier: 3.520A pdb=" N GLN D 487 " --> pdb=" O LEU D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 504 removed outlier: 3.629A pdb=" N LEU D 503 " --> pdb=" O ASP D 499 " (cutoff:3.500A) Processing helix chain 'D' and resid 518 through 525 Processing helix chain 'D' and resid 550 through 562 removed outlier: 3.513A pdb=" N LEU D 554 " --> pdb=" O ASN D 550 " (cutoff:3.500A) Processing helix chain 'D' and resid 564 through 575 removed outlier: 3.697A pdb=" N ALA D 575 " --> pdb=" O LEU D 571 " (cutoff:3.500A) Processing helix chain 'D' and resid 586 through 602 removed outlier: 4.936A pdb=" N LEU D 592 " --> pdb=" O GLU D 588 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ARG D 595 " --> pdb=" O SER D 591 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N VAL D 596 " --> pdb=" O LEU D 592 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG D 597 " --> pdb=" O LEU D 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 606 through 616 Processing helix chain 'D' and resid 623 through 627 Processing helix chain 'D' and resid 628 through 650 Processing helix chain 'D' and resid 652 through 661 Processing helix chain 'D' and resid 669 through 683 removed outlier: 3.789A pdb=" N LEU D 683 " --> pdb=" O LEU D 679 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 705 removed outlier: 5.169A pdb=" N ILE D 694 " --> pdb=" O ASP D 690 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG D 695 " --> pdb=" O ASP D 691 " (cutoff:3.500A) Proline residue: D 699 - end of helix Processing helix chain 'D' and resid 709 through 722 Processing helix chain 'D' and resid 724 through 728 Processing helix chain 'D' and resid 743 through 766 Processing helix chain 'D' and resid 773 through 780 removed outlier: 4.052A pdb=" N LEU D 777 " --> pdb=" O GLU D 773 " (cutoff:3.500A) Processing helix chain 'D' and resid 781 through 784 Processing helix chain 'D' and resid 794 through 812 removed outlier: 3.617A pdb=" N GLY D 812 " --> pdb=" O ILE D 808 " (cutoff:3.500A) Processing helix chain 'D' and resid 814 through 824 removed outlier: 3.578A pdb=" N LEU D 824 " --> pdb=" O THR D 820 " (cutoff:3.500A) Processing helix chain 'D' and resid 831 through 836 Processing helix chain 'D' and resid 839 through 851 Processing helix chain 'D' and resid 860 through 876 Processing helix chain 'D' and resid 879 through 888 Processing helix chain 'D' and resid 901 through 914 Processing helix chain 'D' and resid 917 through 943 removed outlier: 4.140A pdb=" N THR D 934 " --> pdb=" O GLU D 930 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA D 938 " --> pdb=" O THR D 934 " (cutoff:3.500A) Processing helix chain 'D' and resid 951 through 960 Processing helix chain 'D' and resid 972 through 990 removed outlier: 3.704A pdb=" N ASN D 990 " --> pdb=" O ASN D 986 " (cutoff:3.500A) Processing helix chain 'D' and resid 999 through 1002 removed outlier: 3.585A pdb=" N THR D1002 " --> pdb=" O PRO D 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 999 through 1002' Processing helix chain 'D' and resid 1003 through 1008 Processing helix chain 'D' and resid 1015 through 1028 Processing helix chain 'D' and resid 1029 through 1032 Processing helix chain 'D' and resid 1042 through 1052 Processing helix chain 'D' and resid 1058 through 1078 removed outlier: 3.537A pdb=" N ALA D1072 " --> pdb=" O ASN D1068 " (cutoff:3.500A) Processing helix chain 'D' and resid 1200 through 1210 removed outlier: 3.806A pdb=" N LYS D1210 " --> pdb=" O ASN D1206 " (cutoff:3.500A) Processing helix chain 'D' and resid 1261 through 1271 Processing helix chain 'D' and resid 1272 through 1276 Processing helix chain 'D' and resid 1582 through 1586 Processing helix chain 'D' and resid 1612 through 1623 removed outlier: 4.137A pdb=" N ALA D1617 " --> pdb=" O SER D1613 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLU D1618 " --> pdb=" O ARG D1614 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG D1619 " --> pdb=" O LYS D1615 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE D1622 " --> pdb=" O GLU D1618 " (cutoff:3.500A) Processing helix chain 'D' and resid 1623 through 1628 removed outlier: 3.689A pdb=" N VAL D1627 " --> pdb=" O GLY D1623 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LEU D1628 " --> pdb=" O ILE D1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 1623 through 1628' Processing helix chain 'D' and resid 1629 through 1634 removed outlier: 3.532A pdb=" N GLN D1633 " --> pdb=" O SER D1629 " (cutoff:3.500A) Processing helix chain 'D' and resid 1783 through 1792 Processing helix chain 'D' and resid 1792 through 1805 Processing helix chain 'D' and resid 1807 through 1817 removed outlier: 3.860A pdb=" N ARG D1813 " --> pdb=" O THR D1809 " (cutoff:3.500A) Processing helix chain 'D' and resid 1837 through 1842 Processing helix chain 'D' and resid 1855 through 1863 Processing helix chain 'D' and resid 1864 through 1888 Processing helix chain 'D' and resid 1891 through 1910 removed outlier: 3.521A pdb=" N ASN D1896 " --> pdb=" O ARG D1892 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU D1897 " --> pdb=" O ASP D1893 " (cutoff:3.500A) Processing helix chain 'D' and resid 1925 through 1930 Processing helix chain 'D' and resid 1931 through 1947 Processing helix chain 'D' and resid 1969 through 1987 removed outlier: 3.658A pdb=" N GLN D1973 " --> pdb=" O ASN D1969 " (cutoff:3.500A) Processing helix chain 'D' and resid 2034 through 2121 removed outlier: 3.720A pdb=" N LYS D2089 " --> pdb=" O LYS D2085 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY D2107 " --> pdb=" O GLU D2103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU D2121 " --> pdb=" O THR D2117 " (cutoff:3.500A) Processing helix chain 'D' and resid 2124 through 2143 removed outlier: 4.026A pdb=" N THR D2142 " --> pdb=" O SER D2138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER D2143 " --> pdb=" O VAL D2139 " (cutoff:3.500A) Processing helix chain 'D' and resid 2144 through 2155 Processing helix chain 'D' and resid 2171 through 2260 Processing helix chain 'D' and resid 2263 through 2300 removed outlier: 3.506A pdb=" N TYR D2267 " --> pdb=" O ASN D2263 " (cutoff:3.500A) Processing helix chain 'D' and resid 2314 through 2318 Processing helix chain 'D' and resid 2321 through 2341 Processing helix chain 'D' and resid 2353 through 2359 Processing helix chain 'D' and resid 2366 through 2377 removed outlier: 3.817A pdb=" N THR D2372 " --> pdb=" O LYS D2368 " (cutoff:3.500A) Processing helix chain 'D' and resid 2401 through 2405 Processing helix chain 'D' and resid 2406 through 2410 removed outlier: 3.538A pdb=" N THR D2409 " --> pdb=" O ASN D2406 " (cutoff:3.500A) Processing helix chain 'D' and resid 2412 through 2416 removed outlier: 3.647A pdb=" N LEU D2415 " --> pdb=" O PRO D2412 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY D2416 " --> pdb=" O ASP D2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 2412 through 2416' Processing helix chain 'D' and resid 2452 through 2454 No H-bonds generated for 'chain 'D' and resid 2452 through 2454' Processing helix chain 'D' and resid 2503 through 2509 removed outlier: 3.799A pdb=" N LEU D2507 " --> pdb=" O GLN D2503 " (cutoff:3.500A) Processing helix chain 'E' and resid 21 through 28 removed outlier: 4.081A pdb=" N SER E 26 " --> pdb=" O LEU E 22 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N MET E 28 " --> pdb=" O ASN E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 37 Processing helix chain 'E' and resid 43 through 69 Processing helix chain 'E' and resid 72 through 76 Processing helix chain 'E' and resid 88 through 96 Processing helix chain 'E' and resid 98 through 102 Processing helix chain 'E' and resid 114 through 127 Processing helix chain 'E' and resid 137 through 142 Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.326A pdb=" N ALA E 146 " --> pdb=" O ARG E 142 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N SER E 147 " --> pdb=" O PRO E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'E' and resid 151 through 157 Processing helix chain 'E' and resid 162 through 178 Processing helix chain 'E' and resid 180 through 189 Processing helix chain 'E' and resid 200 through 214 Processing helix chain 'E' and resid 217 through 223 removed outlier: 3.501A pdb=" N SER E 221 " --> pdb=" O LEU E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 223 through 228 Processing helix chain 'E' and resid 231 through 240 Processing helix chain 'E' and resid 243 through 252 removed outlier: 3.712A pdb=" N GLU E 252 " --> pdb=" O GLN E 248 " (cutoff:3.500A) Processing helix chain 'E' and resid 258 through 267 removed outlier: 3.757A pdb=" N LYS E 264 " --> pdb=" O THR E 260 " (cutoff:3.500A) Processing helix chain 'E' and resid 277 through 286 removed outlier: 3.564A pdb=" N LEU E 281 " --> pdb=" O SER E 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 288 through 293 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.659A pdb=" N HIS E 341 " --> pdb=" O PHE E 337 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 337 through 341' Processing helix chain 'E' and resid 402 through 408 Processing helix chain 'E' and resid 437 through 456 Processing helix chain 'E' and resid 458 through 470 removed outlier: 3.526A pdb=" N ILE E 469 " --> pdb=" O VAL E 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 476 through 493 removed outlier: 3.520A pdb=" N GLN E 487 " --> pdb=" O LEU E 483 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 504 removed outlier: 3.629A pdb=" N LEU E 503 " --> pdb=" O ASP E 499 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 525 Processing helix chain 'E' and resid 550 through 562 removed outlier: 3.514A pdb=" N LEU E 554 " --> pdb=" O ASN E 550 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 575 removed outlier: 3.696A pdb=" N ALA E 575 " --> pdb=" O LEU E 571 " (cutoff:3.500A) Processing helix chain 'E' and resid 586 through 602 removed outlier: 4.937A pdb=" N LEU E 592 " --> pdb=" O GLU E 588 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ARG E 595 " --> pdb=" O SER E 591 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N VAL E 596 " --> pdb=" O LEU E 592 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ARG E 597 " --> pdb=" O LEU E 593 " (cutoff:3.500A) Processing helix chain 'E' and resid 606 through 616 Processing helix chain 'E' and resid 623 through 627 Processing helix chain 'E' and resid 628 through 650 Processing helix chain 'E' and resid 652 through 661 Processing helix chain 'E' and resid 669 through 683 removed outlier: 3.789A pdb=" N LEU E 683 " --> pdb=" O LEU E 679 " (cutoff:3.500A) Processing helix chain 'E' and resid 688 through 705 removed outlier: 5.168A pdb=" N ILE E 694 " --> pdb=" O ASP E 690 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N ARG E 695 " --> pdb=" O ASP E 691 " (cutoff:3.500A) Proline residue: E 699 - end of helix Processing helix chain 'E' and resid 709 through 722 Processing helix chain 'E' and resid 724 through 728 Processing helix chain 'E' and resid 743 through 766 Processing helix chain 'E' and resid 773 through 780 removed outlier: 4.052A pdb=" N LEU E 777 " --> pdb=" O GLU E 773 " (cutoff:3.500A) Processing helix chain 'E' and resid 781 through 784 Processing helix chain 'E' and resid 794 through 812 removed outlier: 3.619A pdb=" N GLY E 812 " --> pdb=" O ILE E 808 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 824 removed outlier: 3.577A pdb=" N LEU E 824 " --> pdb=" O THR E 820 " (cutoff:3.500A) Processing helix chain 'E' and resid 831 through 836 Processing helix chain 'E' and resid 839 through 851 Processing helix chain 'E' and resid 860 through 876 Processing helix chain 'E' and resid 879 through 888 Processing helix chain 'E' and resid 901 through 914 Processing helix chain 'E' and resid 917 through 943 removed outlier: 4.140A pdb=" N THR E 934 " --> pdb=" O GLU E 930 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ALA E 938 " --> pdb=" O THR E 934 " (cutoff:3.500A) Processing helix chain 'E' and resid 951 through 960 Processing helix chain 'E' and resid 972 through 990 removed outlier: 3.704A pdb=" N ASN E 990 " --> pdb=" O ASN E 986 " (cutoff:3.500A) Processing helix chain 'E' and resid 999 through 1002 removed outlier: 3.585A pdb=" N THR E1002 " --> pdb=" O PRO E 999 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 999 through 1002' Processing helix chain 'E' and resid 1003 through 1008 Processing helix chain 'E' and resid 1015 through 1028 Processing helix chain 'E' and resid 1029 through 1032 Processing helix chain 'E' and resid 1042 through 1052 Processing helix chain 'E' and resid 1058 through 1078 removed outlier: 3.536A pdb=" N ALA E1072 " --> pdb=" O ASN E1068 " (cutoff:3.500A) Processing helix chain 'E' and resid 1200 through 1210 removed outlier: 3.807A pdb=" N LYS E1210 " --> pdb=" O ASN E1206 " (cutoff:3.500A) Processing helix chain 'E' and resid 1261 through 1271 Processing helix chain 'E' and resid 1272 through 1276 Processing helix chain 'E' and resid 1582 through 1586 Processing helix chain 'E' and resid 1612 through 1623 removed outlier: 4.138A pdb=" N ALA E1617 " --> pdb=" O SER E1613 " (cutoff:3.500A) removed outlier: 5.789A pdb=" N GLU E1618 " --> pdb=" O ARG E1614 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG E1619 " --> pdb=" O LYS E1615 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE E1622 " --> pdb=" O GLU E1618 " (cutoff:3.500A) Processing helix chain 'E' and resid 1623 through 1628 removed outlier: 3.689A pdb=" N VAL E1627 " --> pdb=" O GLY E1623 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU E1628 " --> pdb=" O ILE E1624 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 1623 through 1628' Processing helix chain 'E' and resid 1629 through 1634 removed outlier: 3.532A pdb=" N GLN E1633 " --> pdb=" O SER E1629 " (cutoff:3.500A) Processing helix chain 'E' and resid 1783 through 1792 Processing helix chain 'E' and resid 1792 through 1805 Processing helix chain 'E' and resid 1807 through 1817 removed outlier: 3.861A pdb=" N ARG E1813 " --> pdb=" O THR E1809 " (cutoff:3.500A) Processing helix chain 'E' and resid 1837 through 1842 Processing helix chain 'E' and resid 1855 through 1863 Processing helix chain 'E' and resid 1864 through 1888 Processing helix chain 'E' and resid 1891 through 1910 removed outlier: 3.521A pdb=" N ASN E1896 " --> pdb=" O ARG E1892 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU E1897 " --> pdb=" O ASP E1893 " (cutoff:3.500A) Processing helix chain 'E' and resid 1925 through 1930 Processing helix chain 'E' and resid 1931 through 1947 Processing helix chain 'E' and resid 1969 through 1987 removed outlier: 3.659A pdb=" N GLN E1973 " --> pdb=" O ASN E1969 " (cutoff:3.500A) Processing helix chain 'E' and resid 2034 through 2121 removed outlier: 3.720A pdb=" N LYS E2089 " --> pdb=" O LYS E2085 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLY E2107 " --> pdb=" O GLU E2103 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU E2121 " --> pdb=" O THR E2117 " (cutoff:3.500A) Processing helix chain 'E' and resid 2124 through 2143 removed outlier: 4.025A pdb=" N THR E2142 " --> pdb=" O SER E2138 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N SER E2143 " --> pdb=" O VAL E2139 " (cutoff:3.500A) Processing helix chain 'E' and resid 2144 through 2155 Processing helix chain 'E' and resid 2171 through 2260 Processing helix chain 'E' and resid 2263 through 2300 removed outlier: 3.505A pdb=" N TYR E2267 " --> pdb=" O ASN E2263 " (cutoff:3.500A) Processing helix chain 'E' and resid 2314 through 2318 Processing helix chain 'E' and resid 2321 through 2341 Processing helix chain 'E' and resid 2353 through 2359 Processing helix chain 'E' and resid 2366 through 2377 removed outlier: 3.817A pdb=" N THR E2372 " --> pdb=" O LYS E2368 " (cutoff:3.500A) Processing helix chain 'E' and resid 2401 through 2405 Processing helix chain 'E' and resid 2406 through 2410 removed outlier: 3.537A pdb=" N THR E2409 " --> pdb=" O ASN E2406 " (cutoff:3.500A) Processing helix chain 'E' and resid 2412 through 2416 removed outlier: 3.647A pdb=" N LEU E2415 " --> pdb=" O PRO E2412 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY E2416 " --> pdb=" O ASP E2413 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 2412 through 2416' Processing helix chain 'E' and resid 2452 through 2454 No H-bonds generated for 'chain 'E' and resid 2452 through 2454' Processing helix chain 'E' and resid 2503 through 2509 removed outlier: 3.799A pdb=" N LEU E2507 " --> pdb=" O GLN E2503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 317 removed outlier: 7.203A pdb=" N ASN A 375 " --> pdb=" O TYR A 380 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR A 380 " --> pdb=" O ASN A 375 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 342 through 351 removed outlier: 3.708A pdb=" N TYR A 344 " --> pdb=" O SER A 360 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1080 through 1086 removed outlier: 5.775A pdb=" N VAL A1081 " --> pdb=" O TYR A1101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR A1101 " --> pdb=" O VAL A1081 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A1083 " --> pdb=" O ILE A1099 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1146 through 1151 Processing sheet with id=AA5, first strand: chain 'A' and resid 1214 through 1220 Processing sheet with id=AA6, first strand: chain 'A' and resid 1282 through 1284 removed outlier: 4.070A pdb=" N TYR A1282 " --> pdb=" O LEU A1589 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE A1587 " --> pdb=" O VAL A1284 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1292 through 1296 removed outlier: 3.567A pdb=" N VAL A1515 " --> pdb=" O LEU A1507 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1299 through 1300 Processing sheet with id=AA9, first strand: chain 'A' and resid 1317 through 1319 removed outlier: 3.756A pdb=" N VAL A1543 " --> pdb=" O LEU A1328 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1335 through 1337 Processing sheet with id=AB2, first strand: chain 'A' and resid 1690 through 1696 removed outlier: 4.081A pdb=" N THR A1690 " --> pdb=" O LEU A1650 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL A1768 " --> pdb=" O THR A1647 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS A1766 " --> pdb=" O LYS A1649 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1663 through 1668 removed outlier: 6.991A pdb=" N PHE A1664 " --> pdb=" O GLU A1682 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU A1682 " --> pdb=" O PHE A1664 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE A1666 " --> pdb=" O TYR A1680 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR A1680 " --> pdb=" O ILE A1666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 1728 through 1731 Processing sheet with id=AB5, first strand: chain 'A' and resid 1746 through 1749 removed outlier: 6.779A pdb=" N LYS A1756 " --> pdb=" O SER A1747 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET A1749 " --> pdb=" O ILE A1754 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A1754 " --> pdb=" O MET A1749 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1825 through 1826 Processing sheet with id=AB7, first strand: chain 'A' and resid 2346 through 2352 removed outlier: 5.750A pdb=" N THR A2520 " --> pdb=" O ILE A2421 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE A2421 " --> pdb=" O THR A2520 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N ARG A2522 " --> pdb=" O ARG A2419 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG A2419 " --> pdb=" O ARG A2522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU A2484 " --> pdb=" O ILE A2421 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 2381 through 2382 Processing sheet with id=AB9, first strand: chain 'B' and resid 313 through 317 removed outlier: 7.204A pdb=" N ASN B 375 " --> pdb=" O TYR B 380 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR B 380 " --> pdb=" O ASN B 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 342 through 351 removed outlier: 3.708A pdb=" N TYR B 344 " --> pdb=" O SER B 360 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 1080 through 1086 removed outlier: 5.776A pdb=" N VAL B1081 " --> pdb=" O TYR B1101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR B1101 " --> pdb=" O VAL B1081 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER B1083 " --> pdb=" O ILE B1099 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 1146 through 1151 Processing sheet with id=AC4, first strand: chain 'B' and resid 1214 through 1220 Processing sheet with id=AC5, first strand: chain 'B' and resid 1282 through 1284 removed outlier: 4.070A pdb=" N TYR B1282 " --> pdb=" O LEU B1589 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE B1587 " --> pdb=" O VAL B1284 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 1292 through 1296 removed outlier: 3.567A pdb=" N VAL B1515 " --> pdb=" O LEU B1507 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 1299 through 1300 Processing sheet with id=AC8, first strand: chain 'B' and resid 1317 through 1319 removed outlier: 3.756A pdb=" N VAL B1543 " --> pdb=" O LEU B1328 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 1335 through 1337 Processing sheet with id=AD1, first strand: chain 'B' and resid 1690 through 1696 removed outlier: 4.080A pdb=" N THR B1690 " --> pdb=" O LEU B1650 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL B1768 " --> pdb=" O THR B1647 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS B1766 " --> pdb=" O LYS B1649 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1663 through 1668 removed outlier: 6.991A pdb=" N PHE B1664 " --> pdb=" O GLU B1682 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU B1682 " --> pdb=" O PHE B1664 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE B1666 " --> pdb=" O TYR B1680 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR B1680 " --> pdb=" O ILE B1666 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 1728 through 1731 Processing sheet with id=AD4, first strand: chain 'B' and resid 1746 through 1749 removed outlier: 6.779A pdb=" N LYS B1756 " --> pdb=" O SER B1747 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET B1749 " --> pdb=" O ILE B1754 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B1754 " --> pdb=" O MET B1749 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 1825 through 1826 Processing sheet with id=AD6, first strand: chain 'B' and resid 2346 through 2352 removed outlier: 5.749A pdb=" N THR B2520 " --> pdb=" O ILE B2421 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N ILE B2421 " --> pdb=" O THR B2520 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG B2522 " --> pdb=" O ARG B2419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG B2419 " --> pdb=" O ARG B2522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU B2484 " --> pdb=" O ILE B2421 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 2381 through 2382 Processing sheet with id=AD8, first strand: chain 'C' and resid 313 through 317 removed outlier: 7.202A pdb=" N ASN C 375 " --> pdb=" O TYR C 380 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR C 380 " --> pdb=" O ASN C 375 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 342 through 351 removed outlier: 3.708A pdb=" N TYR C 344 " --> pdb=" O SER C 360 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU C 354 " --> pdb=" O ILE C 350 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 1080 through 1086 removed outlier: 5.775A pdb=" N VAL C1081 " --> pdb=" O TYR C1101 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR C1101 " --> pdb=" O VAL C1081 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER C1083 " --> pdb=" O ILE C1099 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 1146 through 1151 Processing sheet with id=AE3, first strand: chain 'C' and resid 1214 through 1220 Processing sheet with id=AE4, first strand: chain 'C' and resid 1282 through 1284 removed outlier: 4.070A pdb=" N TYR C1282 " --> pdb=" O LEU C1589 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ILE C1587 " --> pdb=" O VAL C1284 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 1292 through 1296 removed outlier: 3.567A pdb=" N VAL C1515 " --> pdb=" O LEU C1507 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 1299 through 1300 Processing sheet with id=AE7, first strand: chain 'C' and resid 1317 through 1319 removed outlier: 3.755A pdb=" N VAL C1543 " --> pdb=" O LEU C1328 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 1335 through 1337 Processing sheet with id=AE9, first strand: chain 'C' and resid 1690 through 1696 removed outlier: 4.080A pdb=" N THR C1690 " --> pdb=" O LEU C1650 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL C1768 " --> pdb=" O THR C1647 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS C1766 " --> pdb=" O LYS C1649 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 1663 through 1668 removed outlier: 6.991A pdb=" N PHE C1664 " --> pdb=" O GLU C1682 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU C1682 " --> pdb=" O PHE C1664 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ILE C1666 " --> pdb=" O TYR C1680 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR C1680 " --> pdb=" O ILE C1666 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1728 through 1731 Processing sheet with id=AF3, first strand: chain 'C' and resid 1746 through 1749 removed outlier: 6.778A pdb=" N LYS C1756 " --> pdb=" O SER C1747 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET C1749 " --> pdb=" O ILE C1754 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE C1754 " --> pdb=" O MET C1749 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 1825 through 1826 Processing sheet with id=AF5, first strand: chain 'C' and resid 2346 through 2352 removed outlier: 5.749A pdb=" N THR C2520 " --> pdb=" O ILE C2421 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE C2421 " --> pdb=" O THR C2520 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG C2522 " --> pdb=" O ARG C2419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG C2419 " --> pdb=" O ARG C2522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU C2484 " --> pdb=" O ILE C2421 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 2381 through 2382 Processing sheet with id=AF7, first strand: chain 'D' and resid 313 through 317 removed outlier: 7.203A pdb=" N ASN D 375 " --> pdb=" O TYR D 380 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR D 380 " --> pdb=" O ASN D 375 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 342 through 351 removed outlier: 3.709A pdb=" N TYR D 344 " --> pdb=" O SER D 360 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N GLU D 354 " --> pdb=" O ILE D 350 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 1080 through 1086 removed outlier: 5.775A pdb=" N VAL D1081 " --> pdb=" O TYR D1101 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N TYR D1101 " --> pdb=" O VAL D1081 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER D1083 " --> pdb=" O ILE D1099 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 1146 through 1151 Processing sheet with id=AG2, first strand: chain 'D' and resid 1214 through 1220 Processing sheet with id=AG3, first strand: chain 'D' and resid 1282 through 1284 removed outlier: 4.071A pdb=" N TYR D1282 " --> pdb=" O LEU D1589 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE D1587 " --> pdb=" O VAL D1284 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'D' and resid 1292 through 1296 removed outlier: 3.567A pdb=" N VAL D1515 " --> pdb=" O LEU D1507 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'D' and resid 1299 through 1300 Processing sheet with id=AG6, first strand: chain 'D' and resid 1317 through 1319 removed outlier: 3.755A pdb=" N VAL D1543 " --> pdb=" O LEU D1328 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'D' and resid 1335 through 1337 Processing sheet with id=AG8, first strand: chain 'D' and resid 1690 through 1696 removed outlier: 4.080A pdb=" N THR D1690 " --> pdb=" O LEU D1650 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL D1768 " --> pdb=" O THR D1647 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS D1766 " --> pdb=" O LYS D1649 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'D' and resid 1663 through 1668 removed outlier: 6.991A pdb=" N PHE D1664 " --> pdb=" O GLU D1682 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU D1682 " --> pdb=" O PHE D1664 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ILE D1666 " --> pdb=" O TYR D1680 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR D1680 " --> pdb=" O ILE D1666 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 1728 through 1731 Processing sheet with id=AH2, first strand: chain 'D' and resid 1746 through 1749 removed outlier: 6.778A pdb=" N LYS D1756 " --> pdb=" O SER D1747 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET D1749 " --> pdb=" O ILE D1754 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE D1754 " --> pdb=" O MET D1749 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 1825 through 1826 Processing sheet with id=AH4, first strand: chain 'D' and resid 2346 through 2352 removed outlier: 5.750A pdb=" N THR D2520 " --> pdb=" O ILE D2421 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE D2421 " --> pdb=" O THR D2520 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG D2522 " --> pdb=" O ARG D2419 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ARG D2419 " --> pdb=" O ARG D2522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU D2484 " --> pdb=" O ILE D2421 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'D' and resid 2381 through 2382 Processing sheet with id=AH6, first strand: chain 'E' and resid 313 through 317 removed outlier: 7.203A pdb=" N ASN E 375 " --> pdb=" O TYR E 380 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N TYR E 380 " --> pdb=" O ASN E 375 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 342 through 351 removed outlier: 3.708A pdb=" N TYR E 344 " --> pdb=" O SER E 360 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLU E 354 " --> pdb=" O ILE E 350 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 1080 through 1086 removed outlier: 5.775A pdb=" N VAL E1081 " --> pdb=" O TYR E1101 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N TYR E1101 " --> pdb=" O VAL E1081 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER E1083 " --> pdb=" O ILE E1099 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'E' and resid 1146 through 1151 Processing sheet with id=AI1, first strand: chain 'E' and resid 1214 through 1220 Processing sheet with id=AI2, first strand: chain 'E' and resid 1282 through 1284 removed outlier: 4.070A pdb=" N TYR E1282 " --> pdb=" O LEU E1589 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE E1587 " --> pdb=" O VAL E1284 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'E' and resid 1292 through 1296 removed outlier: 3.567A pdb=" N VAL E1515 " --> pdb=" O LEU E1507 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'E' and resid 1299 through 1300 Processing sheet with id=AI5, first strand: chain 'E' and resid 1317 through 1319 removed outlier: 3.755A pdb=" N VAL E1543 " --> pdb=" O LEU E1328 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'E' and resid 1335 through 1337 Processing sheet with id=AI7, first strand: chain 'E' and resid 1690 through 1696 removed outlier: 4.080A pdb=" N THR E1690 " --> pdb=" O LEU E1650 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL E1768 " --> pdb=" O THR E1647 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N HIS E1766 " --> pdb=" O LYS E1649 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'E' and resid 1663 through 1668 removed outlier: 6.992A pdb=" N PHE E1664 " --> pdb=" O GLU E1682 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU E1682 " --> pdb=" O PHE E1664 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ILE E1666 " --> pdb=" O TYR E1680 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR E1680 " --> pdb=" O ILE E1666 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'E' and resid 1728 through 1731 Processing sheet with id=AJ1, first strand: chain 'E' and resid 1746 through 1749 removed outlier: 6.778A pdb=" N LYS E1756 " --> pdb=" O SER E1747 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N MET E1749 " --> pdb=" O ILE E1754 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE E1754 " --> pdb=" O MET E1749 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'E' and resid 1825 through 1826 Processing sheet with id=AJ3, first strand: chain 'E' and resid 2346 through 2352 removed outlier: 5.749A pdb=" N THR E2520 " --> pdb=" O ILE E2421 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE E2421 " --> pdb=" O THR E2520 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ARG E2522 " --> pdb=" O ARG E2419 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ARG E2419 " --> pdb=" O ARG E2522 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU E2484 " --> pdb=" O ILE E2421 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'E' and resid 2381 through 2382 4795 hydrogen bonds defined for protein. 13785 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: 57.84 Time building geometry restraints manager: 32.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 28849 1.34 - 1.46: 19178 1.46 - 1.58: 46853 1.58 - 1.70: 0 1.70 - 1.82: 620 Bond restraints: 95500 Sorted by residual: bond pdb=" CG1 ILE D1818 " pdb=" CD1 ILE D1818 " ideal model delta sigma weight residual 1.513 1.409 0.104 3.90e-02 6.57e+02 7.05e+00 bond pdb=" CG1 ILE A1818 " pdb=" CD1 ILE A1818 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.97e+00 bond pdb=" CG1 ILE C1818 " pdb=" CD1 ILE C1818 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.96e+00 bond pdb=" CG1 ILE E1818 " pdb=" CD1 ILE E1818 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.96e+00 bond pdb=" CG1 ILE B1818 " pdb=" CD1 ILE B1818 " ideal model delta sigma weight residual 1.513 1.410 0.103 3.90e-02 6.57e+02 6.96e+00 ... (remaining 95495 not shown) Histogram of bond angle deviations from ideal: 96.34 - 106.71: 2722 106.71 - 117.08: 64372 117.08 - 127.44: 61611 127.44 - 137.81: 980 137.81 - 148.18: 5 Bond angle restraints: 129690 Sorted by residual: angle pdb=" C LEU A 668 " pdb=" N THR A 669 " pdb=" CA THR A 669 " ideal model delta sigma weight residual 120.69 148.18 -27.49 2.95e+00 1.15e-01 8.68e+01 angle pdb=" C LEU B 668 " pdb=" N THR B 669 " pdb=" CA THR B 669 " ideal model delta sigma weight residual 120.69 148.16 -27.47 2.95e+00 1.15e-01 8.67e+01 angle pdb=" C LEU C 668 " pdb=" N THR C 669 " pdb=" CA THR C 669 " ideal model delta sigma weight residual 120.69 148.15 -27.46 2.95e+00 1.15e-01 8.66e+01 angle pdb=" C LEU D 668 " pdb=" N THR D 669 " pdb=" CA THR D 669 " ideal model delta sigma weight residual 120.69 148.14 -27.45 2.95e+00 1.15e-01 8.66e+01 angle pdb=" C LEU E 668 " pdb=" N THR E 669 " pdb=" CA THR E 669 " ideal model delta sigma weight residual 120.69 148.14 -27.45 2.95e+00 1.15e-01 8.66e+01 ... (remaining 129685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.49: 54038 15.49 - 30.99: 2743 30.99 - 46.48: 509 46.48 - 61.97: 20 61.97 - 77.47: 60 Dihedral angle restraints: 57370 sinusoidal: 22845 harmonic: 34525 Sorted by residual: dihedral pdb=" CA ALA E2344 " pdb=" C ALA E2344 " pdb=" N LEU E2345 " pdb=" CA LEU E2345 " ideal model delta harmonic sigma weight residual 180.00 140.13 39.87 0 5.00e+00 4.00e-02 6.36e+01 dihedral pdb=" CA ALA B2344 " pdb=" C ALA B2344 " pdb=" N LEU B2345 " pdb=" CA LEU B2345 " ideal model delta harmonic sigma weight residual 180.00 140.16 39.84 0 5.00e+00 4.00e-02 6.35e+01 dihedral pdb=" CA ALA D2344 " pdb=" C ALA D2344 " pdb=" N LEU D2345 " pdb=" CA LEU D2345 " ideal model delta harmonic sigma weight residual 180.00 140.21 39.79 0 5.00e+00 4.00e-02 6.33e+01 ... (remaining 57367 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 11867 0.075 - 0.150: 2437 0.150 - 0.226: 210 0.226 - 0.301: 41 0.301 - 0.376: 10 Chirality restraints: 14565 Sorted by residual: chirality pdb=" CB VAL B 563 " pdb=" CA VAL B 563 " pdb=" CG1 VAL B 563 " pdb=" CG2 VAL B 563 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" CB VAL E 563 " pdb=" CA VAL E 563 " pdb=" CG1 VAL E 563 " pdb=" CG2 VAL E 563 " both_signs ideal model delta sigma weight residual False -2.63 -2.25 -0.37 2.00e-01 2.50e+01 3.51e+00 chirality pdb=" CB VAL A 563 " pdb=" CA VAL A 563 " pdb=" CG1 VAL A 563 " pdb=" CG2 VAL A 563 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.49e+00 ... (remaining 14562 not shown) Planarity restraints: 16710 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN C 420 " 0.052 5.00e-02 4.00e+02 7.91e-02 1.00e+01 pdb=" N PRO C 421 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO C 421 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO C 421 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 420 " 0.052 5.00e-02 4.00e+02 7.89e-02 9.97e+00 pdb=" N PRO D 421 " -0.137 5.00e-02 4.00e+02 pdb=" CA PRO D 421 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO D 421 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN E 420 " -0.052 5.00e-02 4.00e+02 7.88e-02 9.94e+00 pdb=" N PRO E 421 " 0.136 5.00e-02 4.00e+02 pdb=" CA PRO E 421 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO E 421 " -0.043 5.00e-02 4.00e+02 ... (remaining 16707 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 11686 2.75 - 3.29: 89844 3.29 - 3.83: 160701 3.83 - 4.36: 191081 4.36 - 4.90: 325455 Nonbonded interactions: 778767 Sorted by model distance: nonbonded pdb=" OE2 GLU A 817 " pdb=" OG SER E 665 " model vdw 2.215 2.440 nonbonded pdb=" OG SER A 111 " pdb=" OE1 GLN A1967 " model vdw 2.219 2.440 nonbonded pdb=" OG SER E 111 " pdb=" OE1 GLN E1967 " model vdw 2.219 2.440 nonbonded pdb=" OG SER D 111 " pdb=" OE1 GLN D1967 " model vdw 2.220 2.440 nonbonded pdb=" OG SER B 111 " pdb=" OE1 GLN B1967 " model vdw 2.220 2.440 ... (remaining 778762 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 5.020 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: 0.110 Extract box with map and model: 16.220 Check model and map are aligned: 1.010 Set scattering table: 0.700 Process input model: 219.480 Find NCS groups from input model: 4.830 Set up NCS constraints: 0.500 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: 0.030 Load rotamer database and sin/cos tables:11.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 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 : 0.007 0.104 95500 Z= 0.458 Angle : 1.062 27.487 129690 Z= 0.561 Chirality : 0.060 0.376 14565 Planarity : 0.007 0.079 16710 Dihedral : 10.141 77.468 35090 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.30 % Allowed : 6.95 % Favored : 92.75 % Rotamer: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 1.20 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.20 (0.07), residues: 11655 helix: -1.90 (0.06), residues: 5250 sheet: -1.45 (0.12), residues: 1770 loop : -2.50 (0.08), residues: 4635 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.004 TRP D 860 HIS 0.020 0.003 HIS C2314 PHE 0.032 0.003 PHE A 27 TYR 0.051 0.003 TYR C1887 ARG 0.016 0.002 ARG B2204 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1946 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1941 time to evaluate : 10.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1055 SER cc_start: 0.7224 (m) cc_final: 0.7023 (p) REVERT: A 2032 MET cc_start: 0.8437 (mmm) cc_final: 0.8203 (mmm) REVERT: A 2327 MET cc_start: 0.7969 (mmm) cc_final: 0.7763 (mmm) REVERT: B 1064 ASP cc_start: 0.6195 (m-30) cc_final: 0.5865 (m-30) REVERT: B 1893 ASP cc_start: 0.6156 (m-30) cc_final: 0.5920 (m-30) REVERT: D 1064 ASP cc_start: 0.6400 (m-30) cc_final: 0.6127 (m-30) REVERT: E 1055 SER cc_start: 0.7289 (m) cc_final: 0.6976 (p) outliers start: 5 outliers final: 4 residues processed: 1946 average time/residue: 1.9352 time to fit residues: 4966.1851 Evaluate side-chains 832 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 828 time to evaluate : 8.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1241 ASN Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain C residue 745 ASN Chi-restraints excluded: chain D residue 1241 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 983 optimal weight: 3.9990 chunk 883 optimal weight: 5.9990 chunk 489 optimal weight: 3.9990 chunk 301 optimal weight: 1.9990 chunk 595 optimal weight: 5.9990 chunk 471 optimal weight: 1.9990 chunk 913 optimal weight: 0.9990 chunk 353 optimal weight: 0.9980 chunk 555 optimal weight: 4.9990 chunk 679 optimal weight: 0.8980 chunk 1057 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 GLN A 133 ASN A 152 GLN A 171 HIS A 213 GLN A 223 ASN A 306 ASN A 341 HIS A 343 ASN A 374 GLN A 392 ASN A 394 HIS ** A 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 519 HIS A 525 ASN A 608 ASN A 641 GLN ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 793 HIS A 913 GLN A1051 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1197 ASN A1263 ASN A1540 GLN A1621 ASN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1783 ASN ** A1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1866 HIS A1919 ASN A2075 GLN A2109 GLN A2129 GLN A2239 GLN A2268 ASN A2306 HIS A2314 HIS A2390 ASN ** A2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A2503 GLN A2516 HIS B 74 GLN B 152 GLN B 171 HIS B 213 GLN B 223 ASN B 341 HIS B 343 ASN B 374 GLN B 392 ASN B 394 HIS ** B 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 519 HIS B 525 ASN B 608 ASN ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 HIS ** B 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1041 GLN ** B1054 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1197 ASN B1263 ASN B1540 GLN ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1757 ASN ** B1772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1783 ASN B1807 ASN ** B1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1866 HIS B1919 ASN B1995 GLN B2051 GLN B2075 GLN B2109 GLN ** B2268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2306 HIS B2314 HIS B2390 ASN B2397 GLN B2503 GLN B2516 HIS C 74 GLN C 133 ASN C 152 GLN C 171 HIS C 213 GLN C 306 ASN C 341 HIS C 343 ASN C 374 GLN C 383 GLN C 392 ASN C 394 HIS C 525 ASN C 641 GLN ** C 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 793 HIS ** C 913 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 925 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1054 GLN C1068 ASN ** C1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1197 ASN C1263 ASN C1540 GLN C1575 HIS C1621 ASN ** C1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1783 ASN C1800 GLN ** C1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1866 HIS C1919 ASN C1977 GLN C1995 GLN C2051 GLN C2054 ASN C2075 GLN C2109 GLN C2129 GLN C2241 ASN C2268 ASN C2306 HIS C2314 HIS C2390 ASN ** C2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C2503 GLN C2516 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 133 ASN D 152 GLN D 171 HIS D 213 GLN D 306 ASN D 341 HIS D 343 ASN D 374 GLN D 392 ASN D 394 HIS D 430 HIS D 519 HIS D 525 ASN D 634 GLN D 745 ASN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 HIS D1068 ASN ** D1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1197 ASN D1540 GLN D1670 ASN D1735 ASN ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1783 ASN D1800 GLN ** D1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1862 HIS D1866 HIS D1919 ASN D1932 GLN D2054 ASN D2075 GLN D2109 GLN D2129 GLN D2175 ASN D2258 GLN ** D2268 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2306 HIS D2314 HIS D2390 ASN ** D2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D2503 GLN D2516 HIS E 74 GLN E 133 ASN E 152 GLN E 153 ASN E 171 HIS E 213 GLN E 223 ASN E 306 ASN E 341 HIS E 343 ASN E 374 GLN E 383 GLN E 392 ASN E 394 HIS ** E 430 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 519 HIS E 525 ASN E 649 GLN ** E 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 793 HIS E 913 GLN E 925 GLN E1041 GLN E1058 ASN E1068 ASN E1197 ASN E1263 ASN E1323 ASN E1540 GLN E1621 ASN E1670 ASN ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1772 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1783 ASN E1849 ASN E1866 HIS E1889 GLN E1919 ASN E1932 GLN E1977 GLN E2054 ASN E2075 GLN E2129 GLN E2175 ASN E2268 ASN E2306 HIS E2314 HIS E2390 ASN ** E2397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2503 GLN E2516 HIS Total number of N/Q/H flips: 194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 95500 Z= 0.227 Angle : 0.661 14.082 129690 Z= 0.347 Chirality : 0.043 0.217 14565 Planarity : 0.005 0.066 16710 Dihedral : 5.817 51.965 12713 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.11 % Favored : 93.80 % Rotamer: Outliers : 2.60 % Allowed : 11.13 % Favored : 86.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.08), residues: 11655 helix: 0.15 (0.07), residues: 5360 sheet: -0.98 (0.12), residues: 1675 loop : -1.97 (0.09), residues: 4620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 43 HIS 0.008 0.001 HIS B2314 PHE 0.018 0.002 PHE A 804 TYR 0.020 0.001 TYR E1230 ARG 0.009 0.001 ARG C 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 929 time to evaluate : 8.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7104 (mt-10) REVERT: A 1614 ARG cc_start: 0.8026 (OUTLIER) cc_final: 0.7378 (mtp180) REVERT: A 1622 ILE cc_start: 0.8339 (mp) cc_final: 0.8041 (mp) REVERT: A 2032 MET cc_start: 0.8312 (mmm) cc_final: 0.7886 (mmm) REVERT: A 2220 LYS cc_start: 0.7694 (mtmm) cc_final: 0.7389 (mtmm) REVERT: B 1614 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7219 (mtm180) REVERT: C 64 GLU cc_start: 0.6683 (tt0) cc_final: 0.6383 (tt0) REVERT: C 1027 TYR cc_start: 0.7438 (m-80) cc_final: 0.7015 (m-80) REVERT: C 1599 MET cc_start: 0.7168 (ptm) cc_final: 0.6943 (ptm) REVERT: C 2233 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7767 (ttm-80) REVERT: D 153 ASN cc_start: 0.7302 (OUTLIER) cc_final: 0.6898 (t0) REVERT: D 505 HIS cc_start: 0.8029 (OUTLIER) cc_final: 0.7635 (t-90) REVERT: D 1880 ILE cc_start: 0.8865 (OUTLIER) cc_final: 0.8629 (mt) REVERT: E 505 HIS cc_start: 0.8144 (OUTLIER) cc_final: 0.7934 (t-90) REVERT: E 2220 LYS cc_start: 0.7874 (mtmm) cc_final: 0.7607 (mtpt) outliers start: 266 outliers final: 49 residues processed: 1123 average time/residue: 1.7475 time to fit residues: 2664.5425 Evaluate side-chains 784 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 727 time to evaluate : 8.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 770 SER Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1204 ILE Chi-restraints excluded: chain A residue 1614 ARG Chi-restraints excluded: chain A residue 1880 ILE Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1614 ARG Chi-restraints excluded: chain B residue 1832 ASP Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2089 LYS Chi-restraints excluded: chain C residue 2209 GLU Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 153 ASN Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 911 LEU Chi-restraints excluded: chain D residue 1216 MET Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1875 MET Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 505 HIS Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2447 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 587 optimal weight: 1.9990 chunk 328 optimal weight: 1.9990 chunk 880 optimal weight: 0.9980 chunk 720 optimal weight: 3.9990 chunk 291 optimal weight: 6.9990 chunk 1059 optimal weight: 7.9990 chunk 1144 optimal weight: 0.0030 chunk 943 optimal weight: 0.9990 chunk 1051 optimal weight: 6.9990 chunk 361 optimal weight: 9.9990 chunk 850 optimal weight: 2.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1323 ASN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1800 GLN ** A1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2395 GLN A2397 GLN B 80 ASN ** B 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 793 HIS B1041 GLN B1051 GLN B1054 GLN ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1800 GLN ** B1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2268 ASN C 223 ASN C 383 GLN ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1862 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN C1995 GLN C2395 GLN C2397 GLN ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 608 ASN D 943 ASN ** D1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1621 ASN D1626 ASN ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2225 GLN D2268 ASN D2397 GLN E 82 ASN E 153 ASN E 193 GLN ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 ASN E 913 GLN E 943 ASN E1041 GLN E1058 ASN ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1800 GLN ** E1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1977 GLN E2109 GLN E2397 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 95500 Z= 0.200 Angle : 0.605 11.674 129690 Z= 0.314 Chirality : 0.042 0.193 14565 Planarity : 0.004 0.061 16710 Dihedral : 5.284 47.302 12705 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.57 % Favored : 93.37 % Rotamer: Outliers : 2.30 % Allowed : 12.98 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.08), residues: 11655 helix: 1.06 (0.07), residues: 5375 sheet: -0.71 (0.12), residues: 1660 loop : -1.75 (0.09), residues: 4620 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 43 HIS 0.005 0.001 HIS D2461 PHE 0.015 0.001 PHE A 804 TYR 0.017 0.001 TYR E1230 ARG 0.009 0.001 ARG D2189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 820 time to evaluate : 8.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7396 (OUTLIER) cc_final: 0.7102 (mt-10) REVERT: A 1614 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7491 (mtp180) REVERT: A 2032 MET cc_start: 0.8185 (mmm) cc_final: 0.7835 (mmm) REVERT: A 2233 ARG cc_start: 0.7661 (OUTLIER) cc_final: 0.7086 (ttt-90) REVERT: B 911 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 1089 ILE cc_start: 0.8693 (OUTLIER) cc_final: 0.8479 (mm) REVERT: B 1770 MET cc_start: 0.6561 (tmt) cc_final: 0.5903 (tmm) REVERT: C 87 THR cc_start: 0.7558 (p) cc_final: 0.7270 (p) REVERT: C 433 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7322 (ttp) REVERT: C 2233 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7558 (ttm-80) REVERT: D 505 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7656 (t-90) REVERT: D 930 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7212 (mt-10) REVERT: D 1622 ILE cc_start: 0.8385 (mp) cc_final: 0.8103 (mp) REVERT: D 1770 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.5657 (tmm) REVERT: D 1880 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8542 (mt) outliers start: 236 outliers final: 76 residues processed: 997 average time/residue: 1.7450 time to fit residues: 2369.0691 Evaluate side-chains 769 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 682 time to evaluate : 8.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1614 ARG Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1890 LEU Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2233 ARG Chi-restraints excluded: chain A residue 2241 ASN Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 302 LYS Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 539 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1089 ILE Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1249 MET Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1310 THR Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2089 LYS Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 930 GLU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1770 MET Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 2032 MET Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2091 MET Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 1024 GLU Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1506 LEU Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1926 LEU Chi-restraints excluded: chain E residue 1993 ASP Chi-restraints excluded: chain E residue 2159 ASN Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 1047 optimal weight: 9.9990 chunk 796 optimal weight: 0.5980 chunk 550 optimal weight: 6.9990 chunk 117 optimal weight: 6.9990 chunk 505 optimal weight: 3.9990 chunk 711 optimal weight: 5.9990 chunk 1063 optimal weight: 0.9990 chunk 1126 optimal weight: 2.9990 chunk 555 optimal weight: 0.1980 chunk 1008 optimal weight: 0.0020 chunk 303 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 ASN A 943 ASN A1050 GLN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 913 GLN B 925 GLN B 943 ASN ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1773 ASN ** B1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 608 ASN C 943 ASN ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1831 GLN C1862 HIS C1977 GLN D 54 HIS ** D 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 793 HIS ** D1050 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2225 GLN E 383 GLN ** E 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1041 GLN ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1977 GLN E2159 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 95500 Z= 0.166 Angle : 0.575 11.058 129690 Z= 0.297 Chirality : 0.041 0.190 14565 Planarity : 0.004 0.058 16710 Dihedral : 5.024 41.897 12705 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.41 % Favored : 93.55 % Rotamer: Outliers : 2.38 % Allowed : 13.94 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.08), residues: 11655 helix: 1.45 (0.07), residues: 5390 sheet: -0.52 (0.12), residues: 1605 loop : -1.62 (0.09), residues: 4660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 463 HIS 0.006 0.001 HIS D2461 PHE 0.014 0.001 PHE E 804 TYR 0.017 0.001 TYR D1230 ARG 0.009 0.000 ARG D2189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1006 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 762 time to evaluate : 8.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 ASP cc_start: 0.7134 (t0) cc_final: 0.6859 (t70) REVERT: A 930 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7090 (mt-10) REVERT: A 1770 MET cc_start: 0.7431 (tpp) cc_final: 0.7168 (mpp) REVERT: A 2032 MET cc_start: 0.8107 (mmm) cc_final: 0.7783 (mmm) REVERT: B 911 LEU cc_start: 0.9105 (OUTLIER) cc_final: 0.8899 (tp) REVERT: B 1225 ASP cc_start: 0.5827 (t0) cc_final: 0.5486 (t0) REVERT: B 1614 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7804 (mtm180) REVERT: C 87 THR cc_start: 0.7511 (p) cc_final: 0.7228 (p) REVERT: C 433 MET cc_start: 0.7971 (OUTLIER) cc_final: 0.7328 (ttp) REVERT: C 1255 MET cc_start: 0.7515 (mmp) cc_final: 0.7264 (mmp) REVERT: C 2233 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7217 (ttm-80) REVERT: D 505 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7624 (t-90) REVERT: D 930 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: D 1622 ILE cc_start: 0.8251 (mp) cc_final: 0.8015 (mp) outliers start: 244 outliers final: 79 residues processed: 948 average time/residue: 1.7557 time to fit residues: 2277.1153 Evaluate side-chains 765 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 679 time to evaluate : 8.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2241 ASN Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 540 LYS Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1216 MET Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1614 ARG Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2266 LEU Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 582 GLU Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2089 LYS Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2291 MET Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 457 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 505 HIS Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 930 GLU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 2032 MET Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1926 LEU Chi-restraints excluded: chain E residue 2159 ASN Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2447 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 937 optimal weight: 4.9990 chunk 639 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 838 optimal weight: 4.9990 chunk 464 optimal weight: 10.0000 chunk 960 optimal weight: 6.9990 chunk 778 optimal weight: 1.9990 chunk 1 optimal weight: 8.9990 chunk 575 optimal weight: 0.9980 chunk 1010 optimal weight: 0.9980 chunk 284 optimal weight: 6.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1050 GLN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN B 793 HIS ** B1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1323 ASN ** B1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1773 ASN ** B1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1041 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1058 ASN ** C1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 491 GLN D 793 HIS D 943 ASN D1050 GLN D1058 ASN ** D1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 200 HIS E1041 GLN ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1977 GLN E2175 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 95500 Z= 0.225 Angle : 0.592 12.483 129690 Z= 0.306 Chirality : 0.042 0.188 14565 Planarity : 0.004 0.059 16710 Dihedral : 4.964 39.024 12705 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.61 % Favored : 93.35 % Rotamer: Outliers : 2.29 % Allowed : 14.63 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.08), residues: 11655 helix: 1.67 (0.07), residues: 5365 sheet: -0.50 (0.12), residues: 1690 loop : -1.53 (0.10), residues: 4600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E1846 HIS 0.005 0.001 HIS C 492 PHE 0.013 0.001 PHE C 484 TYR 0.019 0.001 TYR C1012 ARG 0.009 0.001 ARG C2189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 959 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 724 time to evaluate : 8.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1614 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7965 (mtt180) REVERT: A 2032 MET cc_start: 0.8050 (mmm) cc_final: 0.7510 (mmm) REVERT: A 2233 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7205 (tpt-90) REVERT: B 911 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8923 (tp) REVERT: B 1225 ASP cc_start: 0.5698 (t0) cc_final: 0.5367 (t0) REVERT: B 1314 PHE cc_start: 0.6861 (m-80) cc_final: 0.6541 (m-10) REVERT: B 2471 MET cc_start: 0.7742 (tpp) cc_final: 0.7368 (tpp) REVERT: C 87 THR cc_start: 0.7564 (p) cc_final: 0.7266 (p) REVERT: C 433 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7334 (ttp) REVERT: C 2233 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7322 (ttm-80) REVERT: D 1255 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.6913 (mpp) REVERT: D 1880 ILE cc_start: 0.8825 (OUTLIER) cc_final: 0.8562 (mt) outliers start: 235 outliers final: 100 residues processed: 896 average time/residue: 1.7155 time to fit residues: 2105.6483 Evaluate side-chains 767 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 660 time to evaluate : 8.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 607 VAL Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1157 LEU Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1614 ARG Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2179 ILE Chi-restraints excluded: chain A residue 2233 ARG Chi-restraints excluded: chain A residue 2241 ASN Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1216 MET Chi-restraints excluded: chain B residue 1218 CYS Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1775 GLU Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 271 ASP Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 584 MET Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2089 LYS Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1255 MET Chi-restraints excluded: chain D residue 1615 LYS Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 2032 MET Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 1024 GLU Chi-restraints excluded: chain E residue 1059 ILE Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1599 MET Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1926 LEU Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 378 optimal weight: 10.0000 chunk 1014 optimal weight: 0.7980 chunk 222 optimal weight: 10.0000 chunk 661 optimal weight: 0.6980 chunk 277 optimal weight: 5.9990 chunk 1127 optimal weight: 0.9990 chunk 935 optimal weight: 5.9990 chunk 521 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 372 optimal weight: 2.9990 chunk 591 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 478 ASN A1626 ASN ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 77 ASN B 478 ASN B1058 ASN ** B1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1626 ASN ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN C1051 GLN C1058 ASN ** C1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 ASN ** D1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1773 ASN ** D1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN E1041 GLN ** E1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1773 ASN ** E1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1977 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 95500 Z= 0.199 Angle : 0.584 13.658 129690 Z= 0.300 Chirality : 0.041 0.192 14565 Planarity : 0.004 0.058 16710 Dihedral : 4.892 35.770 12705 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 2.01 % Allowed : 15.37 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.08), residues: 11655 helix: 1.80 (0.07), residues: 5365 sheet: -0.31 (0.12), residues: 1685 loop : -1.51 (0.10), residues: 4605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E1846 HIS 0.005 0.001 HIS B 492 PHE 0.011 0.001 PHE A 804 TYR 0.022 0.001 TYR B1012 ARG 0.011 0.001 ARG D2169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 913 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 707 time to evaluate : 8.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7114 (mt-10) REVERT: A 1614 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7950 (mtt180) REVERT: A 2032 MET cc_start: 0.8016 (mmm) cc_final: 0.7528 (mmm) REVERT: A 2233 ARG cc_start: 0.7697 (OUTLIER) cc_final: 0.7209 (tpt-90) REVERT: B 911 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8905 (tp) REVERT: B 1225 ASP cc_start: 0.5632 (t0) cc_final: 0.5318 (t0) REVERT: B 2471 MET cc_start: 0.7667 (tpp) cc_final: 0.7222 (tpp) REVERT: C 87 THR cc_start: 0.7566 (p) cc_final: 0.7278 (p) REVERT: C 187 MET cc_start: 0.8241 (tmm) cc_final: 0.7903 (tmm) REVERT: C 433 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7341 (ttp) REVERT: C 1852 ASP cc_start: 0.6562 (m-30) cc_final: 0.6214 (m-30) REVERT: C 2233 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7282 (ttm-80) REVERT: D 930 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7210 (mt-10) REVERT: D 1880 ILE cc_start: 0.8822 (OUTLIER) cc_final: 0.8561 (mt) REVERT: E 302 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7546 (mmmt) REVERT: E 1770 MET cc_start: 0.6401 (ttp) cc_final: 0.6183 (tmm) outliers start: 206 outliers final: 99 residues processed: 872 average time/residue: 1.6978 time to fit residues: 2037.4905 Evaluate side-chains 751 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 643 time to evaluate : 8.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1614 ARG Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2179 ILE Chi-restraints excluded: chain A residue 2233 ARG Chi-restraints excluded: chain A residue 2241 ASN Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1704 ILE Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1775 GLU Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2266 LEU Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2070 GLU Chi-restraints excluded: chain C residue 2089 LYS Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 930 GLU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 656 VAL Chi-restraints excluded: chain E residue 1024 GLU Chi-restraints excluded: chain E residue 1059 ILE Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 1926 LEU Chi-restraints excluded: chain E residue 2159 ASN Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Chi-restraints excluded: chain E residue 2366 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 1086 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 642 optimal weight: 0.2980 chunk 823 optimal weight: 5.9990 chunk 637 optimal weight: 2.9990 chunk 948 optimal weight: 2.9990 chunk 629 optimal weight: 0.9980 chunk 1122 optimal weight: 0.9980 chunk 702 optimal weight: 1.9990 chunk 684 optimal weight: 0.9990 chunk 518 optimal weight: 5.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 77 ASN ** B1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 478 ASN C1051 GLN C1058 ASN ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN ** D 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 386 ASN D1058 ASN ** D1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1041 GLN E1127 ASN ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1849 ASN E1977 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 95500 Z= 0.171 Angle : 0.577 15.100 129690 Z= 0.295 Chirality : 0.041 0.196 14565 Planarity : 0.004 0.058 16710 Dihedral : 4.757 31.637 12705 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 1.90 % Allowed : 15.85 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.08), residues: 11655 helix: 1.92 (0.07), residues: 5365 sheet: -0.22 (0.13), residues: 1650 loop : -1.41 (0.10), residues: 4640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D1846 HIS 0.006 0.001 HIS D2461 PHE 0.012 0.001 PHE A 804 TYR 0.026 0.001 TYR B1012 ARG 0.010 0.000 ARG D2232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 891 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 696 time to evaluate : 9.489 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7405 (OUTLIER) cc_final: 0.7109 (mt-10) REVERT: B 373 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.9008 (tp) REVERT: B 911 LEU cc_start: 0.9093 (OUTLIER) cc_final: 0.8882 (tp) REVERT: B 1225 ASP cc_start: 0.5505 (t0) cc_final: 0.5211 (t0) REVERT: B 2471 MET cc_start: 0.7669 (tpp) cc_final: 0.7260 (tpp) REVERT: C 87 THR cc_start: 0.7493 (p) cc_final: 0.7200 (p) REVERT: C 187 MET cc_start: 0.8207 (tmm) cc_final: 0.7917 (tmm) REVERT: C 433 MET cc_start: 0.7944 (OUTLIER) cc_final: 0.7332 (ttp) REVERT: C 2233 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.7131 (ttm-80) REVERT: D 930 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: E 302 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7471 (mmmt) REVERT: E 490 MET cc_start: 0.7227 (mtm) cc_final: 0.6957 (mtp) outliers start: 195 outliers final: 96 residues processed: 852 average time/residue: 1.7643 time to fit residues: 2061.3080 Evaluate side-chains 750 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 647 time to evaluate : 8.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 505 HIS Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1506 LEU Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2179 ILE Chi-restraints excluded: chain A residue 2241 ASN Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1058 ASN Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 505 HIS Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2089 LYS Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 386 ASN Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 930 GLU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1775 GLU Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 1890 LEU Chi-restraints excluded: chain D residue 1946 ARG Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 522 MET Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 1059 ILE Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1689 GLU Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1926 LEU Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 694 optimal weight: 7.9990 chunk 448 optimal weight: 5.9990 chunk 670 optimal weight: 2.9990 chunk 338 optimal weight: 5.9990 chunk 220 optimal weight: 10.0000 chunk 217 optimal weight: 4.9990 chunk 713 optimal weight: 7.9990 chunk 765 optimal weight: 7.9990 chunk 555 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 882 optimal weight: 5.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 ASN A 200 HIS A1050 GLN ** A1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS B 200 HIS B1241 ASN ** B1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1862 HIS ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 200 HIS C 478 ASN ** C 487 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 ASN ** C 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 ASN ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1626 ASN C1735 ASN ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1831 GLN C1977 GLN C2148 HIS C2175 ASN D 82 ASN D 200 HIS D 576 ASN ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1849 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2148 HIS ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 805 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 943 ASN E1041 GLN E1058 ASN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1626 ASN ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1849 ASN E1862 HIS E1977 GLN E2148 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 95500 Z= 0.409 Angle : 0.709 17.631 129690 Z= 0.365 Chirality : 0.046 0.208 14565 Planarity : 0.005 0.068 16710 Dihedral : 5.252 40.917 12705 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer: Outliers : 2.22 % Allowed : 15.93 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.08), residues: 11655 helix: 1.57 (0.07), residues: 5455 sheet: -0.39 (0.12), residues: 1700 loop : -1.51 (0.10), residues: 4500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 463 HIS 0.007 0.002 HIS E1590 PHE 0.017 0.002 PHE C 484 TYR 0.034 0.002 TYR A1012 ARG 0.012 0.001 ARG E2169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 888 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 661 time to evaluate : 8.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: B 373 LEU cc_start: 0.9295 (OUTLIER) cc_final: 0.9072 (tp) REVERT: B 911 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8935 (tp) REVERT: B 1015 ARG cc_start: 0.7863 (OUTLIER) cc_final: 0.7375 (ptp-110) REVERT: B 2091 MET cc_start: 0.6704 (OUTLIER) cc_final: 0.6466 (mpp) REVERT: B 2471 MET cc_start: 0.7999 (tpp) cc_final: 0.7679 (tpp) REVERT: C 187 MET cc_start: 0.8295 (tmm) cc_final: 0.7897 (tmm) REVERT: C 433 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7310 (ttp) REVERT: D 1060 ASP cc_start: 0.6281 (m-30) cc_final: 0.6056 (m-30) REVERT: D 1880 ILE cc_start: 0.8875 (OUTLIER) cc_final: 0.8658 (mt) REVERT: E 302 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7592 (mmmt) REVERT: E 490 MET cc_start: 0.7412 (mtm) cc_final: 0.7130 (mtp) REVERT: E 1619 ARG cc_start: 0.8086 (mmt-90) cc_final: 0.7780 (mpt180) outliers start: 227 outliers final: 117 residues processed: 843 average time/residue: 1.6670 time to fit residues: 1930.0319 Evaluate side-chains 751 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 626 time to evaluate : 8.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2083 SER Chi-restraints excluded: chain A residue 2179 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1015 ARG Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1290 THR Chi-restraints excluded: chain B residue 1337 ASN Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1832 ASP Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2091 MET Chi-restraints excluded: chain B residue 2132 ASP Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 852 LEU Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1337 ASN Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 1890 LEU Chi-restraints excluded: chain C residue 1906 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 290 ASP Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 852 LEU Chi-restraints excluded: chain D residue 911 LEU Chi-restraints excluded: chain D residue 1058 ASN Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1775 GLU Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 2032 MET Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2083 SER Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2415 LEU Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 302 LYS Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 901 THR Chi-restraints excluded: chain E residue 1149 VAL Chi-restraints excluded: chain E residue 1218 CYS Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1290 THR Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1849 ASN Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 2098 LYS Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 1021 optimal weight: 0.5980 chunk 1075 optimal weight: 2.9990 chunk 981 optimal weight: 5.9990 chunk 1046 optimal weight: 5.9990 chunk 629 optimal weight: 0.9990 chunk 455 optimal weight: 3.9990 chunk 821 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 945 optimal weight: 6.9990 chunk 989 optimal weight: 1.9990 chunk 1042 optimal weight: 0.1980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN A1050 GLN ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A2468 GLN B1287 GLN ** B1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 80 ASN C 487 GLN C1051 GLN ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1735 ASN ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN D 82 ASN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1080 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1127 ASN ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1849 ASN ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1041 GLN E1127 ASN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1849 ASN E1977 GLN E2395 GLN E2468 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.3861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 95500 Z= 0.213 Angle : 0.622 18.250 129690 Z= 0.317 Chirality : 0.042 0.192 14565 Planarity : 0.004 0.058 16710 Dihedral : 5.021 39.147 12705 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 1.62 % Allowed : 16.38 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.08), residues: 11655 helix: 1.81 (0.07), residues: 5410 sheet: -0.35 (0.12), residues: 1720 loop : -1.40 (0.10), residues: 4525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 463 HIS 0.006 0.001 HIS B 492 PHE 0.010 0.001 PHE A 804 TYR 0.037 0.001 TYR B1012 ARG 0.013 0.001 ARG E2169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 166 poor density : 671 time to evaluate : 8.362 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7415 (OUTLIER) cc_final: 0.7083 (mt-10) REVERT: B 373 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.9016 (tp) REVERT: B 911 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8910 (tp) REVERT: B 1770 MET cc_start: 0.6708 (tmt) cc_final: 0.6445 (tmm) REVERT: B 2471 MET cc_start: 0.7935 (tpp) cc_final: 0.7520 (tpp) REVERT: C 87 THR cc_start: 0.7513 (p) cc_final: 0.7205 (p) REVERT: C 433 MET cc_start: 0.7946 (OUTLIER) cc_final: 0.7324 (ttp) REVERT: C 1012 TYR cc_start: 0.7040 (m-80) cc_final: 0.6821 (m-80) REVERT: C 1297 LYS cc_start: 0.7856 (mppt) cc_final: 0.7634 (mtmt) REVERT: C 1770 MET cc_start: 0.6328 (tmm) cc_final: 0.6034 (tmm) REVERT: C 2233 ARG cc_start: 0.7990 (OUTLIER) cc_final: 0.7341 (ttm-80) REVERT: D 1849 ASN cc_start: 0.7752 (OUTLIER) cc_final: 0.7471 (p0) REVERT: D 1880 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8581 (mt) REVERT: E 490 MET cc_start: 0.7413 (mtm) cc_final: 0.7187 (mtp) outliers start: 166 outliers final: 102 residues processed: 801 average time/residue: 1.7230 time to fit residues: 1879.7233 Evaluate side-chains 731 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 622 time to evaluate : 8.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 539 THR Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain A residue 2012 LEU Chi-restraints excluded: chain A residue 2179 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 802 THR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1049 LEU Chi-restraints excluded: chain C residue 1149 VAL Chi-restraints excluded: chain C residue 1218 CYS Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 1735 ASN Chi-restraints excluded: chain C residue 1906 LEU Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1775 GLU Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1849 ASN Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 2032 MET Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2431 LEU Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 1024 GLU Chi-restraints excluded: chain E residue 1058 ASN Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1630 MET Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1849 ASN Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 1885 SER Chi-restraints excluded: chain E residue 2098 LYS Chi-restraints excluded: chain E residue 2159 ASN Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 687 optimal weight: 0.0980 chunk 1106 optimal weight: 5.9990 chunk 675 optimal weight: 0.9980 chunk 524 optimal weight: 6.9990 chunk 769 optimal weight: 0.9990 chunk 1160 optimal weight: 1.9990 chunk 1068 optimal weight: 4.9990 chunk 924 optimal weight: 6.9990 chunk 95 optimal weight: 0.9990 chunk 713 optimal weight: 5.9990 chunk 566 optimal weight: 7.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 HIS B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1051 GLN C1735 ASN ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1773 ASN C1977 GLN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1127 ASN ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2468 GLN ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E1127 ASN ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1849 ASN ** E1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.3933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 95500 Z= 0.191 Angle : 0.622 18.319 129690 Z= 0.314 Chirality : 0.042 0.197 14565 Planarity : 0.004 0.063 16710 Dihedral : 4.883 35.700 12705 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.86 % Favored : 93.11 % Rotamer: Outliers : 1.27 % Allowed : 16.94 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.08), residues: 11655 helix: 1.87 (0.07), residues: 5425 sheet: -0.30 (0.12), residues: 1730 loop : -1.38 (0.10), residues: 4500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 463 HIS 0.010 0.001 HIS D2461 PHE 0.011 0.001 PHE A 804 TYR 0.031 0.001 TYR A1012 ARG 0.014 0.001 ARG D2169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 23310 Ramachandran restraints generated. 11655 Oldfield, 0 Emsley, 11655 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 648 time to evaluate : 8.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 930 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7066 (mt-10) REVERT: B 373 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8992 (tp) REVERT: B 911 LEU cc_start: 0.9125 (OUTLIER) cc_final: 0.8902 (tp) REVERT: B 1770 MET cc_start: 0.6671 (tmt) cc_final: 0.6439 (tmm) REVERT: B 2471 MET cc_start: 0.7913 (tpp) cc_final: 0.7490 (tpp) REVERT: C 87 THR cc_start: 0.7503 (p) cc_final: 0.7215 (p) REVERT: C 187 MET cc_start: 0.8188 (tmm) cc_final: 0.7924 (tmm) REVERT: C 433 MET cc_start: 0.7945 (OUTLIER) cc_final: 0.7305 (ttp) REVERT: C 1012 TYR cc_start: 0.7005 (m-80) cc_final: 0.6796 (m-80) REVERT: C 1297 LYS cc_start: 0.7834 (mppt) cc_final: 0.7618 (mtmt) REVERT: C 2233 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.7285 (ttm-80) REVERT: D 740 ARG cc_start: 0.7091 (mpp80) cc_final: 0.6843 (mpp80) REVERT: D 1880 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8549 (mt) REVERT: E 490 MET cc_start: 0.7397 (mtm) cc_final: 0.7145 (mtp) outliers start: 130 outliers final: 97 residues processed: 755 average time/residue: 1.7113 time to fit residues: 1768.5212 Evaluate side-chains 728 residues out of total 10260 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 625 time to evaluate : 8.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 290 ASP Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 298 LEU Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 483 LEU Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 901 THR Chi-restraints excluded: chain A residue 911 LEU Chi-restraints excluded: chain A residue 930 GLU Chi-restraints excluded: chain A residue 1011 THR Chi-restraints excluded: chain A residue 1149 VAL Chi-restraints excluded: chain A residue 1226 VAL Chi-restraints excluded: chain A residue 1251 ILE Chi-restraints excluded: chain A residue 1290 THR Chi-restraints excluded: chain A residue 1708 VAL Chi-restraints excluded: chain A residue 1832 ASP Chi-restraints excluded: chain A residue 1885 SER Chi-restraints excluded: chain A residue 1935 ARG Chi-restraints excluded: chain A residue 2179 ILE Chi-restraints excluded: chain A residue 2316 THR Chi-restraints excluded: chain A residue 2396 LEU Chi-restraints excluded: chain A residue 2431 LEU Chi-restraints excluded: chain A residue 2486 VAL Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 361 VAL Chi-restraints excluded: chain B residue 373 LEU Chi-restraints excluded: chain B residue 474 THR Chi-restraints excluded: chain B residue 513 THR Chi-restraints excluded: chain B residue 563 VAL Chi-restraints excluded: chain B residue 798 LEU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 901 THR Chi-restraints excluded: chain B residue 911 LEU Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1044 MET Chi-restraints excluded: chain B residue 1226 VAL Chi-restraints excluded: chain B residue 1251 ILE Chi-restraints excluded: chain B residue 1708 VAL Chi-restraints excluded: chain B residue 1885 SER Chi-restraints excluded: chain B residue 1890 LEU Chi-restraints excluded: chain B residue 1926 LEU Chi-restraints excluded: chain B residue 2316 THR Chi-restraints excluded: chain C residue 84 THR Chi-restraints excluded: chain C residue 290 ASP Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 433 MET Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 539 THR Chi-restraints excluded: chain C residue 563 VAL Chi-restraints excluded: chain C residue 775 THR Chi-restraints excluded: chain C residue 901 THR Chi-restraints excluded: chain C residue 1048 LEU Chi-restraints excluded: chain C residue 1226 VAL Chi-restraints excluded: chain C residue 1251 ILE Chi-restraints excluded: chain C residue 1290 THR Chi-restraints excluded: chain C residue 1622 ILE Chi-restraints excluded: chain C residue 1708 VAL Chi-restraints excluded: chain C residue 1777 MET Chi-restraints excluded: chain C residue 2012 LEU Chi-restraints excluded: chain C residue 2233 ARG Chi-restraints excluded: chain C residue 2316 THR Chi-restraints excluded: chain D residue 292 LEU Chi-restraints excluded: chain D residue 361 VAL Chi-restraints excluded: chain D residue 373 LEU Chi-restraints excluded: chain D residue 440 ILE Chi-restraints excluded: chain D residue 474 THR Chi-restraints excluded: chain D residue 539 THR Chi-restraints excluded: chain D residue 798 LEU Chi-restraints excluded: chain D residue 1063 GLU Chi-restraints excluded: chain D residue 1149 VAL Chi-restraints excluded: chain D residue 1251 ILE Chi-restraints excluded: chain D residue 1310 THR Chi-restraints excluded: chain D residue 1708 VAL Chi-restraints excluded: chain D residue 1775 GLU Chi-restraints excluded: chain D residue 1832 ASP Chi-restraints excluded: chain D residue 1880 ILE Chi-restraints excluded: chain D residue 2032 MET Chi-restraints excluded: chain D residue 2066 GLU Chi-restraints excluded: chain D residue 2266 LEU Chi-restraints excluded: chain D residue 2316 THR Chi-restraints excluded: chain D residue 2448 THR Chi-restraints excluded: chain E residue 290 ASP Chi-restraints excluded: chain E residue 361 VAL Chi-restraints excluded: chain E residue 373 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 513 THR Chi-restraints excluded: chain E residue 539 THR Chi-restraints excluded: chain E residue 563 VAL Chi-restraints excluded: chain E residue 584 MET Chi-restraints excluded: chain E residue 606 THR Chi-restraints excluded: chain E residue 852 LEU Chi-restraints excluded: chain E residue 1251 ILE Chi-restraints excluded: chain E residue 1310 THR Chi-restraints excluded: chain E residue 1708 VAL Chi-restraints excluded: chain E residue 1849 ASN Chi-restraints excluded: chain E residue 1880 ILE Chi-restraints excluded: chain E residue 2098 LYS Chi-restraints excluded: chain E residue 2179 ILE Chi-restraints excluded: chain E residue 2291 MET Chi-restraints excluded: chain E residue 2316 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1165 random chunks: chunk 734 optimal weight: 6.9990 chunk 984 optimal weight: 10.0000 chunk 283 optimal weight: 0.5980 chunk 852 optimal weight: 7.9990 chunk 136 optimal weight: 8.9990 chunk 256 optimal weight: 5.9990 chunk 925 optimal weight: 6.9990 chunk 387 optimal weight: 0.0670 chunk 950 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 170 optimal weight: 4.9990 overall best weight: 2.1324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1670 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1287 GLN ** B1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B1735 ASN ** B1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1058 ASN ** C1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1735 ASN ** C1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C1977 GLN ** D 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 785 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1127 ASN ** D1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D1773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1849 ASN ** E 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 386 ASN E 805 HIS E1127 ASN ** E1522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E1741 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E1849 ASN ** E1977 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E2159 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.064607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.053122 restraints weight = 274322.674| |-----------------------------------------------------------------------------| r_work (start): 0.2874 rms_B_bonded: 2.51 r_work: 0.2745 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2621 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.3951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 95500 Z= 0.277 Angle : 0.655 17.350 129690 Z= 0.332 Chirality : 0.043 0.199 14565 Planarity : 0.004 0.067 16710 Dihedral : 4.973 36.694 12705 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.98 % Favored : 92.96 % Rotamer: Outliers : 1.32 % Allowed : 16.91 % Favored : 81.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.08), residues: 11655 helix: 1.83 (0.07), residues: 5415 sheet: -0.24 (0.12), residues: 1690 loop : -1.37 (0.10), residues: 4550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 463 HIS 0.009 0.001 HIS D2461 PHE 0.013 0.001 PHE C 484 TYR 0.036 0.001 TYR A1012 ARG 0.014 0.001 ARG D2169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32595.67 seconds wall clock time: 568 minutes 42.01 seconds (34122.01 seconds total)