Starting phenix.real_space_refine (version: 1.21rc1) on Sun Aug 27 20:25:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/08_2023/6rui_10006.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/08_2023/6rui_10006.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/08_2023/6rui_10006.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/08_2023/6rui_10006.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/08_2023/6rui_10006.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rui_10006/08_2023/6rui_10006.pdb" } resolution = 2.7 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 93 5.49 5 S 238 5.16 5 C 32426 2.51 5 N 8884 2.21 5 O 9883 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 244": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ARG 422": "NH1" <-> "NH2" Residue "A TYR 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 771": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 786": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 225": "NH1" <-> "NH2" Residue "B ARG 261": "NH1" <-> "NH2" Residue "B PHE 262": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 448": "NH1" <-> "NH2" Residue "B PHE 769": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 781": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 817": "NH1" <-> "NH2" Residue "B TYR 874": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 895": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1014": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1033": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1065": "NH1" <-> "NH2" Residue "C TYR 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 300": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 6": "NH1" <-> "NH2" Residue "E TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 167": "NH1" <-> "NH2" Residue "E TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 42": "NH1" <-> "NH2" Residue "O PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 18": "NH1" <-> "NH2" Residue "Q ARG 26": "NH1" <-> "NH2" Residue "Q ARG 27": "NH1" <-> "NH2" Residue "Q ARG 114": "NH1" <-> "NH2" Residue "Q ARG 117": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 305": "NH1" <-> "NH2" Residue "Q ARG 324": "NH1" <-> "NH2" Residue "Q ARG 350": "NH1" <-> "NH2" Residue "Q TYR 366": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 411": "NH1" <-> "NH2" Residue "Q ARG 421": "NH1" <-> "NH2" Residue "Q ARG 478": "NH1" <-> "NH2" Residue "Q ARG 504": "NH1" <-> "NH2" Residue "S ARG 44": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S TYR 205": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 221": "NH1" <-> "NH2" Residue "S ARG 257": "NH1" <-> "NH2" Residue "S ARG 377": "NH1" <-> "NH2" Residue "S PHE 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 407": "NH1" <-> "NH2" Residue "S ARG 419": "NH1" <-> "NH2" Residue "S ARG 434": "NH1" <-> "NH2" Residue "S ARG 472": "NH1" <-> "NH2" Residue "S ARG 484": "NH1" <-> "NH2" Residue "S PHE 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 542": "NH1" <-> "NH2" Residue "S PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 746": "NH1" <-> "NH2" Residue "S ARG 762": "NH1" <-> "NH2" Residue "R ARG 17": "NH1" <-> "NH2" Residue "R ARG 29": "NH1" <-> "NH2" Residue "R ARG 30": "NH1" <-> "NH2" Residue "R ARG 33": "NH1" <-> "NH2" Residue "R ARG 209": "NH1" <-> "NH2" Residue "R ARG 241": "NH1" <-> "NH2" Residue "R ARG 283": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "R PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 381": "NH1" <-> "NH2" Residue "R ARG 397": "NH1" <-> "NH2" Residue "R ARG 441": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 51525 Number of models: 1 Model: "" Number of chains: 21 Chain: "T" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 958 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain breaks: 1 Chain: "U" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 965 Classifications: {'DNA': 46} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 45} Chain breaks: 1 Chain: "I" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 942 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 4, 'TRANS': 119} Chain: "N" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1103 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 129} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "M" Number of atoms: 856 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 856 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "A" Number of atoms: 11565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1465, 11565 Classifications: {'peptide': 1465} Link IDs: {'PTRANS': 59, 'TRANS': 1405} Chain breaks: 7 Chain: "B" Number of atoms: 9365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1180, 9365 Classifications: {'peptide': 1180} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 59, 'TRANS': 1120} Chain breaks: 2 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "C" Number of atoms: 2418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2418 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 19, 'TRANS': 284} Chain breaks: 1 Chain: "D" Number of atoms: 551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 551 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 3, 'TRANS': 66} Chain breaks: 1 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1759 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain: "F" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 823 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} Chain: "G" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1600 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 2 Chain: "H" Number of atoms: 1072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1072 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "K" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 810 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "L" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 359 Classifications: {'peptide': 45} Modifications used: {'COO': 1} Link IDs: {'TRANS': 44} Chain: "O" Number of atoms: 4139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 504, 4139 Classifications: {'peptide': 504} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 13, 'TRANS': 490} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "Q" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 477, 3936 Classifications: {'peptide': 477} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 19, 'TRANS': 457} Chain breaks: 3 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "S" Number of atoms: 4963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4963 Classifications: {'peptide': 610} Link IDs: {'PTRANS': 21, 'TRANS': 588} Chain breaks: 7 Chain: "R" Number of atoms: 2771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2771 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 12, 'TRANS': 317} Chain breaks: 3 Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 40069 SG CYS Q 29 64.350 77.582 61.343 1.00 96.26 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" P DT T 40 " occ=0.00 ... (18 atoms not shown) pdb=" C6 DT T 40 " occ=0.00 residue: pdb=" P DG U 12 " occ=0.00 ... (20 atoms not shown) pdb=" C4 DG U 12 " occ=0.00 residue: pdb=" P DA U 19 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 19 " occ=0.00 residue: pdb=" P DA U 31 " occ=0.00 ... (19 atoms not shown) pdb=" C4 DA U 31 " occ=0.00 Time building chain proxies: 19.03, per 1000 atoms: 0.37 Number of scatterers: 51525 At special positions: 0 Unit cell: (159.12, 217.36, 190.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 238 16.00 P 93 15.00 O 9883 8.00 N 8884 7.00 C 32426 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: 16.69 Conformation dependent library (CDL) restraints added in 5.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Q 601 " pdb="ZN ZN Q 601 " - pdb=" SG CYS Q 29 " 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11720 Finding SS restraints... Secondary structure from input PDB file: 218 helices and 64 sheets defined 38.6% alpha, 15.4% beta 13 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 14.01 Creating SS restraints... Processing helix chain 'I' and resid 58 through 63 removed outlier: 3.585A pdb=" N LYS I 63 " --> pdb=" O SER I 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 149 through 154 Processing helix chain 'M' and resid 67 through 72 removed outlier: 3.777A pdb=" N ALA M 72 " --> pdb=" O SER M 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 28 removed outlier: 3.638A pdb=" N LEU A 27 " --> pdb=" O LYS A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 99 removed outlier: 3.808A pdb=" N ILE A 96 " --> pdb=" O ASN A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 125 removed outlier: 3.611A pdb=" N TYR A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 124 " --> pdb=" O CYS A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 135 Processing helix chain 'A' and resid 174 through 199 removed outlier: 3.642A pdb=" N LEU A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU A 180 " --> pdb=" O THR A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 224 removed outlier: 3.550A pdb=" N HIS A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.679A pdb=" N ARG A 265 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL A 266 " --> pdb=" O THR A 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 261 through 266' Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.619A pdb=" N ASN A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 326 " --> pdb=" O ASN A 322 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG A 329 " --> pdb=" O ASP A 325 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 330 " --> pdb=" O THR A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 339 removed outlier: 4.417A pdb=" N TYR A 337 " --> pdb=" O CYS A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 354 Processing helix chain 'A' and resid 365 through 369 removed outlier: 3.968A pdb=" N LEU A 369 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 406 removed outlier: 3.789A pdb=" N LEU A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEU A 386 " --> pdb=" O GLN A 382 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS A 388 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG A 397 " --> pdb=" O SER A 393 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ASP A 401 " --> pdb=" O ARG A 397 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 403 " --> pdb=" O LEU A 399 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS A 405 " --> pdb=" O ASP A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 439 removed outlier: 3.511A pdb=" N THR A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A 434 " --> pdb=" O ILE A 430 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA A 436 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 459 removed outlier: 3.863A pdb=" N GLN A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 471 Processing helix chain 'A' and resid 498 through 503 Processing helix chain 'A' and resid 515 through 526 removed outlier: 3.824A pdb=" N GLN A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 559 Processing helix chain 'A' and resid 596 through 598 No H-bonds generated for 'chain 'A' and resid 596 through 598' Processing helix chain 'A' and resid 617 through 621 Processing helix chain 'A' and resid 640 through 650 Processing helix chain 'A' and resid 673 through 681 removed outlier: 3.507A pdb=" N VAL A 678 " --> pdb=" O ILE A 674 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TRP A 679 " --> pdb=" O SER A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 688 through 700 removed outlier: 3.652A pdb=" N CYS A 699 " --> pdb=" O TYR A 695 " (cutoff:3.500A) Processing helix chain 'A' and resid 728 through 740 removed outlier: 3.662A pdb=" N ILE A 732 " --> pdb=" O GLY A 728 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 739 " --> pdb=" O VAL A 735 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 761 removed outlier: 3.545A pdb=" N GLY A 761 " --> pdb=" O GLU A 758 " (cutoff:3.500A) Processing helix chain 'A' and resid 782 through 787 Processing helix chain 'A' and resid 792 through 801 Processing helix chain 'A' and resid 802 through 824 Processing helix chain 'A' and resid 830 through 834 removed outlier: 3.541A pdb=" N ARG A 834 " --> pdb=" O ASP A 831 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 848 removed outlier: 3.747A pdb=" N THR A 844 " --> pdb=" O ASN A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 849 through 851 No H-bonds generated for 'chain 'A' and resid 849 through 851' Processing helix chain 'A' and resid 852 through 862 Processing helix chain 'A' and resid 872 through 884 removed outlier: 3.718A pdb=" N ARG A 878 " --> pdb=" O GLU A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 912 removed outlier: 3.501A pdb=" N SER A 898 " --> pdb=" O ALA A 894 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A 903 " --> pdb=" O LYS A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 932 removed outlier: 3.544A pdb=" N ALA A 929 " --> pdb=" O MET A 925 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLY A 932 " --> pdb=" O MET A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 936 through 945 Processing helix chain 'A' and resid 976 through 979 Processing helix chain 'A' and resid 991 through 1010 removed outlier: 4.282A pdb=" N GLY A1005 " --> pdb=" O ALA A1001 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU A1006 " --> pdb=" O GLY A1002 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A1008 " --> pdb=" O GLU A1004 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1027 removed outlier: 3.605A pdb=" N GLN A1020 " --> pdb=" O SER A1016 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A1021 " --> pdb=" O GLY A1017 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN A1026 " --> pdb=" O CYS A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1049 through 1053 Processing helix chain 'A' and resid 1056 through 1060 removed outlier: 3.531A pdb=" N GLU A1060 " --> pdb=" O ILE A1057 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1072 Processing helix chain 'A' and resid 1072 through 1080 removed outlier: 3.675A pdb=" N LYS A1078 " --> pdb=" O TYR A1074 " (cutoff:3.500A) Processing helix chain 'A' and resid 1082 through 1086 removed outlier: 3.589A pdb=" N LEU A1085 " --> pdb=" O PRO A1082 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ILE A1086 " --> pdb=" O SER A1083 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1082 through 1086' Processing helix chain 'A' and resid 1092 through 1108 removed outlier: 3.505A pdb=" N LYS A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LYS A1107 " --> pdb=" O LYS A1103 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N HIS A1108 " --> pdb=" O TYR A1104 " (cutoff:3.500A) Processing helix chain 'A' and resid 1122 through 1127 removed outlier: 3.680A pdb=" N LYS A1126 " --> pdb=" O PRO A1122 " (cutoff:3.500A) Processing helix chain 'A' and resid 1137 through 1150 Processing helix chain 'A' and resid 1163 through 1176 removed outlier: 3.628A pdb=" N ALA A1168 " --> pdb=" O LYS A1164 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A1169 " --> pdb=" O LYS A1165 " (cutoff:3.500A) Processing helix chain 'A' and resid 1184 through 1195 Processing helix chain 'A' and resid 1217 through 1226 removed outlier: 3.585A pdb=" N GLU A1224 " --> pdb=" O PRO A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1247 through 1257 removed outlier: 3.512A pdb=" N LYS A1256 " --> pdb=" O ASP A1252 " (cutoff:3.500A) Processing helix chain 'A' and resid 1298 through 1307 Processing helix chain 'A' and resid 1309 through 1318 removed outlier: 3.508A pdb=" N GLN A1314 " --> pdb=" O LYS A1310 " (cutoff:3.500A) Processing helix chain 'A' and resid 1320 through 1338 removed outlier: 3.557A pdb=" N LYS A1331 " --> pdb=" O ALA A1327 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG A1338 " --> pdb=" O LYS A1334 " (cutoff:3.500A) Processing helix chain 'A' and resid 1440 through 1454 removed outlier: 3.525A pdb=" N ILE A1450 " --> pdb=" O ARG A1446 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER A1452 " --> pdb=" O SER A1448 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N HIS A1453 " --> pdb=" O ALA A1449 " (cutoff:3.500A) Processing helix chain 'A' and resid 1484 through 1494 Processing helix chain 'A' and resid 1512 through 1516 removed outlier: 4.219A pdb=" N GLY A1515 " --> pdb=" O PRO A1512 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A1516 " --> pdb=" O GLU A1513 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1512 through 1516' Processing helix chain 'A' and resid 1525 through 1530 removed outlier: 3.614A pdb=" N MET A1529 " --> pdb=" O ASN A1525 " (cutoff:3.500A) Processing helix chain 'A' and resid 1531 through 1533 No H-bonds generated for 'chain 'A' and resid 1531 through 1533' Processing helix chain 'A' and resid 1537 through 1541 removed outlier: 3.794A pdb=" N ILE A1541 " --> pdb=" O VAL A1538 " (cutoff:3.500A) Processing helix chain 'A' and resid 1545 through 1553 Processing helix chain 'A' and resid 1554 through 1572 removed outlier: 3.766A pdb=" N ARG A1572 " --> pdb=" O ASN A1568 " (cutoff:3.500A) Processing helix chain 'A' and resid 1578 through 1590 removed outlier: 3.604A pdb=" N LEU A1582 " --> pdb=" O SER A1578 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU A1584 " --> pdb=" O ARG A1580 " (cutoff:3.500A) Processing helix chain 'A' and resid 1599 through 1604 Processing helix chain 'A' and resid 1608 through 1616 removed outlier: 3.775A pdb=" N LYS A1612 " --> pdb=" O SER A1608 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU A1616 " --> pdb=" O LYS A1612 " (cutoff:3.500A) Processing helix chain 'A' and resid 1617 through 1627 Processing helix chain 'A' and resid 1636 through 1644 removed outlier: 3.547A pdb=" N VAL A1642 " --> pdb=" O SER A1638 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL A1643 " --> pdb=" O ALA A1639 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 35 through 40 removed outlier: 3.981A pdb=" N GLN B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 51 removed outlier: 3.934A pdb=" N SER B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.539A pdb=" N GLY B 58 " --> pdb=" O GLY B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 removed outlier: 3.629A pdb=" N SER B 126 " --> pdb=" O TYR B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 183 Processing helix chain 'B' and resid 219 through 224 removed outlier: 4.182A pdb=" N ALA B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ASN B 224 " --> pdb=" O PRO B 220 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 219 through 224' Processing helix chain 'B' and resid 273 through 281 removed outlier: 4.272A pdb=" N CYS B 281 " --> pdb=" O LEU B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.852A pdb=" N ILE B 288 " --> pdb=" O SER B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 317 removed outlier: 3.632A pdb=" N ASP B 304 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU B 306 " --> pdb=" O LEU B 302 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 307 " --> pdb=" O THR B 303 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LEU B 308 " --> pdb=" O ASP B 304 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 313 " --> pdb=" O LEU B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 334 removed outlier: 4.633A pdb=" N GLN B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 357 removed outlier: 4.354A pdb=" N GLN B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 386 removed outlier: 3.537A pdb=" N ARG B 379 " --> pdb=" O LEU B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 433 removed outlier: 3.582A pdb=" N ILE B 425 " --> pdb=" O LEU B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 451 removed outlier: 3.533A pdb=" N SER B 447 " --> pdb=" O LYS B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 492 through 498 Processing helix chain 'B' and resid 506 through 510 Processing helix chain 'B' and resid 521 through 525 removed outlier: 3.532A pdb=" N TRP B 525 " --> pdb=" O PRO B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 568 Processing helix chain 'B' and resid 574 through 576 No H-bonds generated for 'chain 'B' and resid 574 through 576' Processing helix chain 'B' and resid 597 through 614 removed outlier: 3.637A pdb=" N ARG B 609 " --> pdb=" O ALA B 605 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU B 614 " --> pdb=" O TYR B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 668 through 672 removed outlier: 3.541A pdb=" N MET B 672 " --> pdb=" O GLN B 669 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 692 through 697 removed outlier: 3.665A pdb=" N ILE B 696 " --> pdb=" O PRO B 693 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU B 697 " --> pdb=" O THR B 694 " (cutoff:3.500A) Processing helix chain 'B' and resid 706 through 710 removed outlier: 3.540A pdb=" N ASN B 710 " --> pdb=" O SER B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 711 through 722 removed outlier: 3.591A pdb=" N ASN B 715 " --> pdb=" O GLN B 711 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLN B 720 " --> pdb=" O MET B 716 " (cutoff:3.500A) Processing helix chain 'B' and resid 723 through 725 No H-bonds generated for 'chain 'B' and resid 723 through 725' Processing helix chain 'B' and resid 732 through 736 Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.948A pdb=" N ASP B 759 " --> pdb=" O ASN B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 761 through 765 Processing helix chain 'B' and resid 791 through 796 Processing helix chain 'B' and resid 835 through 839 removed outlier: 3.639A pdb=" N GLU B 838 " --> pdb=" O GLU B 835 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 839 " --> pdb=" O TRP B 836 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 835 through 839' Processing helix chain 'B' and resid 932 through 936 Processing helix chain 'B' and resid 950 through 954 Processing helix chain 'B' and resid 960 through 976 removed outlier: 3.649A pdb=" N LEU B 967 " --> pdb=" O PHE B 963 " (cutoff:3.500A) Processing helix chain 'B' and resid 991 through 1004 Processing helix chain 'B' and resid 1040 through 1044 removed outlier: 3.952A pdb=" N LYS B1043 " --> pdb=" O VAL B1040 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE B1044 " --> pdb=" O ASN B1041 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1040 through 1044' Processing helix chain 'B' and resid 1072 through 1082 Processing helix chain 'B' and resid 1084 through 1093 Processing helix chain 'B' and resid 1180 through 1191 Processing helix chain 'C' and resid 33 through 40 removed outlier: 3.976A pdb=" N ASP C 39 " --> pdb=" O LYS C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 74 removed outlier: 3.559A pdb=" N ILE C 72 " --> pdb=" O ARG C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 103 Processing helix chain 'C' and resid 121 through 126 removed outlier: 4.557A pdb=" N PHE C 126 " --> pdb=" O ASP C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 167 No H-bonds generated for 'chain 'C' and resid 165 through 167' Processing helix chain 'C' and resid 172 through 177 removed outlier: 3.703A pdb=" N GLN C 175 " --> pdb=" O GLN C 172 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER C 176 " --> pdb=" O GLY C 173 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR C 177 " --> pdb=" O ARG C 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 177' Processing helix chain 'C' and resid 216 through 220 Processing helix chain 'C' and resid 241 through 249 removed outlier: 4.020A pdb=" N PHE C 247 " --> pdb=" O SER C 243 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS C 249 " --> pdb=" O ARG C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 277 through 282 removed outlier: 3.567A pdb=" N ARG C 281 " --> pdb=" O GLU C 278 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR C 282 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 330 removed outlier: 3.534A pdb=" N PHE C 315 " --> pdb=" O GLU C 311 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER C 317 " --> pdb=" O ILE C 313 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU C 328 " --> pdb=" O LYS C 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 32 through 47 removed outlier: 3.689A pdb=" N GLN D 38 " --> pdb=" O ASP D 34 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N SER D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS D 47 " --> pdb=" O PHE D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 removed outlier: 3.526A pdb=" N ASP D 95 " --> pdb=" O ARG D 91 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE D 96 " --> pdb=" O ILE D 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 26 removed outlier: 3.513A pdb=" N LEU E 12 " --> pdb=" O ASN E 8 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ALA E 15 " --> pdb=" O ARG E 11 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 31 through 36 Processing helix chain 'E' and resid 38 through 47 Processing helix chain 'E' and resid 65 through 72 removed outlier: 3.520A pdb=" N SER E 70 " --> pdb=" O GLU E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 104 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 143 through 147 Processing helix chain 'E' and resid 157 through 169 Processing helix chain 'E' and resid 171 through 175 removed outlier: 3.518A pdb=" N GLN E 174 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 175 " --> pdb=" O GLU E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 171 through 175' Processing helix chain 'E' and resid 184 through 189 Processing helix chain 'F' and resid 56 through 72 removed outlier: 3.646A pdb=" N GLN F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 79 removed outlier: 3.814A pdb=" N ARG F 79 " --> pdb=" O LYS F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 102 Processing helix chain 'F' and resid 116 through 125 Processing helix chain 'G' and resid 13 through 18 Processing helix chain 'G' and resid 19 through 21 No H-bonds generated for 'chain 'G' and resid 19 through 21' Processing helix chain 'G' and resid 56 through 65 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 160 through 162 No H-bonds generated for 'chain 'G' and resid 160 through 162' Processing helix chain 'H' and resid 88 through 92 removed outlier: 3.555A pdb=" N ASP H 92 " --> pdb=" O LEU H 89 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 27 Processing helix chain 'J' and resid 31 through 39 Processing helix chain 'J' and resid 43 through 52 removed outlier: 3.971A pdb=" N MET J 49 " --> pdb=" O CYS J 45 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE J 50 " --> pdb=" O CYS J 46 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'K' and resid 69 through 81 removed outlier: 3.844A pdb=" N ALA K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL K 79 " --> pdb=" O ALA K 75 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 140 removed outlier: 3.587A pdb=" N VAL K 131 " --> pdb=" O LEU K 127 " (cutoff:3.500A) Processing helix chain 'O' and resid 50 through 61 removed outlier: 3.597A pdb=" N VAL O 56 " --> pdb=" O TYR O 52 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS O 57 " --> pdb=" O SER O 53 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP O 61 " --> pdb=" O LYS O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 79 removed outlier: 4.038A pdb=" N ASN O 76 " --> pdb=" O GLY O 72 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA O 79 " --> pdb=" O ALA O 75 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 101 removed outlier: 3.757A pdb=" N ASN O 94 " --> pdb=" O ASP O 90 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASP O 98 " --> pdb=" O ASN O 94 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE O 99 " --> pdb=" O ILE O 95 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU O 100 " --> pdb=" O LEU O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 112 through 121 removed outlier: 4.045A pdb=" N ILE O 116 " --> pdb=" O GLY O 112 " (cutoff:3.500A) Processing helix chain 'O' and resid 129 through 147 removed outlier: 5.084A pdb=" N LYS O 135 " --> pdb=" O HIS O 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE O 142 " --> pdb=" O TYR O 138 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER O 145 " --> pdb=" O LYS O 141 " (cutoff:3.500A) Processing helix chain 'O' and resid 150 through 160 removed outlier: 3.583A pdb=" N SER O 155 " --> pdb=" O TRP O 151 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N MET O 156 " --> pdb=" O GLN O 152 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE O 157 " --> pdb=" O ASP O 153 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER O 160 " --> pdb=" O MET O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 169 through 183 removed outlier: 3.567A pdb=" N HIS O 173 " --> pdb=" O THR O 169 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU O 180 " --> pdb=" O LEU O 176 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ARG O 181 " --> pdb=" O LYS O 177 " (cutoff:3.500A) Processing helix chain 'O' and resid 186 through 195 removed outlier: 3.715A pdb=" N ASP O 191 " --> pdb=" O MET O 187 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N THR O 192 " --> pdb=" O GLY O 188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR O 193 " --> pdb=" O PHE O 189 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA O 195 " --> pdb=" O ASP O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 204 through 221 removed outlier: 4.276A pdb=" N LEU O 208 " --> pdb=" O THR O 204 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR O 212 " --> pdb=" O LEU O 208 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER O 213 " --> pdb=" O VAL O 209 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG O 219 " --> pdb=" O LEU O 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY O 220 " --> pdb=" O LEU O 216 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR O 221 " --> pdb=" O LYS O 217 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 246 removed outlier: 3.801A pdb=" N LYS O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER O 239 " --> pdb=" O GLU O 235 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE O 240 " --> pdb=" O LYS O 236 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLU O 243 " --> pdb=" O SER O 239 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU O 244 " --> pdb=" O ILE O 240 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLN O 245 " --> pdb=" O ASP O 241 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN O 246 " --> pdb=" O VAL O 242 " (cutoff:3.500A) Processing helix chain 'O' and resid 326 through 347 removed outlier: 3.649A pdb=" N THR O 330 " --> pdb=" O LYS O 326 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU O 332 " --> pdb=" O LEU O 328 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU O 338 " --> pdb=" O SER O 334 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER O 340 " --> pdb=" O LEU O 336 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLU O 345 " --> pdb=" O THR O 341 " (cutoff:3.500A) Processing helix chain 'O' and resid 356 through 369 removed outlier: 3.530A pdb=" N PHE O 361 " --> pdb=" O GLY O 357 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N LEU O 367 " --> pdb=" O THR O 363 " (cutoff:3.500A) Processing helix chain 'O' and resid 382 through 389 Processing helix chain 'O' and resid 392 through 397 removed outlier: 3.515A pdb=" N MET O 396 " --> pdb=" O LEU O 393 " (cutoff:3.500A) Processing helix chain 'O' and resid 401 through 408 Processing helix chain 'O' and resid 413 through 431 removed outlier: 3.687A pdb=" N LYS O 417 " --> pdb=" O ALA O 413 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER O 426 " --> pdb=" O GLN O 422 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA O 431 " --> pdb=" O TYR O 427 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 458 removed outlier: 3.890A pdb=" N ILE O 440 " --> pdb=" O ARG O 436 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N PHE O 441 " --> pdb=" O THR O 437 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N TYR O 445 " --> pdb=" O PHE O 441 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N THR O 447 " --> pdb=" O ALA O 443 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU O 458 " --> pdb=" O VAL O 454 " (cutoff:3.500A) Processing helix chain 'O' and resid 466 through 469 removed outlier: 3.634A pdb=" N ARG O 469 " --> pdb=" O GLY O 466 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 466 through 469' Processing helix chain 'O' and resid 470 through 487 removed outlier: 4.104A pdb=" N ILE O 483 " --> pdb=" O ALA O 479 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE O 486 " --> pdb=" O TYR O 482 " (cutoff:3.500A) Processing helix chain 'O' and resid 501 through 510 removed outlier: 3.764A pdb=" N GLN O 507 " --> pdb=" O ASP O 503 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG O 508 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 521 through 535 removed outlier: 3.836A pdb=" N GLN O 534 " --> pdb=" O ARG O 530 " (cutoff:3.500A) Processing helix chain 'O' and resid 540 through 551 Processing helix chain 'O' and resid 582 through 587 Processing helix chain 'O' and resid 601 through 607 removed outlier: 4.466A pdb=" N LEU O 605 " --> pdb=" O ASN O 601 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N MET O 606 " --> pdb=" O TYR O 602 " (cutoff:3.500A) Processing helix chain 'Q' and resid 84 through 90 removed outlier: 3.867A pdb=" N SER Q 88 " --> pdb=" O GLN Q 84 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LYS Q 90 " --> pdb=" O ARG Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 98 through 122 removed outlier: 3.779A pdb=" N LEU Q 105 " --> pdb=" O LYS Q 101 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU Q 112 " --> pdb=" O PHE Q 108 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG Q 114 " --> pdb=" O PHE Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 146 removed outlier: 4.365A pdb=" N HIS Q 131 " --> pdb=" O LYS Q 127 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ILE Q 135 " --> pdb=" O HIS Q 131 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU Q 141 " --> pdb=" O TRP Q 137 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS Q 142 " --> pdb=" O LEU Q 138 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR Q 143 " --> pdb=" O LYS Q 139 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE Q 144 " --> pdb=" O ILE Q 140 " (cutoff:3.500A) Processing helix chain 'Q' and resid 159 through 172 removed outlier: 3.742A pdb=" N LEU Q 165 " --> pdb=" O THR Q 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA Q 168 " --> pdb=" O ILE Q 164 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N SER Q 169 " --> pdb=" O LEU Q 165 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU Q 172 " --> pdb=" O ALA Q 168 " (cutoff:3.500A) Processing helix chain 'Q' and resid 177 through 184 Processing helix chain 'Q' and resid 208 through 214 removed outlier: 3.566A pdb=" N ILE Q 214 " --> pdb=" O TYR Q 210 " (cutoff:3.500A) Processing helix chain 'Q' and resid 224 through 237 Processing helix chain 'Q' and resid 248 through 261 removed outlier: 4.009A pdb=" N CYS Q 260 " --> pdb=" O LEU Q 256 " (cutoff:3.500A) Processing helix chain 'Q' and resid 264 through 277 removed outlier: 3.700A pdb=" N PHE Q 268 " --> pdb=" O PRO Q 264 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU Q 277 " --> pdb=" O VAL Q 273 " (cutoff:3.500A) Processing helix chain 'Q' and resid 301 through 320 removed outlier: 3.725A pdb=" N SER Q 308 " --> pdb=" O LEU Q 304 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N MET Q 311 " --> pdb=" O LEU Q 307 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR Q 313 " --> pdb=" O TYR Q 309 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE Q 314 " --> pdb=" O PHE Q 310 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ASN Q 315 " --> pdb=" O MET Q 311 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET Q 317 " --> pdb=" O THR Q 313 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU Q 318 " --> pdb=" O ILE Q 314 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N PHE Q 320 " --> pdb=" O TRP Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 327 through 339 removed outlier: 3.670A pdb=" N SER Q 333 " --> pdb=" O LYS Q 329 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Q 339 " --> pdb=" O THR Q 335 " (cutoff:3.500A) Processing helix chain 'Q' and resid 346 through 357 removed outlier: 3.687A pdb=" N VAL Q 353 " --> pdb=" O GLY Q 349 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS Q 354 " --> pdb=" O ARG Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 364 through 369 removed outlier: 3.635A pdb=" N PHE Q 367 " --> pdb=" O SER Q 364 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TRP Q 369 " --> pdb=" O TYR Q 366 " (cutoff:3.500A) Processing helix chain 'Q' and resid 370 through 386 removed outlier: 3.776A pdb=" N LYS Q 383 " --> pdb=" O LYS Q 379 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU Q 386 " --> pdb=" O GLU Q 382 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 417 removed outlier: 4.118A pdb=" N ARG Q 410 " --> pdb=" O GLN Q 406 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LYS Q 412 " --> pdb=" O ILE Q 408 " (cutoff:3.500A) Processing helix chain 'Q' and resid 437 through 449 removed outlier: 4.250A pdb=" N LEU Q 442 " --> pdb=" O PHE Q 438 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN Q 443 " --> pdb=" O ILE Q 439 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA Q 447 " --> pdb=" O GLN Q 443 " (cutoff:3.500A) Processing helix chain 'Q' and resid 476 through 490 removed outlier: 3.850A pdb=" N LEU Q 480 " --> pdb=" O ILE Q 476 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN Q 486 " --> pdb=" O HIS Q 482 " (cutoff:3.500A) Processing helix chain 'Q' and resid 494 through 514 removed outlier: 3.834A pdb=" N LEU Q 498 " --> pdb=" O SER Q 494 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N SER Q 503 " --> pdb=" O LYS Q 499 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA Q 508 " --> pdb=" O ARG Q 504 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N HIS Q 511 " --> pdb=" O ASN Q 507 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ARG Q 512 " --> pdb=" O ALA Q 508 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET Q 513 " --> pdb=" O CYS Q 509 " (cutoff:3.500A) Processing helix chain 'S' and resid 189 through 193 removed outlier: 3.511A pdb=" N LEU S 193 " --> pdb=" O ALA S 190 " (cutoff:3.500A) Processing helix chain 'S' and resid 571 through 576 removed outlier: 3.870A pdb=" N ALA S 575 " --> pdb=" O HIS S 571 " (cutoff:3.500A) Processing helix chain 'S' and resid 585 through 612 removed outlier: 4.689A pdb=" N LEU S 592 " --> pdb=" O SER S 588 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL S 593 " --> pdb=" O ILE S 589 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LYS S 597 " --> pdb=" O VAL S 593 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LEU S 598 " --> pdb=" O SER S 594 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG S 601 " --> pdb=" O LYS S 597 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG S 603 " --> pdb=" O LYS S 599 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL S 607 " --> pdb=" O ARG S 603 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLN S 608 " --> pdb=" O ILE S 604 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU S 610 " --> pdb=" O ARG S 606 " (cutoff:3.500A) Processing helix chain 'S' and resid 616 through 639 removed outlier: 3.601A pdb=" N TYR S 628 " --> pdb=" O GLN S 624 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG S 629 " --> pdb=" O ASP S 625 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ALA S 633 " --> pdb=" O ARG S 629 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLU S 639 " --> pdb=" O ASN S 635 " (cutoff:3.500A) Processing helix chain 'S' and resid 671 through 685 removed outlier: 3.593A pdb=" N PHE S 675 " --> pdb=" O SER S 671 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR S 685 " --> pdb=" O GLN S 681 " (cutoff:3.500A) Processing helix chain 'S' and resid 699 through 703 removed outlier: 3.761A pdb=" N LEU S 702 " --> pdb=" O LEU S 699 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N PHE S 703 " --> pdb=" O LEU S 700 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 699 through 703' Processing helix chain 'S' and resid 711 through 720 removed outlier: 3.631A pdb=" N LEU S 718 " --> pdb=" O PHE S 714 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN S 720 " --> pdb=" O ASN S 716 " (cutoff:3.500A) Processing helix chain 'S' and resid 730 through 744 removed outlier: 4.160A pdb=" N ILE S 741 " --> pdb=" O VAL S 737 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N TRP S 742 " --> pdb=" O LYS S 738 " (cutoff:3.500A) Processing helix chain 'S' and resid 752 through 766 removed outlier: 3.529A pdb=" N ILE S 756 " --> pdb=" O LEU S 752 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASN S 758 " --> pdb=" O GLU S 754 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N SER S 761 " --> pdb=" O GLN S 757 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ARG S 762 " --> pdb=" O ASN S 758 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER S 763 " --> pdb=" O GLU S 759 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU S 764 " --> pdb=" O ILE S 760 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 38 removed outlier: 3.720A pdb=" N TYR R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ASN R 25 " --> pdb=" O TYR R 21 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR R 26 " --> pdb=" O GLN R 22 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP R 32 " --> pdb=" O SER R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 126 through 131 removed outlier: 3.773A pdb=" N LYS R 129 " --> pdb=" O LYS R 126 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR R 131 " --> pdb=" O TRP R 128 " (cutoff:3.500A) Processing helix chain 'R' and resid 158 through 166 removed outlier: 3.744A pdb=" N LYS R 164 " --> pdb=" O HIS R 160 " (cutoff:3.500A) Processing helix chain 'R' and resid 166 through 174 removed outlier: 3.817A pdb=" N GLU R 174 " --> pdb=" O LEU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 180 removed outlier: 3.845A pdb=" N HIS R 179 " --> pdb=" O ILE R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 192 Processing helix chain 'R' and resid 209 through 226 removed outlier: 3.618A pdb=" N LEU R 222 " --> pdb=" O ASP R 218 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN R 223 " --> pdb=" O LEU R 219 " (cutoff:3.500A) Processing helix chain 'R' and resid 228 through 240 removed outlier: 3.580A pdb=" N LYS R 234 " --> pdb=" O SER R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 246 through 253 removed outlier: 3.894A pdb=" N LEU R 250 " --> pdb=" O GLN R 246 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N GLY R 252 " --> pdb=" O LYS R 248 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ILE R 253 " --> pdb=" O SER R 249 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 259 removed outlier: 3.790A pdb=" N LEU R 258 " --> pdb=" O GLY R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 278 Processing helix chain 'R' and resid 294 through 299 removed outlier: 3.939A pdb=" N GLN R 298 " --> pdb=" O VAL R 294 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 322 removed outlier: 3.510A pdb=" N ASN R 319 " --> pdb=" O SER R 315 " (cutoff:3.500A) Processing helix chain 'R' and resid 346 through 355 removed outlier: 3.570A pdb=" N THR R 355 " --> pdb=" O GLU R 351 " (cutoff:3.500A) Processing helix chain 'R' and resid 362 through 379 removed outlier: 3.758A pdb=" N HIS R 372 " --> pdb=" O TYR R 368 " (cutoff:3.500A) Processing helix chain 'R' and resid 398 through 421 removed outlier: 4.278A pdb=" N ASN R 402 " --> pdb=" O ASP R 398 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN R 403 " --> pdb=" O ILE R 399 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL R 404 " --> pdb=" O LYS R 400 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE R 405 " --> pdb=" O ILE R 401 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS R 416 " --> pdb=" O ARG R 412 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LYS R 421 " --> pdb=" O ILE R 417 " (cutoff:3.500A) Processing helix chain 'R' and resid 427 through 441 removed outlier: 3.704A pdb=" N GLU R 432 " --> pdb=" O SER R 428 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLN R 434 " --> pdb=" O LEU R 430 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG R 441 " --> pdb=" O SER R 437 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'I' and resid 47 through 50 removed outlier: 6.495A pdb=" N ARG A1295 " --> pdb=" O ASP A1268 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N VAL A1270 " --> pdb=" O HIS A1293 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N HIS A1293 " --> pdb=" O VAL A1270 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL A1272 " --> pdb=" O VAL A1291 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N VAL A1291 " --> pdb=" O VAL A1272 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU A1274 " --> pdb=" O SER A1289 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N SER A1289 " --> pdb=" O GLU A1274 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLU A1471 " --> pdb=" O ASN A1461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 94 through 95 Processing sheet with id=AA4, first strand: chain 'N' and resid 29 through 31 removed outlier: 4.836A pdb=" N THR M 37 " --> pdb=" O GLU M 56 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N GLU M 56 " --> pdb=" O THR M 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU M 50 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL M 23 " --> pdb=" O LEU M 96 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N SER M 98 " --> pdb=" O VAL M 23 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N SER M 25 " --> pdb=" O SER M 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 80 through 82 removed outlier: 3.544A pdb=" N HIS N 85 " --> pdb=" O ILE N 82 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP N 86 " --> pdb=" O THR N 142 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LYS N 135 " --> pdb=" O VAL N 53 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N GLU N 141 " --> pdb=" O PRO N 59 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N TYR M 76 " --> pdb=" O ALA M 93 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU M 80 " --> pdb=" O GLN M 89 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN M 89 " --> pdb=" O LEU M 80 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ILE M 12 " --> pdb=" O ILE M 88 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N LEU M 90 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N SER M 14 " --> pdb=" O LEU M 90 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N LYS M 92 " --> pdb=" O SER M 14 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLN M 16 " --> pdb=" O LYS M 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1631 through 1632 Processing sheet with id=AA7, first strand: chain 'A' and resid 77 through 86 removed outlier: 5.824A pdb=" N ASP A 358 " --> pdb=" O LEU A 81 " (cutoff:3.500A) removed outlier: 10.304A pdb=" N VAL A 83 " --> pdb=" O PHE A 356 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N PHE A 356 " --> pdb=" O VAL A 83 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 243 through 245 Processing sheet with id=AA9, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AB1, first strand: chain 'A' and resid 474 through 476 removed outlier: 3.648A pdb=" N ILE B1069 " --> pdb=" O VAL A 476 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 1045 through 1047 removed outlier: 7.085A pdb=" N LEU A 614 " --> pdb=" O ARG A 481 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL A 483 " --> pdb=" O LEU A 614 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N LEU A 616 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N SER A 485 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 506 through 510 removed outlier: 4.132A pdb=" N GLN A 535 " --> pdb=" O TYR A 578 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N HIS A 580 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA A 533 " --> pdb=" O HIS A 580 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 686 through 687 Processing sheet with id=AB5, first strand: chain 'A' and resid 748 through 752 removed outlier: 6.402A pdb=" N LEU A 770 " --> pdb=" O LEU A 777 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 948 through 949 Processing sheet with id=AB7, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 6.594A pdb=" N ILE A1038 " --> pdb=" O VAL A1046 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1506 through 1508 removed outlier: 3.956A pdb=" N ARG A1506 " --> pdb=" O GLU A1522 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 1261 through 1262 removed outlier: 6.755A pdb=" N VAL A1261 " --> pdb=" O ILE A1498 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 22 through 24 removed outlier: 3.675A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS G 106 " --> pdb=" O PHE G 115 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TRP G 117 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 9.604A pdb=" N LEU G 104 " --> pdb=" O TRP G 117 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N VAL A1656 " --> pdb=" O ILE G 107 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 29 through 30 removed outlier: 3.675A pdb=" N VAL G 120 " --> pdb=" O ILE G 43 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ASN G 121 " --> pdb=" O GLY G 86 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N GLY G 86 " --> pdb=" O ASN G 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 71 through 74 removed outlier: 7.082A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLU B 150 " --> pdb=" O VAL B 145 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 71 through 74 removed outlier: 7.082A pdb=" N LYS B 140 " --> pdb=" O GLU B 100 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N VAL B 102 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU B 138 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE B 104 " --> pdb=" O LYS B 136 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LYS B 136 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLY B 135 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N GLY B 160 " --> pdb=" O GLY B 135 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU B 137 " --> pdb=" O CYS B 158 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 108 through 109 Processing sheet with id=AC6, first strand: chain 'B' and resid 194 through 196 Processing sheet with id=AC7, first strand: chain 'B' and resid 400 through 403 removed outlier: 4.246A pdb=" N MET B 205 " --> pdb=" O MET B 502 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 215 through 218 removed outlier: 5.308A pdb=" N TYR B 232 " --> pdb=" O TYR B 252 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR B 252 " --> pdb=" O TYR B 232 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N THR B 247 " --> pdb=" O SER B 263 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 263 " --> pdb=" O THR B 247 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD1, first strand: chain 'B' and resid 550 through 551 Processing sheet with id=AD2, first strand: chain 'B' and resid 571 through 572 removed outlier: 5.498A pdb=" N ILE B 592 " --> pdb=" O ILE B 588 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 588 " --> pdb=" O ILE B 592 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS B 585 " --> pdb=" O LEU B 640 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU B 642 " --> pdb=" O CYS B 585 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N GLN B 587 " --> pdb=" O LEU B 642 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.168A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 740 through 744 removed outlier: 4.168A pdb=" N THR B 900 " --> pdb=" O ILE B 888 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ARG B 906 " --> pdb=" O ILE B 882 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 882 " --> pdb=" O ARG B 906 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N ARG B 908 " --> pdb=" O ALA B 880 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N ALA B 880 " --> pdb=" O ARG B 908 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N VAL B 885 " --> pdb=" O LYS L 58 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 752 through 753 Processing sheet with id=AD6, first strand: chain 'B' and resid 1010 through 1011 removed outlier: 7.458A pdb=" N MET B 787 " --> pdb=" O SER B 928 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N LYS B 930 " --> pdb=" O MET B 787 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ILE B 789 " --> pdb=" O LYS B 930 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N ILE B 947 " --> pdb=" O ASN B 770 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 772 " --> pdb=" O ILE B 947 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE B 949 " --> pdb=" O VAL B 772 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA B 774 " --> pdb=" O ILE B 949 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N TYR B1027 " --> pdb=" O VAL B 775 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 823 through 825 removed outlier: 3.564A pdb=" N LYS B 868 " --> pdb=" O ASP B 863 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 938 through 939 Processing sheet with id=AD9, first strand: chain 'B' and resid 1098 through 1104 Processing sheet with id=AE1, first strand: chain 'B' and resid 1113 through 1115 Processing sheet with id=AE2, first strand: chain 'B' and resid 1133 through 1134 Processing sheet with id=AE3, first strand: chain 'C' and resid 41 through 47 removed outlier: 6.638A pdb=" N ASN C 53 " --> pdb=" O SER C 45 " (cutoff:3.500A) removed outlier: 10.387A pdb=" N ARG C 293 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N ASN C 234 " --> pdb=" O ARG C 293 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N ARG C 295 " --> pdb=" O GLN C 232 " (cutoff:3.500A) removed outlier: 10.803A pdb=" N GLN C 232 " --> pdb=" O ARG C 295 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N HIS C 297 " --> pdb=" O LEU C 230 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 87 through 88 removed outlier: 4.543A pdb=" N VAL C 133 " --> pdb=" O GLU C 170 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 87 through 88 removed outlier: 7.348A pdb=" N SER C 203 " --> pdb=" O PHE C 85 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N PHE C 85 " --> pdb=" O SER C 203 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N LYS C 205 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N VAL C 83 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N HIS C 207 " --> pdb=" O GLU C 81 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 141 through 142 Processing sheet with id=AE7, first strand: chain 'C' and resid 161 through 163 Processing sheet with id=AE8, first strand: chain 'C' and resid 256 through 257 Processing sheet with id=AE9, first strand: chain 'E' and resid 60 through 62 Processing sheet with id=AF1, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=AF2, first strand: chain 'E' and resid 152 through 155 removed outlier: 3.973A pdb=" N LYS E 152 " --> pdb=" O ILE E 199 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'G' and resid 132 through 140 removed outlier: 3.689A pdb=" N TYR G 136 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLY G 146 " --> pdb=" O PHE G 138 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N GLN G 140 " --> pdb=" O HIS G 144 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N HIS G 144 " --> pdb=" O GLN G 140 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ASN G 154 " --> pdb=" O VAL G 245 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N GLY G 247 " --> pdb=" O ASN G 154 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N SER G 156 " --> pdb=" O GLY G 247 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N SER G 244 " --> pdb=" O HIS G 237 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N THR G 248 " --> pdb=" O VAL G 233 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL G 233 " --> pdb=" O THR G 248 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 167 through 168 Processing sheet with id=AF5, first strand: chain 'H' and resid 4 through 16 removed outlier: 6.711A pdb=" N GLU H 27 " --> pdb=" O SER H 13 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N VAL H 15 " --> pdb=" O ARG H 25 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N ARG H 25 " --> pdb=" O VAL H 15 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N LEU H 122 " --> pdb=" O ASP H 41 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU H 111 " --> pdb=" O VAL H 107 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS H 103 " --> pdb=" O TYR H 115 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N SER H 117 " --> pdb=" O ALA H 101 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ALA H 101 " --> pdb=" O SER H 117 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N LEU H 55 " --> pdb=" O ILE H 9 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ILE H 9 " --> pdb=" O LEU H 55 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL H 57 " --> pdb=" O ASP H 7 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ASP H 7 " --> pdb=" O VAL H 57 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N ILE H 59 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 47 through 49 removed outlier: 3.542A pdb=" N ILE K 103 " --> pdb=" O PHE K 63 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASN K 102 " --> pdb=" O TYR K 91 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N TYR K 91 " --> pdb=" O ASN K 102 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ARG K 104 " --> pdb=" O CYS K 89 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N CYS K 89 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N GLN K 106 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 20 through 21 Processing sheet with id=AF8, first strand: chain 'Q' and resid 63 through 64 removed outlier: 4.114A pdb=" N THR Q 63 " --> pdb=" O SER Q 72 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'S' and resid 63 through 66 removed outlier: 7.561A pdb=" N VAL S 547 " --> pdb=" O LEU S 65 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 173 through 174 removed outlier: 3.620A pdb=" N GLU R 196 " --> pdb=" O TRP S 174 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'S' and resid 184 through 187 removed outlier: 3.519A pdb=" N ILE S 202 " --> pdb=" O GLN S 185 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'S' and resid 213 through 214 removed outlier: 3.709A pdb=" N LEU S 214 " --> pdb=" O ILE S 236 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.571A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER S 268 " --> pdb=" O THR S 265 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'S' and resid 242 through 246 removed outlier: 6.571A pdb=" N ILE S 264 " --> pdb=" O LYS S 243 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N ILE S 245 " --> pdb=" O GLY S 262 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N GLY S 262 " --> pdb=" O ILE S 245 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N SER S 268 " --> pdb=" O THR S 265 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'S' and resid 302 through 303 removed outlier: 3.723A pdb=" N VAL S 302 " --> pdb=" O ASP S 319 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE S 318 " --> pdb=" O SER S 325 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER S 325 " --> pdb=" O ILE S 318 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE S 326 " --> pdb=" O LEU S 347 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N LEU S 347 " --> pdb=" O ILE S 326 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'S' and resid 362 through 366 removed outlier: 4.038A pdb=" N LYS S 371 " --> pdb=" O PHE S 366 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N MET S 380 " --> pdb=" O VAL S 393 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP S 389 " --> pdb=" O ASP S 384 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 402 through 406 Processing sheet with id=AG9, first strand: chain 'S' and resid 449 through 457 removed outlier: 3.563A pdb=" N SER S 495 " --> pdb=" O MET S 478 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY S 493 " --> pdb=" O VAL S 480 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N SER S 482 " --> pdb=" O SER S 491 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N SER S 491 " --> pdb=" O SER S 482 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'S' and resid 504 through 505 removed outlier: 3.750A pdb=" N THR S 504 " --> pdb=" O ARG S 542 " (cutoff:3.500A) 1788 hydrogen bonds defined for protein. 5004 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 23.32 Time building geometry restraints manager: 18.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 16527 1.34 - 1.48: 13698 1.48 - 1.61: 22150 1.61 - 1.75: 7 1.75 - 1.89: 372 Bond restraints: 52754 Sorted by residual: bond pdb=" CA PRO B 28 " pdb=" C PRO B 28 " ideal model delta sigma weight residual 1.514 1.487 0.028 5.50e-03 3.31e+04 2.51e+01 bond pdb=" C LYS A1110 " pdb=" N GLU A1111 " ideal model delta sigma weight residual 1.329 1.250 0.079 1.86e-02 2.89e+03 1.81e+01 bond pdb=" CA LEU B 542 " pdb=" CB LEU B 542 " ideal model delta sigma weight residual 1.529 1.481 0.048 1.38e-02 5.25e+03 1.19e+01 bond pdb=" CB ARG C 69 " pdb=" CG ARG C 69 " ideal model delta sigma weight residual 1.520 1.417 0.103 3.00e-02 1.11e+03 1.18e+01 bond pdb=" N MET Q 35 " pdb=" CA MET Q 35 " ideal model delta sigma weight residual 1.452 1.494 -0.042 1.25e-02 6.40e+03 1.12e+01 ... (remaining 52749 not shown) Histogram of bond angle deviations from ideal: 97.03 - 104.83: 1222 104.83 - 112.63: 27038 112.63 - 120.43: 23616 120.43 - 128.23: 19278 128.23 - 136.03: 521 Bond angle restraints: 71675 Sorted by residual: angle pdb=" N PHE Q 125 " pdb=" CA PHE Q 125 " pdb=" C PHE Q 125 " ideal model delta sigma weight residual 109.42 98.55 10.87 1.48e+00 4.57e-01 5.39e+01 angle pdb=" N VAL J 14 " pdb=" CA VAL J 14 " pdb=" C VAL J 14 " ideal model delta sigma weight residual 113.71 108.22 5.49 9.50e-01 1.11e+00 3.34e+01 angle pdb=" C GLY A1218 " pdb=" N ILE A1219 " pdb=" CA ILE A1219 " ideal model delta sigma weight residual 120.24 123.85 -3.61 6.30e-01 2.52e+00 3.28e+01 angle pdb=" C MET B 783 " pdb=" N ASP B 784 " pdb=" CA ASP B 784 " ideal model delta sigma weight residual 121.54 132.44 -10.90 1.91e+00 2.74e-01 3.26e+01 angle pdb=" C LEU R 354 " pdb=" N THR R 355 " pdb=" CA THR R 355 " ideal model delta sigma weight residual 120.09 126.98 -6.89 1.25e+00 6.40e-01 3.04e+01 ... (remaining 71670 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.42: 30852 30.42 - 60.84: 792 60.84 - 91.26: 52 91.26 - 121.68: 0 121.68 - 152.11: 3 Dihedral angle restraints: 31699 sinusoidal: 13626 harmonic: 18073 Sorted by residual: dihedral pdb=" CA GLN S 728 " pdb=" C GLN S 728 " pdb=" N ALA S 729 " pdb=" CA ALA S 729 " ideal model delta harmonic sigma weight residual 180.00 150.12 29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA LYS A 919 " pdb=" C LYS A 919 " pdb=" N PHE A 920 " pdb=" CA PHE A 920 " ideal model delta harmonic sigma weight residual -180.00 -151.15 -28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY I 90 " pdb=" C GLY I 90 " pdb=" N ASN I 91 " pdb=" CA ASN I 91 " ideal model delta harmonic sigma weight residual 180.00 -151.69 -28.31 0 5.00e+00 4.00e-02 3.21e+01 ... (remaining 31696 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 7425 0.112 - 0.224: 538 0.224 - 0.336: 24 0.336 - 0.448: 3 0.448 - 0.560: 4 Chirality restraints: 7994 Sorted by residual: chirality pdb=" CB ILE R 175 " pdb=" CA ILE R 175 " pdb=" CG1 ILE R 175 " pdb=" CG2 ILE R 175 " both_signs ideal model delta sigma weight residual False 2.64 2.08 0.56 2.00e-01 2.50e+01 7.84e+00 chirality pdb=" CB ILE R 168 " pdb=" CA ILE R 168 " pdb=" CG1 ILE R 168 " pdb=" CG2 ILE R 168 " both_signs ideal model delta sigma weight residual False 2.64 2.15 0.49 2.00e-01 2.50e+01 6.08e+00 chirality pdb=" CA PHE Q 125 " pdb=" N PHE Q 125 " pdb=" C PHE Q 125 " pdb=" CB PHE Q 125 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 7991 not shown) Planarity restraints: 8874 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER O 239 " -0.020 2.00e-02 2.50e+03 3.93e-02 1.55e+01 pdb=" C SER O 239 " 0.068 2.00e-02 2.50e+03 pdb=" O SER O 239 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE O 240 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 368 " -0.033 2.00e-02 2.50e+03 2.67e-02 1.42e+01 pdb=" CG TYR R 368 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TYR R 368 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR R 368 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 368 " -0.014 2.00e-02 2.50e+03 pdb=" CZ TYR R 368 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 368 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR O 221 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C TYR O 221 " -0.061 2.00e-02 2.50e+03 pdb=" O TYR O 221 " 0.023 2.00e-02 2.50e+03 pdb=" N CYS O 222 " 0.020 2.00e-02 2.50e+03 ... (remaining 8871 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 1004 2.66 - 3.22: 45393 3.22 - 3.78: 78890 3.78 - 4.34: 110365 4.34 - 4.90: 178533 Nonbonded interactions: 414185 Sorted by model distance: nonbonded pdb=" OG1 THR Q 12 " pdb="ZN ZN Q 601 " model vdw 2.098 2.230 nonbonded pdb=" OG1 THR A1458 " pdb=" OE1 GLU A1475 " model vdw 2.214 2.440 nonbonded pdb=" OE1 GLN S 21 " pdb=" OG SER S 24 " model vdw 2.231 2.440 nonbonded pdb=" OE2 GLU S 355 " pdb=" OH TYR R 131 " model vdw 2.249 2.440 nonbonded pdb=" O ILE R 257 " pdb=" OG SER R 264 " model vdw 2.261 2.440 ... (remaining 414180 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.00 max=1.00 mean=0.99 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 14.450 Check model and map are aligned: 0.630 Set scattering table: 0.380 Process input model: 126.450 Find NCS groups from input model: 1.070 Set up NCS constraints: 0.150 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 158.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.010 0.103 52754 Z= 0.674 Angle : 1.096 11.029 71675 Z= 0.605 Chirality : 0.064 0.560 7994 Planarity : 0.008 0.082 8874 Dihedral : 12.868 152.105 19979 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.30 % Favored : 92.65 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % 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: -4.42 (0.08), residues: 6079 helix: -3.98 (0.06), residues: 2069 sheet: -2.04 (0.17), residues: 746 loop : -2.41 (0.09), residues: 3264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1434 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1389 time to evaluate : 4.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 17 residues processed: 1415 average time/residue: 1.5906 time to fit residues: 2774.6712 Evaluate side-chains 740 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 723 time to evaluate : 4.462 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 7 average time/residue: 0.3980 time to fit residues: 11.3200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 522 optimal weight: 5.9990 chunk 469 optimal weight: 1.9990 chunk 260 optimal weight: 0.9980 chunk 160 optimal weight: 0.6980 chunk 316 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 485 optimal weight: 0.9990 chunk 187 optimal weight: 0.8980 chunk 295 optimal weight: 0.5980 chunk 361 optimal weight: 0.9980 chunk 562 optimal weight: 4.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN M 74 ASN A 107 HIS A 382 GLN A 590 ASN A 706 HIS A 795 HIS A 819 ASN A1062 HIS A1336 GLN A1487 ASN A1500 GLN A1648 ASN B 479 GLN ** B 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 735 HIS ** B 770 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1165 ASN C 330 ASN G 126 GLN G 150 HIS G 221 ASN H 35 GLN J 53 HIS O 117 GLN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 115 GLN Q 300 ASN Q 486 GLN S 259 ASN S 267 ASN S 387 ASN S 395 GLN S 554 ASN S 656 HIS R 10 ASN R 153 ASN R 189 GLN R 223 ASN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 319 ASN R 434 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 52754 Z= 0.215 Angle : 0.690 12.768 71675 Z= 0.368 Chirality : 0.045 0.242 7994 Planarity : 0.006 0.063 8874 Dihedral : 12.771 146.184 7612 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.98 (0.09), residues: 6079 helix: -2.04 (0.09), residues: 2137 sheet: -1.60 (0.18), residues: 743 loop : -1.99 (0.10), residues: 3199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 858 time to evaluate : 4.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 75 residues processed: 985 average time/residue: 1.4090 time to fit residues: 1751.8807 Evaluate side-chains 729 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 654 time to evaluate : 4.385 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 48 residues processed: 29 average time/residue: 0.5211 time to fit residues: 32.1096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 312 optimal weight: 3.9990 chunk 174 optimal weight: 0.7980 chunk 467 optimal weight: 0.7980 chunk 382 optimal weight: 6.9990 chunk 155 optimal weight: 0.8980 chunk 563 optimal weight: 6.9990 chunk 608 optimal weight: 0.0570 chunk 501 optimal weight: 1.9990 chunk 558 optimal weight: 6.9990 chunk 191 optimal weight: 1.9990 chunk 451 optimal weight: 0.9980 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN M 54 HIS A 260 GLN A 344 ASN A 425 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1108 HIS A1487 ASN A1648 ASN B 166 GLN B 168 ASN B 235 GLN ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN B 695 ASN B1157 GLN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 20 HIS H 35 GLN O 546 ASN O 549 ASN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 259 GLN Q 300 ASN S 267 ASN S 387 ASN R 10 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 433 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 52754 Z= 0.185 Angle : 0.611 11.966 71675 Z= 0.323 Chirality : 0.044 0.239 7994 Planarity : 0.005 0.061 8874 Dihedral : 12.587 146.773 7612 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.68 % Favored : 94.31 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.18 (0.10), residues: 6079 helix: -1.02 (0.10), residues: 2167 sheet: -1.38 (0.18), residues: 772 loop : -1.75 (0.10), residues: 3140 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 219 poor density : 746 time to evaluate : 4.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 219 outliers final: 94 residues processed: 887 average time/residue: 1.3369 time to fit residues: 1499.4050 Evaluate side-chains 739 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 645 time to evaluate : 4.842 Switching outliers to nearest non-outliers outliers start: 94 outliers final: 66 residues processed: 31 average time/residue: 0.5451 time to fit residues: 33.5085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 556 optimal weight: 6.9990 chunk 423 optimal weight: 0.8980 chunk 292 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 268 optimal weight: 5.9990 chunk 378 optimal weight: 4.9990 chunk 565 optimal weight: 0.0870 chunk 598 optimal weight: 0.9990 chunk 295 optimal weight: 0.9990 chunk 535 optimal weight: 0.9980 chunk 161 optimal weight: 0.3980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN M 74 ASN A 344 ASN A 425 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 671 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1487 ASN A1648 ASN B 93 ASN B 166 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN L 66 GLN O 438 GLN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 301 HIS S 267 ASN ** S 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 189 GLN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.061 52754 Z= 0.175 Angle : 0.581 12.325 71675 Z= 0.307 Chirality : 0.043 0.300 7994 Planarity : 0.004 0.059 8874 Dihedral : 12.507 146.655 7612 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.70 (0.10), residues: 6079 helix: -0.46 (0.11), residues: 2179 sheet: -1.24 (0.18), residues: 790 loop : -1.56 (0.11), residues: 3110 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 692 time to evaluate : 4.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 216 outliers final: 102 residues processed: 841 average time/residue: 1.2652 time to fit residues: 1354.1684 Evaluate side-chains 725 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 623 time to evaluate : 4.270 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 81 residues processed: 24 average time/residue: 0.6285 time to fit residues: 29.2198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 498 optimal weight: 2.9990 chunk 339 optimal weight: 0.0000 chunk 8 optimal weight: 6.9990 chunk 445 optimal weight: 5.9990 chunk 246 optimal weight: 0.3980 chunk 510 optimal weight: 6.9990 chunk 413 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 537 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 overall best weight: 1.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN M 74 ASN A 106 HIS A 344 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1299 ASN A1487 ASN B 231 HIS ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 673 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 146 HIS E 179 GLN G 221 ASN H 35 GLN H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 301 HIS Q 434 HIS S 188 GLN S 387 ASN ** S 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 635 ASN R 189 GLN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 52754 Z= 0.230 Angle : 0.619 12.974 71675 Z= 0.324 Chirality : 0.045 0.289 7994 Planarity : 0.005 0.060 8874 Dihedral : 12.601 147.133 7612 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 4.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.49 (0.10), residues: 6079 helix: -0.21 (0.11), residues: 2188 sheet: -1.17 (0.18), residues: 808 loop : -1.49 (0.11), residues: 3083 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 663 time to evaluate : 4.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 242 outliers final: 132 residues processed: 833 average time/residue: 1.2608 time to fit residues: 1341.0013 Evaluate side-chains 742 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 610 time to evaluate : 4.286 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 103 residues processed: 34 average time/residue: 0.5090 time to fit residues: 34.8063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 201 optimal weight: 1.9990 chunk 538 optimal weight: 0.0970 chunk 118 optimal weight: 0.8980 chunk 351 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 598 optimal weight: 3.9990 chunk 497 optimal weight: 0.7980 chunk 277 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 314 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN I 95 ASN A 26 ASN A 344 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1487 ASN B 166 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN O 92 ASN ** O 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 301 HIS S 461 HIS R 189 GLN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7091 moved from start: 0.3987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 52754 Z= 0.168 Angle : 0.576 12.228 71675 Z= 0.300 Chirality : 0.043 0.293 7994 Planarity : 0.004 0.060 8874 Dihedral : 12.521 147.194 7612 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer Outliers : 3.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.11), residues: 6079 helix: 0.08 (0.11), residues: 2195 sheet: -0.99 (0.18), residues: 796 loop : -1.39 (0.11), residues: 3088 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 656 time to evaluate : 4.287 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 132 residues processed: 807 average time/residue: 1.2101 time to fit residues: 1249.7908 Evaluate side-chains 736 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 604 time to evaluate : 4.159 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 102 residues processed: 34 average time/residue: 0.5670 time to fit residues: 36.1973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 577 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 341 optimal weight: 2.9990 chunk 437 optimal weight: 1.9990 chunk 338 optimal weight: 4.9990 chunk 504 optimal weight: 0.8980 chunk 334 optimal weight: 4.9990 chunk 596 optimal weight: 2.9990 chunk 373 optimal weight: 0.5980 chunk 363 optimal weight: 1.9990 chunk 275 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN I 95 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1026 GLN A1487 ASN B 166 GLN ** B 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 301 HIS ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 388 ASN ** S 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 286 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7126 moved from start: 0.4085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 52754 Z= 0.227 Angle : 0.616 13.637 71675 Z= 0.320 Chirality : 0.044 0.307 7994 Planarity : 0.004 0.061 8874 Dihedral : 12.599 147.244 7612 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer Outliers : 4.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.18 (0.11), residues: 6079 helix: 0.11 (0.11), residues: 2192 sheet: -0.93 (0.18), residues: 801 loop : -1.38 (0.11), residues: 3086 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 862 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 639 time to evaluate : 4.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 223 outliers final: 146 residues processed: 795 average time/residue: 1.1935 time to fit residues: 1215.3729 Evaluate side-chains 746 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 600 time to evaluate : 4.193 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 115 residues processed: 36 average time/residue: 0.5158 time to fit residues: 35.0935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 369 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 356 optimal weight: 0.7980 chunk 179 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 115 optimal weight: 0.9980 chunk 379 optimal weight: 1.9990 chunk 406 optimal weight: 3.9990 chunk 294 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 chunk 468 optimal weight: 0.0060 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 344 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN B 166 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN ** E 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 232 ASN ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 286 GLN ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.076 52754 Z= 0.182 Angle : 0.584 13.285 71675 Z= 0.304 Chirality : 0.043 0.310 7994 Planarity : 0.004 0.084 8874 Dihedral : 12.540 147.174 7612 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 3.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.11), residues: 6079 helix: 0.27 (0.11), residues: 2194 sheet: -0.86 (0.18), residues: 809 loop : -1.33 (0.11), residues: 3076 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 628 time to evaluate : 3.851 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 184 outliers final: 136 residues processed: 773 average time/residue: 1.1823 time to fit residues: 1168.6543 Evaluate side-chains 734 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 598 time to evaluate : 3.817 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 120 residues processed: 21 average time/residue: 0.5390 time to fit residues: 23.2936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 542 optimal weight: 4.9990 chunk 571 optimal weight: 0.9990 chunk 521 optimal weight: 6.9990 chunk 555 optimal weight: 1.9990 chunk 334 optimal weight: 3.9990 chunk 242 optimal weight: 4.9990 chunk 436 optimal weight: 0.0870 chunk 170 optimal weight: 1.9990 chunk 502 optimal weight: 5.9990 chunk 525 optimal weight: 7.9990 chunk 554 optimal weight: 0.0060 overall best weight: 1.0180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN I 95 ASN ** A 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 HIS A1487 ASN B 166 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 683 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 340 GLN Q 434 HIS ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.049 52754 Z= 0.206 Angle : 0.605 14.380 71675 Z= 0.314 Chirality : 0.044 0.325 7994 Planarity : 0.004 0.071 8874 Dihedral : 12.574 147.130 7612 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.02 (0.11), residues: 6079 helix: 0.27 (0.11), residues: 2199 sheet: -0.87 (0.18), residues: 826 loop : -1.31 (0.11), residues: 3054 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 794 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 175 poor density : 619 time to evaluate : 4.349 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 175 outliers final: 136 residues processed: 752 average time/residue: 1.1450 time to fit residues: 1101.5122 Evaluate side-chains 728 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 592 time to evaluate : 4.223 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 117 residues processed: 24 average time/residue: 0.4920 time to fit residues: 24.8463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 365 optimal weight: 0.7980 chunk 587 optimal weight: 1.9990 chunk 358 optimal weight: 0.8980 chunk 278 optimal weight: 0.0770 chunk 408 optimal weight: 1.9990 chunk 616 optimal weight: 3.9990 chunk 567 optimal weight: 0.8980 chunk 491 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 379 optimal weight: 0.8980 chunk 301 optimal weight: 6.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN A 31 GLN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN B 166 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 488 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN Q 486 GLN ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 571 HIS ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 52754 Z= 0.177 Angle : 0.586 14.267 71675 Z= 0.303 Chirality : 0.043 0.312 7994 Planarity : 0.004 0.065 8874 Dihedral : 12.533 147.008 7612 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer Outliers : 2.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.11), residues: 6079 helix: 0.38 (0.11), residues: 2200 sheet: -0.87 (0.18), residues: 826 loop : -1.26 (0.11), residues: 3053 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12158 Ramachandran restraints generated. 6079 Oldfield, 0 Emsley, 6079 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 619 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 145 outliers final: 121 residues processed: 737 average time/residue: 1.1338 time to fit residues: 1068.7962 Evaluate side-chains 711 residues out of total 5567 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 590 time to evaluate : 3.732 Switching outliers to nearest non-outliers outliers start: 121 outliers final: 110 residues processed: 14 average time/residue: 0.4784 time to fit residues: 16.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 619 random chunks: chunk 390 optimal weight: 7.9990 chunk 523 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 452 optimal weight: 0.0870 chunk 72 optimal weight: 0.4980 chunk 136 optimal weight: 0.9990 chunk 491 optimal weight: 0.5980 chunk 205 optimal weight: 0.6980 chunk 505 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 0.5760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 19 ASN A 344 ASN ** A 590 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1487 ASN B 166 GLN ** B 547 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 684 ASN C 207 HIS ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 171 ASN H 137 GLN ** K 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 66 GLN ** O 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 300 ASN ** S 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.213247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 93)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.170753 restraints weight = 69849.422| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 1.78 r_work: 0.3824 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3741 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 52754 Z= 0.165 Angle : 0.580 13.641 71675 Z= 0.300 Chirality : 0.043 0.308 7994 Planarity : 0.004 0.064 8874 Dihedral : 12.500 146.843 7612 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 2.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.83 (0.11), residues: 6079 helix: 0.46 (0.11), residues: 2202 sheet: -0.82 (0.18), residues: 820 loop : -1.21 (0.11), residues: 3057 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19766.22 seconds wall clock time: 342 minutes 40.29 seconds (20560.29 seconds total)