Starting phenix.real_space_refine (version: dev) on Wed May 18 08:43:42 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lsr_0963/05_2022/6lsr_0963_neut_updated.pdb" } resolution = 3.13 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.002 sd= 0.014 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "0 TYR 284": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 141172 Number of models: 1 Model: "" Number of chains: 57 Chain: "0" Number of atoms: 1537 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1537 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 182, 'PCIS': 1} Chain breaks: 2 Chain: "1" Number of atoms: 988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 988 Classifications: {'peptide': 247} Incomplete info: {'backbone_only': 238} Link IDs: {'PTRANS': 17, 'TRANS': 229} Chain breaks: 11 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 1081 Unresolved non-hydrogen angles: 1559 Unresolved non-hydrogen dihedrals: 715 Unresolved non-hydrogen chiralities: 310 Planarities with less than four sites: {'GLN:plan1': 9, 'HIS:plan': 7, 'TYR:plan': 10, 'ASN:plan1': 6, 'TRP:plan': 5, 'ASP:plan': 13, 'PHE:plan': 8, 'GLU:plan': 22, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 508 Chain: "2" Number of atoms: 74786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3482, 74786 Classifications: {'RNA': 3482} Modifications used: {'5*END': 1, 'rna3p': 68, 'rna2p_pyr': 220, 'rna3p_pur': 1515, 'rna2p': 15, 'rna3p_pyr': 1313, 'rna2p_pur': 336} Link IDs: {'rna3p': 2911, 'rna2p': 570} Chain breaks: 17 Unresolved non-hydrogen bonds: 84 Unresolved non-hydrogen angles: 252 Unresolved non-hydrogen dihedrals: 41 Chain: "3" Number of atoms: 2053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 2053 Classifications: {'peptide': 255} Link IDs: {'PTRANS': 8, 'TRANS': 246} Chain breaks: 1 Chain: "5" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna3p_pur': 55, 'rna2p_pyr': 5, 'rna3p_pyr': 54} Link IDs: {'rna3p': 108, 'rna2p': 11} Chain: "6" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1704 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 6, 'TRANS': 217} Chain: "8" Number of atoms: 3294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3294 Classifications: {'RNA': 155} Modifications used: {'rna3p_pyr': 66, 'rna2p_pur': 14, 'rna3p_pur': 62, 'rna2p_pyr': 13, '5*END': 1} Link IDs: {'rna3p': 127, 'rna2p': 27} Chain breaks: 1 Chain: "A" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1708 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 203} Chain: "B" Number of atoms: 3238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3238 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 14, 'TRANS': 386, 'PCIS': 1} Chain: "C" Number of atoms: 757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 757 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 3, 'TRANS': 88} Chain breaks: 1 Chain: "D" Number of atoms: 2846 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2846 Classifications: {'peptide': 357} Link IDs: {'PTRANS': 18, 'TRANS': 338} Chain: "E" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 868 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "G" Number of atoms: 1853 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1853 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 14, 'CIS': 1, 'TRANS': 215} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "I" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "K" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "L" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "M" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 2, 'TRANS': 82, 'PCIS': 1} Chain: "N" Number of atoms: 1302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1302 Classifications: {'peptide': 162} Link IDs: {'PTRANS': 3, 'CIS': 1, 'TRANS': 157} Chain: "O" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 559 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 2, 'TRANS': 65} Chain: "P" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Q" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1701 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "S" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1103 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 4, 'TRANS': 129} Chain: "T" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "U" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "V" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1634 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "W" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 862 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 4, 'CIS': 1, 'TRANS': 99} Chain: "X" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "Y" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Z" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1513 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "a" Number of atoms: 1217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1217 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 3, 'TRANS': 141} Chain: "b" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1453 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 163, 'PCIS': 1} Chain: "c" Number of atoms: 1284 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1284 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 9, 'TRANS': 147} Chain: "d" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "e" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "f" Number of atoms: 519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 519 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 2, 'TRANS': 59} Chain: "g" Number of atoms: 958 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 958 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 108} Chain: "h" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "i" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "l" Number of atoms: 1002 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1002 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "m" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "r" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2237 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 265} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "t" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "u" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "v" Number of atoms: 1897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1897 Classifications: {'peptide': 235} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain breaks: 1 Chain: "w" Number of atoms: 1878 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Conformer: "B" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} bond proxies already assigned to first conformer: 1896 Chain: "z" Number of atoms: 2837 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 354, 2764 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 12, 'TRANS': 341} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 354, 2764 Classifications: {'peptide': 354} Link IDs: {'PTRANS': 12, 'TRANS': 341} Chain breaks: 1 bond proxies already assigned to first conformer: 2723 Chain: "2" Number of atoms: 236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 236 Unusual residues: {' MG': 236} Classifications: {'undetermined': 236} Link IDs: {None: 235} Chain: "5" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "2" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N ASER z 39 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER z 39 " occ=0.50 residue: pdb=" N ALYS z 158 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS z 158 " occ=0.50 residue: pdb=" N AMET z 185 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET z 185 " occ=0.50 residue: pdb=" N LYS z 215 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS z 215 " occ=0.50 residue: pdb=" N AGLU z 217 " occ=0.50 ... (16 atoms not shown) pdb=" OE2BGLU z 217 " occ=0.50 Time building chain proxies: 57.82, per 1000 atoms: 0.41 Number of scatterers: 141172 At special positions: 0 Unit cell: (231.702, 244.398, 283.544, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 281 16.00 P 3754 15.00 Mg 246 11.99 O 36502 8.00 N 26419 7.00 C 73970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS 3 308 " - pdb=" SG CYS 3 383 " distance=2.04 Simple disulfide: pdb=" SG CYS E 52 " - pdb=" SG CYS E 92 " distance=2.03 Simple disulfide: pdb=" SG CYS M 19 " - pdb=" SG CYS M 37 " distance=2.05 Simple disulfide: pdb=" SG CYS X 39 " - pdb=" SG CYS X 60 " distance=2.04 Simple disulfide: pdb=" SG CYS X 42 " - pdb=" SG CYS X 60 " distance=2.02 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 42.96 Conformation dependent library (CDL) restraints added in 7.4 seconds 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13722 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 264 helices and 71 sheets defined 41.4% alpha, 14.2% beta 1120 base pairs and 2032 stacking pairs defined. Time for finding SS restraints: 58.77 Creating SS restraints... Processing helix chain '0' and resid 263 through 275 removed outlier: 3.551A pdb=" N VAL 0 268 " --> pdb=" O LEU 0 264 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N ALA 0 269 " --> pdb=" O MET 0 265 " (cutoff:3.500A) Processing helix chain '0' and resid 287 through 301 removed outlier: 3.779A pdb=" N LEU 0 291 " --> pdb=" O ASP 0 287 " (cutoff:3.500A) Processing helix chain '0' and resid 317 through 329 removed outlier: 4.173A pdb=" N ASN 0 326 " --> pdb=" O GLN 0 322 " (cutoff:3.500A) Processing helix chain '0' and resid 336 through 344 removed outlier: 6.142A pdb=" N ALA 0 340 " --> pdb=" O ASP 0 336 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU 0 341 " --> pdb=" O GLY 0 337 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ALA 0 344 " --> pdb=" O ALA 0 340 " (cutoff:3.500A) Processing helix chain '0' and resid 396 through 402 Processing helix chain '0' and resid 435 through 469 removed outlier: 3.853A pdb=" N GLU 0 442 " --> pdb=" O ALA 0 438 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG 0 443 " --> pdb=" O LEU 0 439 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP 0 444 " --> pdb=" O MET 0 440 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR 0 447 " --> pdb=" O ARG 0 443 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG 0 450 " --> pdb=" O GLN 0 446 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN 0 464 " --> pdb=" O GLY 0 460 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA 0 465 " --> pdb=" O MET 0 461 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN 0 468 " --> pdb=" O ASN 0 464 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N MET 0 469 " --> pdb=" O ALA 0 465 " (cutoff:3.500A) Processing helix chain '1' and resid 128 through 150 removed outlier: 4.252A pdb=" N TRP 1 139 " --> pdb=" O ASN 1 135 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N ARG 1 140 " --> pdb=" O PHE 1 136 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N ARG 1 141 " --> pdb=" O LEU 1 137 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N GLN 1 142 " --> pdb=" O GLU 1 138 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU 1 143 " --> pdb=" O TRP 1 139 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL 1 144 " --> pdb=" O ARG 1 140 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLN 1 150 " --> pdb=" O LEU 1 146 " (cutoff:3.500A) Processing helix chain '1' and resid 161 through 170 removed outlier: 3.605A pdb=" N ARG 1 169 " --> pdb=" O ARG 1 165 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N VAL 1 170 " --> pdb=" O GLN 1 166 " (cutoff:3.500A) Processing helix chain '1' and resid 185 through 190 Processing helix chain '1' and resid 194 through 201 removed outlier: 4.858A pdb=" N MET 1 201 " --> pdb=" O TYR 1 197 " (cutoff:3.500A) Processing helix chain '1' and resid 218 through 233 removed outlier: 6.604A pdb=" N ARG 1 222 " --> pdb=" O THR 1 218 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER 1 223 " --> pdb=" O ALA 1 219 " (cutoff:3.500A) Processing helix chain '1' and resid 398 through 406 removed outlier: 3.970A pdb=" N ASN 1 404 " --> pdb=" O SER 1 400 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N THR 1 405 " --> pdb=" O SER 1 401 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ILE 1 406 " --> pdb=" O THR 1 402 " (cutoff:3.500A) Processing helix chain '1' and resid 449 through 456 removed outlier: 3.836A pdb=" N SER 1 456 " --> pdb=" O GLU 1 452 " (cutoff:3.500A) Processing helix chain '1' and resid 467 through 477 Processing helix chain '1' and resid 479 through 487 removed outlier: 3.931A pdb=" N LEU 1 483 " --> pdb=" O PRO 1 479 " (cutoff:3.500A) Processing helix chain '1' and resid 505 through 516 removed outlier: 5.423A pdb=" N LEU 1 509 " --> pdb=" O THR 1 505 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU 1 510 " --> pdb=" O SER 1 506 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N THR 1 511 " --> pdb=" O GLU 1 507 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N ALA 1 512 " --> pdb=" O GLU 1 508 " (cutoff:3.500A) Processing helix chain '1' and resid 528 through 540 removed outlier: 4.065A pdb=" N TYR 1 534 " --> pdb=" O ARG 1 530 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ILE 1 535 " --> pdb=" O SER 1 531 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ASP 1 538 " --> pdb=" O TYR 1 534 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N VAL 1 540 " --> pdb=" O LEU 1 536 " (cutoff:3.500A) Processing helix chain '3' and resid 166 through 180 Processing helix chain '3' and resid 201 through 216 Processing helix chain '3' and resid 258 through 266 removed outlier: 4.268A pdb=" N GLY 3 266 " --> pdb=" O ALA 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 295 through 303 removed outlier: 5.174A pdb=" N TRP 3 300 " --> pdb=" O GLY 3 296 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N SER 3 301 " --> pdb=" O SER 3 297 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS 3 302 " --> pdb=" O THR 3 298 " (cutoff:3.500A) Proline residue: 3 303 - end of helix Processing helix chain '3' and resid 365 through 370 removed outlier: 3.707A pdb=" N LEU 3 369 " --> pdb=" O LEU 3 365 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ASN 3 370 " --> pdb=" O GLY 3 366 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 365 through 370' Processing helix chain '3' and resid 379 through 384 removed outlier: 6.428A pdb=" N CYS 3 383 " --> pdb=" O ASP 3 379 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN 3 384 " --> pdb=" O LEU 3 380 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 379 through 384' Processing helix chain '3' and resid 387 through 394 removed outlier: 5.661A pdb=" N ASN 3 394 " --> pdb=" O VAL 3 390 " (cutoff:3.500A) Processing helix chain '6' and resid 12 through 17 removed outlier: 4.139A pdb=" N PHE 6 16 " --> pdb=" O GLU 6 12 " (cutoff:3.500A) Processing helix chain '6' and resid 31 through 43 removed outlier: 3.793A pdb=" N TYR 6 35 " --> pdb=" O SER 6 31 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N GLU 6 41 " --> pdb=" O VAL 6 37 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 63 removed outlier: 4.888A pdb=" N MET 6 62 " --> pdb=" O ILE 6 58 " (cutoff:3.500A) Processing helix chain '6' and resid 77 through 89 removed outlier: 3.841A pdb=" N HIS 6 83 " --> pdb=" O GLN 6 79 " (cutoff:3.500A) Proline residue: 6 89 - end of helix Processing helix chain '6' and resid 103 through 108 removed outlier: 3.516A pdb=" N VAL 6 107 " --> pdb=" O ALA 6 103 " (cutoff:3.500A) Processing helix chain '6' and resid 122 through 133 removed outlier: 3.775A pdb=" N GLU 6 127 " --> pdb=" O ARG 6 123 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE 6 128 " --> pdb=" O GLU 6 124 " (cutoff:3.500A) Processing helix chain '6' and resid 147 through 152 removed outlier: 3.523A pdb=" N TYR 6 151 " --> pdb=" O LEU 6 147 " (cutoff:3.500A) Processing helix chain '6' and resid 166 through 178 removed outlier: 3.603A pdb=" N GLU 6 172 " --> pdb=" O GLU 6 168 " (cutoff:3.500A) Processing helix chain '6' and resid 192 through 197 removed outlier: 5.133A pdb=" N GLY 6 196 " --> pdb=" O VAL 6 192 " (cutoff:3.500A) Processing helix chain '6' and resid 211 through 223 removed outlier: 3.680A pdb=" N SER 6 216 " --> pdb=" O SER 6 212 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N VAL 6 217 " --> pdb=" O THR 6 213 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS 6 223 " --> pdb=" O GLU 6 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 6 through 11 removed outlier: 5.267A pdb=" N LEU A 10 " --> pdb=" O SER A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 removed outlier: 4.384A pdb=" N ALA A 77 " --> pdb=" O HIS A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 95 removed outlier: 3.934A pdb=" N LYS A 92 " --> pdb=" O GLU A 88 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LEU A 93 " --> pdb=" O ALA A 89 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N LYS A 95 " --> pdb=" O LYS A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 108 removed outlier: 4.494A pdb=" N VAL A 100 " --> pdb=" O ASN A 96 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS A 101 " --> pdb=" O LYS A 97 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS A 102 " --> pdb=" O LYS A 98 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR A 107 " --> pdb=" O LEU A 103 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ASP A 108 " --> pdb=" O ALA A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 123 removed outlier: 6.890A pdb=" N LYS A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLN A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Proline residue: A 121 - end of helix Processing helix chain 'A' and resid 124 through 132 removed outlier: 4.887A pdb=" N LYS A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N ALA A 131 " --> pdb=" O GLY A 127 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLY A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 155 removed outlier: 3.765A pdb=" N LYS A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N ILE A 155 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 194 removed outlier: 3.727A pdb=" N LEU A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N VAL A 180 " --> pdb=" O ASP A 176 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR A 181 " --> pdb=" O ASP A 177 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N HIS A 184 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LEU A 185 " --> pdb=" O TYR A 181 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N SER A 192 " --> pdb=" O ASN A 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.167A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 140 removed outlier: 4.326A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N GLU B 140 " --> pdb=" O LYS B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 156 removed outlier: 3.935A pdb=" N GLN B 145 " --> pdb=" O ASP B 141 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU B 146 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N SER B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER B 152 " --> pdb=" O LYS B 148 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LYS B 155 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N TYR B 156 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.394A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 removed outlier: 3.821A pdb=" N ARG B 200 " --> pdb=" O TRP B 196 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LEU B 201 " --> pdb=" O ALA B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.987A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 356 through 361 removed outlier: 4.663A pdb=" N LEU B 360 " --> pdb=" O LYS B 356 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 356 through 361' Processing helix chain 'B' and resid 381 through 390 removed outlier: 3.555A pdb=" N LYS B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY B 390 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 403 removed outlier: 4.391A pdb=" N GLU B 401 " --> pdb=" O ILE B 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 20 removed outlier: 3.751A pdb=" N ARG C 18 " --> pdb=" O ARG C 14 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N ASN C 19 " --> pdb=" O LYS C 15 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N GLY C 20 " --> pdb=" O TRP C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 54 removed outlier: 3.862A pdb=" N ASN C 42 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS C 51 " --> pdb=" O LYS C 47 " (cutoff:3.500A) removed outlier: 5.587A pdb=" N LYS C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N GLY C 53 " --> pdb=" O HIS C 49 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N LEU C 54 " --> pdb=" O ASN C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 55 through 67 Processing helix chain 'C' and resid 91 through 101 removed outlier: 3.971A pdb=" N ALA C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N HIS C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 118 removed outlier: 3.833A pdb=" N LEU C 116 " --> pdb=" O ILE C 112 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG C 117 " --> pdb=" O ALA C 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 25 through 30 removed outlier: 4.569A pdb=" N LYS D 29 " --> pdb=" O PRO D 25 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA D 30 " --> pdb=" O ALA D 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 25 through 30' Processing helix chain 'D' and resid 33 through 49 removed outlier: 4.445A pdb=" N LYS D 46 " --> pdb=" O THR D 42 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ASN D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ASN D 48 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 5.056A pdb=" N ARG D 49 " --> pdb=" O ARG D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 134 removed outlier: 3.544A pdb=" N ILE D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA D 130 " --> pdb=" O SER D 126 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER D 131 " --> pdb=" O ALA D 127 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ALA D 132 " --> pdb=" O LEU D 128 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LEU D 133 " --> pdb=" O ALA D 129 " (cutoff:3.500A) Proline residue: D 134 - end of helix Processing helix chain 'D' and resid 135 through 141 removed outlier: 3.578A pdb=" N SER D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LYS D 140 " --> pdb=" O LEU D 136 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLY D 141 " --> pdb=" O VAL D 137 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 135 through 141' Processing helix chain 'D' and resid 156 through 161 removed outlier: 4.406A pdb=" N GLY D 160 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N TYR D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 156 through 161' Processing helix chain 'D' and resid 163 through 175 removed outlier: 3.773A pdb=" N ALA D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LEU D 171 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS D 172 " --> pdb=" O VAL D 168 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LYS D 175 " --> pdb=" O LEU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 187 removed outlier: 4.008A pdb=" N ILE D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLN D 187 " --> pdb=" O VAL D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 198 removed outlier: 4.052A pdb=" N ARG D 197 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ASN D 198 " --> pdb=" O GLY D 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 193 through 198' Processing helix chain 'D' and resid 216 through 222 removed outlier: 3.731A pdb=" N ARG D 222 " --> pdb=" O ILE D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 236 through 242 Proline residue: D 242 - end of helix Processing helix chain 'D' and resid 253 through 264 removed outlier: 3.937A pdb=" N LYS D 259 " --> pdb=" O SER D 255 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N LEU D 260 " --> pdb=" O ALA D 256 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP D 261 " --> pdb=" O PHE D 257 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLU D 262 " --> pdb=" O ARG D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 295 removed outlier: 4.955A pdb=" N LYS D 294 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N SER D 295 " --> pdb=" O ARG D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 302 removed outlier: 3.974A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU D 302 " --> pdb=" O ILE D 298 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 329 removed outlier: 3.652A pdb=" N LEU D 328 " --> pdb=" O ILE D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 359 removed outlier: 4.661A pdb=" N THR D 334 " --> pdb=" O PRO D 330 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ALA D 358 " --> pdb=" O ALA D 354 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 24 removed outlier: 4.125A pdb=" N LEU E 20 " --> pdb=" O SER E 16 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LYS E 23 " --> pdb=" O GLN E 19 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER E 24 " --> pdb=" O LEU E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 41 Processing helix chain 'E' and resid 53 through 68 Processing helix chain 'E' and resid 77 through 86 Processing helix chain 'F' and resid 60 through 68 removed outlier: 4.068A pdb=" N MET F 65 " --> pdb=" O PRO F 61 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N ARG F 66 " --> pdb=" O LYS F 62 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU F 67 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N SER F 68 " --> pdb=" O LEU F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 110 removed outlier: 3.736A pdb=" N LYS F 92 " --> pdb=" O ARG F 88 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU F 98 " --> pdb=" O ALA F 94 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS F 101 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ILE F 102 " --> pdb=" O GLU F 98 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N LYS F 105 " --> pdb=" O LYS F 101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU F 107 " --> pdb=" O VAL F 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.583A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE G 69 " --> pdb=" O ARG G 65 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU G 74 " --> pdb=" O LEU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 5.101A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.689A pdb=" N LEU G 98 " --> pdb=" O GLN G 94 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ARG G 103 " --> pdb=" O ALA G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 124 removed outlier: 3.752A pdb=" N GLU G 119 " --> pdb=" O LEU G 115 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLY G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 150 removed outlier: 4.376A pdb=" N THR G 145 " --> pdb=" O ASN G 141 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN G 149 " --> pdb=" O THR G 145 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 removed outlier: 5.595A pdb=" N VAL G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N PHE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N LEU G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.851A pdb=" N LEU G 190 " --> pdb=" O GLY G 186 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 226 removed outlier: 3.907A pdb=" N GLU G 220 " --> pdb=" O ALA G 216 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR G 224 " --> pdb=" O GLU G 220 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 259 Processing helix chain 'H' and resid 5 through 13 removed outlier: 3.501A pdb=" N LEU H 9 " --> pdb=" O LYS H 5 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ARG H 10 " --> pdb=" O ALA H 6 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N GLY H 11 " --> pdb=" O ARG H 7 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS H 12 " --> pdb=" O ASP H 8 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LYS H 13 " --> pdb=" O LEU H 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 5 through 13' Processing helix chain 'H' and resid 14 through 38 removed outlier: 3.519A pdb=" N LEU H 24 " --> pdb=" O GLN H 20 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N VAL H 26 " --> pdb=" O ASP H 22 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY H 38 " --> pdb=" O ALA H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 74 removed outlier: 3.955A pdb=" N LYS H 46 " --> pdb=" O SER H 42 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE H 47 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ARG H 48 " --> pdb=" O LEU H 44 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL H 49 " --> pdb=" O SER H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 85 Proline residue: H 85 - end of helix Processing helix chain 'H' and resid 88 through 95 removed outlier: 4.041A pdb=" N ARG H 94 " --> pdb=" O ALA H 90 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N LEU H 95 " --> pdb=" O MET H 91 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 102 Processing helix chain 'H' and resid 104 through 114 Processing helix chain 'I' and resid 63 through 86 removed outlier: 4.786A pdb=" N THR I 69 " --> pdb=" O LYS I 65 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N VAL I 70 " --> pdb=" O GLU I 66 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ARG I 71 " --> pdb=" O LEU I 67 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N THR I 72 " --> pdb=" O ALA I 68 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 166 removed outlier: 3.549A pdb=" N ILE I 161 " --> pdb=" O SER I 157 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N THR I 166 " --> pdb=" O GLN I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 171 through 176 removed outlier: 3.913A pdb=" N PHE I 175 " --> pdb=" O ASP I 171 " (cutoff:3.500A) Processing helix chain 'K' and resid 25 through 30 removed outlier: 5.553A pdb=" N ARG K 29 " --> pdb=" O ARG K 25 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ARG K 30 " --> pdb=" O HIS K 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 25 through 30' Processing helix chain 'K' and resid 34 through 49 removed outlier: 3.626A pdb=" N ARG K 45 " --> pdb=" O ARG K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 64 removed outlier: 3.885A pdb=" N VAL K 63 " --> pdb=" O GLU K 59 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER K 64 " --> pdb=" O LEU K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 78 Processing helix chain 'K' and resid 79 through 103 removed outlier: 3.501A pdb=" N GLU K 88 " --> pdb=" O LYS K 84 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N LYS K 99 " --> pdb=" O ALA K 95 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ALA K 102 " --> pdb=" O ARG K 98 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS K 103 " --> pdb=" O LYS K 99 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 removed outlier: 4.016A pdb=" N ARG L 6 " --> pdb=" O PRO L 2 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N LYS L 7 " --> pdb=" O SER L 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 2 through 7' Processing helix chain 'L' and resid 41 through 48 Processing helix chain 'L' and resid 64 through 69 removed outlier: 4.436A pdb=" N SER L 68 " --> pdb=" O LYS L 64 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE L 69 " --> pdb=" O ARG L 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 64 through 69' Processing helix chain 'L' and resid 74 through 79 removed outlier: 3.847A pdb=" N LEU L 78 " --> pdb=" O ASN L 74 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N TRP L 79 " --> pdb=" O LEU L 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 74 through 79' Processing helix chain 'L' and resid 83 through 93 removed outlier: 3.880A pdb=" N ARG L 87 " --> pdb=" O SER L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 102 through 107 removed outlier: 3.873A pdb=" N SER L 106 " --> pdb=" O ASP L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 141 removed outlier: 3.784A pdb=" N SER L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 141 " --> pdb=" O ILE L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 11 removed outlier: 3.625A pdb=" N PHE M 8 " --> pdb=" O GLY M 4 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N GLY M 9 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N LYS M 10 " --> pdb=" O SER M 6 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ARG M 11 " --> pdb=" O SER M 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 4 through 11' Processing helix chain 'M' and resid 50 through 58 removed outlier: 3.531A pdb=" N ARG M 55 " --> pdb=" O ALA M 51 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG M 56 " --> pdb=" O LYS M 52 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASN M 57 " --> pdb=" O ALA M 53 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N THR M 58 " --> pdb=" O LYS M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 64 through 77 removed outlier: 4.432A pdb=" N ILE M 69 " --> pdb=" O ARG M 65 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG M 72 " --> pdb=" O LYS M 68 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ARG M 75 " --> pdb=" O TYR M 71 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N HIS M 76 " --> pdb=" O ARG M 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 30 through 44 removed outlier: 4.437A pdb=" N THR N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL N 39 " --> pdb=" O ARG N 35 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU N 40 " --> pdb=" O ALA N 36 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU N 41 " --> pdb=" O ALA N 37 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU N 43 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 91 removed outlier: 3.565A pdb=" N LYS N 88 " --> pdb=" O GLU N 84 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL N 89 " --> pdb=" O LYS N 85 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ARG N 90 " --> pdb=" O GLY N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 111 through 116 removed outlier: 4.742A pdb=" N LEU N 115 " --> pdb=" O GLU N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 144 removed outlier: 4.757A pdb=" N ASP N 143 " --> pdb=" O PHE N 139 " (cutoff:3.500A) Processing helix chain 'N' and resid 158 through 170 removed outlier: 3.559A pdb=" N MET N 163 " --> pdb=" O LYS N 159 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLN N 168 " --> pdb=" O ARG N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 17 removed outlier: 4.174A pdb=" N LEU O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N LEU O 13 " --> pdb=" O LYS O 9 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR O 14 " --> pdb=" O ASP O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 60 removed outlier: 4.190A pdb=" N GLU O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU O 60 " --> pdb=" O LEU O 56 " (cutoff:3.500A) Processing helix chain 'P' and resid 6 through 21 removed outlier: 3.610A pdb=" N PHE P 12 " --> pdb=" O ARG P 8 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ARG P 21 " --> pdb=" O GLN P 17 " (cutoff:3.500A) Processing helix chain 'P' and resid 24 through 30 removed outlier: 4.420A pdb=" N ARG P 28 " --> pdb=" O PRO P 24 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N MET P 29 " --> pdb=" O GLN P 25 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LYS P 30 " --> pdb=" O TRP P 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 24 through 30' Processing helix chain 'Q' and resid 17 through 22 removed outlier: 4.546A pdb=" N ARG Q 21 " --> pdb=" O ASP Q 17 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N VAL Q 22 " --> pdb=" O TRP Q 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 17 through 22' Processing helix chain 'Q' and resid 27 through 47 removed outlier: 3.702A pdb=" N ARG Q 45 " --> pdb=" O ALA Q 41 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ALA Q 47 " --> pdb=" O ALA Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 85 removed outlier: 3.744A pdb=" N VAL Q 83 " --> pdb=" O GLU Q 79 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 95 removed outlier: 4.792A pdb=" N ARG Q 92 " --> pdb=" O LYS Q 88 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR Q 93 " --> pdb=" O LYS Q 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 124 removed outlier: 3.764A pdb=" N LEU Q 110 " --> pdb=" O SER Q 106 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASN Q 113 " --> pdb=" O SER Q 109 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 145 removed outlier: 3.875A pdb=" N LEU Q 144 " --> pdb=" O SER Q 140 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS Q 145 " --> pdb=" O ALA Q 141 " (cutoff:3.500A) Processing helix chain 'Q' and resid 170 through 176 Processing helix chain 'Q' and resid 177 through 192 removed outlier: 3.795A pdb=" N ALA Q 189 " --> pdb=" O ALA Q 185 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG Q 190 " --> pdb=" O ARG Q 186 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N LEU Q 191 " --> pdb=" O ALA Q 187 " (cutoff:3.500A) Processing helix chain 'Q' and resid 193 through 209 removed outlier: 5.093A pdb=" N GLN Q 205 " --> pdb=" O GLU Q 201 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASP Q 206 " --> pdb=" O ALA Q 202 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N VAL Q 207 " --> pdb=" O ALA Q 203 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N GLU Q 208 " --> pdb=" O GLU Q 204 " (cutoff:3.500A) Processing helix chain 'S' and resid 51 through 56 removed outlier: 3.986A pdb=" N MET S 55 " --> pdb=" O PRO S 51 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N GLN S 56 " --> pdb=" O PHE S 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 51 through 56' Processing helix chain 'S' and resid 69 through 81 removed outlier: 5.045A pdb=" N ALA S 80 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP S 81 " --> pdb=" O TRP S 77 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 90 removed outlier: 4.505A pdb=" N ALA S 87 " --> pdb=" O ASN S 83 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA S 88 " --> pdb=" O THR S 84 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N THR S 89 " --> pdb=" O LYS S 85 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ARG S 90 " --> pdb=" O TRP S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 104 removed outlier: 3.740A pdb=" N ALA S 97 " --> pdb=" O LYS S 93 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N MET S 104 " --> pdb=" O ARG S 100 " (cutoff:3.500A) Processing helix chain 'S' and resid 105 through 135 removed outlier: 3.760A pdb=" N MET S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS S 128 " --> pdb=" O LYS S 124 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS S 132 " --> pdb=" O LYS S 128 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ALA S 133 " --> pdb=" O LYS S 129 " (cutoff:3.500A) Processing helix chain 'T' and resid 28 through 34 removed outlier: 4.098A pdb=" N ARG T 32 " --> pdb=" O ASN T 28 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS T 34 " --> pdb=" O HIS T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 40 through 57 Processing helix chain 'T' and resid 65 through 74 Processing helix chain 'U' and resid 2 through 14 removed outlier: 4.013A pdb=" N TYR U 6 " --> pdb=" O GLY U 2 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS U 13 " --> pdb=" O GLU U 9 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N LYS U 14 " --> pdb=" O LEU U 10 " (cutoff:3.500A) Processing helix chain 'U' and resid 16 through 34 removed outlier: 3.707A pdb=" N GLN U 32 " --> pdb=" O TRP U 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LEU U 33 " --> pdb=" O GLN U 29 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N SER U 34 " --> pdb=" O TYR U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 52 Processing helix chain 'U' and resid 83 through 88 removed outlier: 4.144A pdb=" N HIS U 87 " --> pdb=" O LYS U 83 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLY U 88 " --> pdb=" O PRO U 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 83 through 88' Processing helix chain 'U' and resid 97 through 111 removed outlier: 4.158A pdb=" N VAL U 101 " --> pdb=" O SER U 97 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY U 111 " --> pdb=" O GLY U 107 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 146 removed outlier: 4.915A pdb=" N ASN U 145 " --> pdb=" O ALA U 141 " (cutoff:3.500A) Proline residue: U 146 - end of helix Processing helix chain 'U' and resid 148 through 153 removed outlier: 4.599A pdb=" N THR U 152 " --> pdb=" O THR U 148 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N LYS U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 148 through 153' Processing helix chain 'U' and resid 158 through 163 Processing helix chain 'U' and resid 165 through 173 removed outlier: 3.747A pdb=" N LYS U 170 " --> pdb=" O SER U 166 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N SER U 171 " --> pdb=" O ALA U 167 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ARG U 172 " --> pdb=" O GLY U 168 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N GLY U 173 " --> pdb=" O ARG U 169 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 197 Processing helix chain 'V' and resid 15 through 30 removed outlier: 3.568A pdb=" N ALA V 21 " --> pdb=" O GLY V 17 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS V 25 " --> pdb=" O ALA V 21 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU V 28 " --> pdb=" O ALA V 24 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LEU V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLY V 30 " --> pdb=" O GLN V 26 " (cutoff:3.500A) Processing helix chain 'V' and resid 46 through 61 removed outlier: 3.806A pdb=" N LYS V 60 " --> pdb=" O ALA V 56 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ARG V 61 " --> pdb=" O PHE V 57 " (cutoff:3.500A) Processing helix chain 'V' and resid 65 through 70 removed outlier: 3.911A pdb=" N GLY V 69 " --> pdb=" O ASN V 65 " (cutoff:3.500A) Proline residue: V 70 - end of helix No H-bonds generated for 'chain 'V' and resid 65 through 70' Processing helix chain 'V' and resid 75 through 89 removed outlier: 3.934A pdb=" N MET V 87 " --> pdb=" O THR V 83 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU V 88 " --> pdb=" O VAL V 84 " (cutoff:3.500A) Proline residue: V 89 - end of helix Processing helix chain 'V' and resid 92 through 103 removed outlier: 4.209A pdb=" N LEU V 102 " --> pdb=" O ALA V 98 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS V 103 " --> pdb=" O LEU V 99 " (cutoff:3.500A) Processing helix chain 'V' and resid 124 through 129 Processing helix chain 'V' and resid 137 through 146 removed outlier: 3.581A pdb=" N HIS V 143 " --> pdb=" O GLY V 139 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N VAL V 145 " --> pdb=" O LEU V 141 " (cutoff:3.500A) Processing helix chain 'V' and resid 150 through 190 removed outlier: 3.792A pdb=" N LYS V 159 " --> pdb=" O THR V 155 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLU V 162 " --> pdb=" O GLU V 158 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS V 163 " --> pdb=" O LYS V 159 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU V 186 " --> pdb=" O GLU V 182 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LYS V 187 " --> pdb=" O LYS V 183 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N LYS V 188 " --> pdb=" O ASN V 184 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE V 189 " --> pdb=" O VAL V 185 " (cutoff:3.500A) Processing helix chain 'V' and resid 191 through 200 removed outlier: 4.233A pdb=" N VAL V 195 " --> pdb=" O LYS V 191 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR V 198 " --> pdb=" O GLU V 194 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY V 200 " --> pdb=" O LEU V 196 " (cutoff:3.500A) Processing helix chain 'W' and resid 35 through 46 Processing helix chain 'X' and resid 19 through 35 removed outlier: 3.633A pdb=" N LYS X 24 " --> pdb=" O ALA X 20 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ILE X 29 " --> pdb=" O MET X 25 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE X 31 " --> pdb=" O LYS X 27 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER X 32 " --> pdb=" O LYS X 28 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS X 34 " --> pdb=" O GLU X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 73 through 92 removed outlier: 4.024A pdb=" N THR X 78 " --> pdb=" O THR X 74 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER X 81 " --> pdb=" O VAL X 77 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU X 86 " --> pdb=" O ALA X 82 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ASP X 91 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN X 92 " --> pdb=" O GLU X 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 15 removed outlier: 4.433A pdb=" N SER Y 14 " --> pdb=" O ASN Y 10 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N CYS Y 15 " --> pdb=" O PRO Y 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 10 through 15' Processing helix chain 'Y' and resid 25 through 37 Processing helix chain 'Y' and resid 40 through 54 removed outlier: 3.879A pdb=" N THR Y 52 " --> pdb=" O LEU Y 48 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU Y 53 " --> pdb=" O LYS Y 49 " (cutoff:3.500A) Processing helix chain 'Y' and resid 72 through 77 removed outlier: 4.949A pdb=" N TRP Y 76 " --> pdb=" O GLN Y 72 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N GLY Y 77 " --> pdb=" O ALA Y 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 72 through 77' Processing helix chain 'Y' and resid 84 through 106 removed outlier: 3.512A pdb=" N ALA Y 88 " --> pdb=" O PRO Y 84 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU Y 103 " --> pdb=" O GLU Y 99 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS Y 105 " --> pdb=" O ASN Y 101 " (cutoff:3.500A) Processing helix chain 'Y' and resid 108 through 113 removed outlier: 3.969A pdb=" N LEU Y 112 " --> pdb=" O ASP Y 108 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL Y 113 " --> pdb=" O VAL Y 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 108 through 113' Processing helix chain 'Z' and resid 22 through 39 removed outlier: 3.519A pdb=" N THR Z 39 " --> pdb=" O LEU Z 35 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 54 removed outlier: 4.474A pdb=" N GLN Z 45 " --> pdb=" O SER Z 41 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL Z 46 " --> pdb=" O THR Z 42 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N MET Z 53 " --> pdb=" O LYS Z 49 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SER Z 54 " --> pdb=" O ARG Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 62 through 72 removed outlier: 3.637A pdb=" N MET Z 66 " --> pdb=" O SER Z 62 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU Z 72 " --> pdb=" O ARG Z 68 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 117 Processing helix chain 'Z' and resid 122 through 130 removed outlier: 4.233A pdb=" N LEU Z 128 " --> pdb=" O ASP Z 124 " (cutoff:3.500A) Processing helix chain 'Z' and resid 146 through 153 removed outlier: 4.303A pdb=" N ARG Z 150 " --> pdb=" O ARG Z 146 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N HIS Z 151 " --> pdb=" O GLU Z 147 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE Z 152 " --> pdb=" O VAL Z 148 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N GLY Z 153 " --> pdb=" O TYR Z 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 146 through 153' Processing helix chain 'Z' and resid 171 through 176 removed outlier: 5.393A pdb=" N GLU Z 175 " --> pdb=" O GLY Z 171 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG Z 176 " --> pdb=" O ARG Z 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 171 through 176' Processing helix chain 'a' and resid 4 through 16 removed outlier: 3.512A pdb=" N SER a 12 " --> pdb=" O LYS a 8 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER a 13 " --> pdb=" O ARG a 9 " (cutoff:3.500A) Processing helix chain 'a' and resid 18 through 23 removed outlier: 3.693A pdb=" N VAL a 22 " --> pdb=" O GLY a 18 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N TRP a 23 " --> pdb=" O LYS a 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 18 through 23' Processing helix chain 'a' and resid 28 through 36 removed outlier: 4.289A pdb=" N ILE a 32 " --> pdb=" O GLU a 28 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN a 34 " --> pdb=" O ASN a 30 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ALA a 35 " --> pdb=" O GLU a 31 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ASN a 36 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing helix chain 'a' and resid 37 through 48 removed outlier: 6.308A pdb=" N ARG a 42 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LYS a 43 " --> pdb=" O GLN a 39 " (cutoff:3.500A) Processing helix chain 'a' and resid 60 through 73 removed outlier: 3.712A pdb=" N LYS a 72 " --> pdb=" O LEU a 68 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY a 73 " --> pdb=" O ALA a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 84 through 113 Proline residue: a 90 - end of helix removed outlier: 6.704A pdb=" N VAL a 93 " --> pdb=" O MET a 89 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ILE a 101 " --> pdb=" O ARG a 97 " (cutoff:3.500A) Processing helix chain 'a' and resid 116 through 130 removed outlier: 4.337A pdb=" N SER a 122 " --> pdb=" O HIS a 118 " (cutoff:3.500A) Processing helix chain 'a' and resid 134 through 146 Processing helix chain 'b' and resid 36 through 52 Processing helix chain 'b' and resid 101 through 117 removed outlier: 3.753A pdb=" N GLY b 114 " --> pdb=" O TYR b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 125 removed outlier: 3.886A pdb=" N ILE b 124 " --> pdb=" O ARG b 120 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLN b 125 " --> pdb=" O ALA b 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 120 through 125' Processing helix chain 'b' and resid 139 through 147 removed outlier: 4.910A pdb=" N PHE b 145 " --> pdb=" O ALA b 141 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N HIS b 146 " --> pdb=" O VAL b 142 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ASP b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 161 through 166 Proline residue: b 165 - end of helix No H-bonds generated for 'chain 'b' and resid 161 through 166' Processing helix chain 'c' and resid 11 through 16 removed outlier: 4.309A pdb=" N SER c 16 " --> pdb=" O ARG c 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 32 removed outlier: 3.970A pdb=" N MET c 31 " --> pdb=" O LEU c 27 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG c 32 " --> pdb=" O ALA c 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 27 through 32' Processing helix chain 'c' and resid 54 through 59 removed outlier: 3.513A pdb=" N HIS c 58 " --> pdb=" O HIS c 54 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY c 59 " --> pdb=" O LYS c 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 54 through 59' Processing helix chain 'c' and resid 92 through 97 removed outlier: 4.109A pdb=" N ILE c 96 " --> pdb=" O ARG c 92 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS c 97 " --> pdb=" O ILE c 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 92 through 97' Processing helix chain 'c' and resid 99 through 123 removed outlier: 3.951A pdb=" N PHE c 105 " --> pdb=" O SER c 101 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU c 106 " --> pdb=" O ARG c 102 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LYS c 107 " --> pdb=" O ASP c 103 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS c 110 " --> pdb=" O LEU c 106 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS c 120 " --> pdb=" O LYS c 116 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N GLU c 121 " --> pdb=" O LYS c 117 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS c 122 " --> pdb=" O GLU c 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 32 removed outlier: 3.694A pdb=" N ASP d 31 " --> pdb=" O HIS d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 36 through 47 removed outlier: 3.998A pdb=" N GLU d 40 " --> pdb=" O ALA d 36 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN d 41 " --> pdb=" O ALA d 37 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N GLN d 44 " --> pdb=" O GLU d 40 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE d 47 " --> pdb=" O LEU d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 79 through 95 removed outlier: 4.710A pdb=" N LEU d 83 " --> pdb=" O SER d 79 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS d 84 " --> pdb=" O LYS d 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 74 removed outlier: 3.798A pdb=" N ARG e 73 " --> pdb=" O LYS e 69 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N LYS e 74 " --> pdb=" O PRO e 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 69 through 74' Processing helix chain 'e' and resid 122 through 130 removed outlier: 4.390A pdb=" N LEU e 128 " --> pdb=" O GLU e 124 " (cutoff:3.500A) Proline residue: e 130 - end of helix Processing helix chain 'e' and resid 131 through 137 removed outlier: 5.232A pdb=" N ASN e 135 " --> pdb=" O ARG e 131 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLY e 137 " --> pdb=" O ALA e 133 " (cutoff:3.500A) Processing helix chain 'f' and resid 33 through 43 removed outlier: 3.735A pdb=" N PHE f 40 " --> pdb=" O CYS f 36 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N LYS f 43 " --> pdb=" O ALA f 39 " (cutoff:3.500A) Processing helix chain 'f' and resid 45 through 50 removed outlier: 4.124A pdb=" N ILE f 49 " --> pdb=" O ASN f 45 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N ASN f 50 " --> pdb=" O PRO f 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 45 through 50' Processing helix chain 'f' and resid 52 through 60 Processing helix chain 'g' and resid 72 through 78 removed outlier: 3.587A pdb=" N ILE g 77 " --> pdb=" O HIS g 73 " (cutoff:3.500A) removed outlier: 4.984A pdb=" N LYS g 78 " --> pdb=" O TYR g 74 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 93 Processing helix chain 'g' and resid 105 through 117 removed outlier: 3.543A pdb=" N LYS g 110 " --> pdb=" O LYS g 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLN g 111 " --> pdb=" O HIS g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 145 through 154 removed outlier: 3.827A pdb=" N VAL g 149 " --> pdb=" O ASP g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 21 removed outlier: 3.893A pdb=" N ASN h 14 " --> pdb=" O ASP h 10 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALA h 21 " --> pdb=" O ARG h 17 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 31 removed outlier: 3.879A pdb=" N LYS h 28 " --> pdb=" O HIS h 24 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N SER h 31 " --> pdb=" O ARG h 27 " (cutoff:3.500A) Processing helix chain 'h' and resid 35 through 43 removed outlier: 3.633A pdb=" N GLN h 40 " --> pdb=" O LYS h 36 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ASN h 43 " --> pdb=" O ARG h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 100 through 105 removed outlier: 4.124A pdb=" N VAL h 104 " --> pdb=" O HIS h 100 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N VAL h 105 " --> pdb=" O PRO h 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 100 through 105' Processing helix chain 'h' and resid 112 through 134 removed outlier: 4.652A pdb=" N LEU h 119 " --> pdb=" O ARG h 115 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ARG h 126 " --> pdb=" O LYS h 122 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN h 127 " --> pdb=" O ALA h 123 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLU h 131 " --> pdb=" O GLN h 127 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N LYS h 132 " --> pdb=" O VAL h 128 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS h 134 " --> pdb=" O LYS h 130 " (cutoff:3.500A) Processing helix chain 'i' and resid 58 through 67 removed outlier: 4.425A pdb=" N LYS i 67 " --> pdb=" O ALA i 63 " (cutoff:3.500A) Processing helix chain 'i' and resid 76 through 81 removed outlier: 3.910A pdb=" N LEU i 80 " --> pdb=" O ASN i 76 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N MET i 81 " --> pdb=" O TYR i 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 76 through 81' Processing helix chain 'i' and resid 92 through 97 removed outlier: 4.155A pdb=" N VAL i 96 " --> pdb=" O ASP i 92 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN i 97 " --> pdb=" O LYS i 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 92 through 97' Processing helix chain 'i' and resid 103 through 125 removed outlier: 3.694A pdb=" N LYS i 109 " --> pdb=" O ALA i 105 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N THR i 124 " --> pdb=" O GLU i 120 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N GLY i 125 " --> pdb=" O ARG i 121 " (cutoff:3.500A) Processing helix chain 'i' and resid 127 through 133 removed outlier: 4.081A pdb=" N PHE i 131 " --> pdb=" O ASN i 127 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N GLN i 132 " --> pdb=" O LYS i 128 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N LYS i 133 " --> pdb=" O TRP i 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 127 through 133' Processing helix chain 'l' and resid 2 through 13 removed outlier: 5.686A pdb=" N ASN l 12 " --> pdb=" O MET l 8 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N CYS l 13 " --> pdb=" O VAL l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 85 through 101 removed outlier: 4.126A pdb=" N LEU l 90 " --> pdb=" O ALA l 86 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE l 93 " --> pdb=" O THR l 89 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ILE l 97 " --> pdb=" O ILE l 93 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ASN l 100 " --> pdb=" O MET l 96 " (cutoff:3.500A) Processing helix chain 'l' and resid 106 through 123 removed outlier: 4.330A pdb=" N ARG l 112 " --> pdb=" O MET l 108 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) Proline residue: l 123 - end of helix Processing helix chain 'm' and resid 5 through 13 removed outlier: 6.201A pdb=" N LYS m 10 " --> pdb=" O ARG m 6 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLY m 11 " --> pdb=" O GLY m 7 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ALA m 12 " --> pdb=" O GLN m 8 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLY m 13 " --> pdb=" O ARG m 9 " (cutoff:3.500A) Processing helix chain 'm' and resid 33 through 38 Processing helix chain 'm' and resid 103 through 108 removed outlier: 4.225A pdb=" N MET m 107 " --> pdb=" O PRO m 103 " (cutoff:3.500A) Proline residue: m 108 - end of helix No H-bonds generated for 'chain 'm' and resid 103 through 108' Processing helix chain 'm' and resid 181 through 193 removed outlier: 3.583A pdb=" N ALA m 185 " --> pdb=" O LYS m 181 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA m 191 " --> pdb=" O HIS m 187 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LYS m 192 " --> pdb=" O LYS m 188 " (cutoff:3.500A) Processing helix chain 'm' and resid 200 through 205 removed outlier: 4.117A pdb=" N MET m 204 " --> pdb=" O ARG m 200 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN m 205 " --> pdb=" O GLY m 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 200 through 205' Processing helix chain 'm' and resid 173 through 178 removed outlier: 3.920A pdb=" N LYS m 177 " --> pdb=" O ARG m 174 " (cutoff:3.500A) Proline residue: m 178 - end of helix Processing helix chain 'r' and resid 9 through 16 Processing helix chain 'r' and resid 20 through 26 Processing helix chain 'r' and resid 29 through 37 removed outlier: 3.610A pdb=" N ARG r 35 " --> pdb=" O TYR r 31 " (cutoff:3.500A) Processing helix chain 'r' and resid 82 through 87 removed outlier: 4.497A pdb=" N TYR r 86 " --> pdb=" O GLU r 82 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLY r 87 " --> pdb=" O LEU r 83 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 82 through 87' Processing helix chain 'r' and resid 94 through 114 removed outlier: 3.629A pdb=" N ARG r 112 " --> pdb=" O ARG r 108 " (cutoff:3.500A) Processing helix chain 'r' and resid 115 through 120 removed outlier: 4.675A pdb=" N TYR r 119 " --> pdb=" O MET r 115 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU r 120 " --> pdb=" O ASP r 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 115 through 120' Processing helix chain 'r' and resid 157 through 170 removed outlier: 3.873A pdb=" N GLY r 161 " --> pdb=" O ASN r 157 " (cutoff:3.500A) Processing helix chain 'r' and resid 191 through 201 removed outlier: 6.419A pdb=" N HIS r 195 " --> pdb=" O ASN r 191 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N ARG r 196 " --> pdb=" O ALA r 192 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N MET r 200 " --> pdb=" O ARG r 196 " (cutoff:3.500A) Processing helix chain 'r' and resid 202 through 215 removed outlier: 3.947A pdb=" N MET r 212 " --> pdb=" O MET r 208 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU r 213 " --> pdb=" O ARG r 209 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU r 214 " --> pdb=" O TYR r 210 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ASP r 215 " --> pdb=" O LEU r 211 " (cutoff:3.500A) Processing helix chain 'r' and resid 216 through 224 removed outlier: 3.675A pdb=" N SER r 224 " --> pdb=" O LYS r 220 " (cutoff:3.500A) Processing helix chain 'r' and resid 225 through 230 removed outlier: 4.766A pdb=" N ASN r 229 " --> pdb=" O GLN r 225 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER r 230 " --> pdb=" O TYR r 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 225 through 230' Processing helix chain 'r' and resid 235 through 251 Proline residue: r 251 - end of helix Processing helix chain 'r' and resid 272 through 281 removed outlier: 4.600A pdb=" N ASP r 278 " --> pdb=" O ALA r 274 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N VAL r 280 " --> pdb=" O LYS r 276 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ALA r 281 " --> pdb=" O LYS r 277 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 29 removed outlier: 3.825A pdb=" N TYR t 28 " --> pdb=" O GLN t 24 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL t 29 " --> pdb=" O SER t 25 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 24 through 29' Processing helix chain 't' and resid 43 through 48 Processing helix chain 't' and resid 81 through 89 removed outlier: 4.724A pdb=" N VAL t 87 " --> pdb=" O LYS t 83 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU t 88 " --> pdb=" O GLU t 84 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N LEU t 89 " --> pdb=" O LEU t 85 " (cutoff:3.500A) Processing helix chain 't' and resid 104 through 119 removed outlier: 3.726A pdb=" N LYS t 109 " --> pdb=" O SER t 105 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ALA t 110 " --> pdb=" O LYS t 106 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLN t 117 " --> pdb=" O GLU t 113 " (cutoff:3.500A) Processing helix chain 'u' and resid 35 through 40 removed outlier: 3.877A pdb=" N THR u 39 " --> pdb=" O ALA u 35 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU u 40 " --> pdb=" O ARG u 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 35 through 40' Processing helix chain 'v' and resid 58 through 67 Processing helix chain 'v' and resid 190 through 195 removed outlier: 4.511A pdb=" N VAL v 194 " --> pdb=" O HIS v 190 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE v 195 " --> pdb=" O GLN v 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 190 through 195' Processing helix chain 'v' and resid 213 through 218 removed outlier: 3.606A pdb=" N PHE v 217 " --> pdb=" O THR v 213 " (cutoff:3.500A) Processing helix chain 'v' and resid 243 through 262 removed outlier: 3.809A pdb=" N LYS v 247 " --> pdb=" O THR v 243 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLN v 250 " --> pdb=" O ARG v 246 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLN v 256 " --> pdb=" O ALA v 252 " (cutoff:3.500A) Proline residue: v 259 - end of helix Processing helix chain 'v' and resid 266 through 274 removed outlier: 5.403A pdb=" N VAL v 274 " --> pdb=" O TYR v 270 " (cutoff:3.500A) Processing helix chain 'v' and resid 282 through 287 removed outlier: 3.512A pdb=" N LEU v 286 " --> pdb=" O TYR v 282 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N VAL v 287 " --> pdb=" O PRO v 283 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 282 through 287' Processing helix chain 'w' and resid 24 through 79 removed outlier: 4.945A pdb=" N LEU w 28 " --> pdb=" O ASN w 24 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N LYS w 29 " --> pdb=" O PHE w 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA w 54 " --> pdb=" O ILE w 50 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE w 69 " --> pdb=" O TYR w 65 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ALA w 72 " --> pdb=" O GLU w 68 " (cutoff:3.500A) Processing helix chain 'w' and resid 102 through 113 removed outlier: 3.561A pdb=" N GLN w 110 " --> pdb=" O ARG w 106 " (cutoff:3.500A) Processing helix chain 'w' and resid 126 through 137 removed outlier: 3.732A pdb=" N MET w 132 " --> pdb=" O ALA w 128 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILE w 135 " --> pdb=" O ASN w 131 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL w 136 " --> pdb=" O MET w 132 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU w 137 " --> pdb=" O LEU w 133 " (cutoff:3.500A) Processing helix chain 'w' and resid 146 through 156 Processing helix chain 'w' and resid 171 through 179 removed outlier: 4.183A pdb=" N ILE w 175 " --> pdb=" O ASP w 171 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER w 178 " --> pdb=" O LEU w 174 " (cutoff:3.500A) Processing helix chain 'w' and resid 186 through 197 removed outlier: 4.199A pdb=" N VAL w 197 " --> pdb=" O GLU w 193 " (cutoff:3.500A) Processing helix chain 'w' and resid 200 through 209 removed outlier: 5.087A pdb=" N TRP w 209 " --> pdb=" O ASN w 205 " (cutoff:3.500A) Processing helix chain 'w' and resid 239 through 248 removed outlier: 3.672A pdb=" N LEU w 243 " --> pdb=" O GLN w 239 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG w 246 " --> pdb=" O ARG w 242 " (cutoff:3.500A) Processing helix chain 'z' and resid 14 through 40 removed outlier: 5.414A pdb=" N SER z 40 " --> pdb=" O VAL z 36 " (cutoff:3.500A) Processing helix chain 'z' and resid 44 through 64 removed outlier: 3.820A pdb=" N ILE z 63 " --> pdb=" O GLU z 59 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N PHE z 64 " --> pdb=" O THR z 60 " (cutoff:3.500A) Processing helix chain 'z' and resid 137 through 157 Processing helix chain 'z' and resid 162 through 178 removed outlier: 3.879A pdb=" N VAL z 166 " --> pdb=" O GLN z 162 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N PHE z 177 " --> pdb=" O VAL z 173 " (cutoff:3.500A) Processing helix chain 'z' and resid 206 through 213 Processing helix chain 'z' and resid 259 through 273 Processing helix chain 'z' and resid 286 through 300 removed outlier: 3.589A pdb=" N ARG z 290 " --> pdb=" O GLU z 286 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N MET z 291 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL z 294 " --> pdb=" O ARG z 290 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU z 295 " --> pdb=" O MET z 291 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS z 296 " --> pdb=" O GLY z 292 " (cutoff:3.500A) Processing helix chain 'z' and resid 351 through 361 removed outlier: 5.481A pdb=" N SER z 361 " --> pdb=" O LEU z 357 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '1' and resid 180 through 183 Processing sheet with id= 2, first strand: chain '1' and resid 388 through 394 removed outlier: 5.572A pdb=" N GLY 1 393 " --> pdb=" O CYS 1 438 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N GLY 1 440 " --> pdb=" O GLY 1 393 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 186 through 190 removed outlier: 3.853A pdb=" N ARG 3 187 " --> pdb=" O TYR 3 198 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU 3 195 " --> pdb=" O VAL 3 159 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N LYS 3 154 " --> pdb=" O TYR 3 238 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '3' and resid 253 through 256 removed outlier: 4.626A pdb=" N ASN 3 253 " --> pdb=" O CYS 3 274 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N HIS 3 282 " --> pdb=" O ILE 3 275 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN 3 290 " --> pdb=" O ASP 3 285 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain '3' and resid 314 through 319 removed outlier: 4.428A pdb=" N ASP 3 373 " --> pdb=" O VAL 3 318 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '3' and resid 320 through 323 Processing sheet with id= 7, first strand: chain '3' and resid 227 through 230 removed outlier: 3.768A pdb=" N THR 3 235 " --> pdb=" O ASP 3 230 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '6' and resid 23 through 27 Processing sheet with id= 9, first strand: chain '6' and resid 69 through 72 removed outlier: 3.796A pdb=" N LEU 6 70 " --> pdb=" O GLN 6 93 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '6' and resid 114 through 117 Processing sheet with id= 11, first strand: chain 'A' and resid 30 through 38 removed outlier: 9.030A pdb=" N GLU A 30 " --> pdb=" O HIS A 171 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N HIS A 171 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 32 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU A 163 " --> pdb=" O LEU A 38 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'A' and resid 65 through 69 removed outlier: 4.297A pdb=" N CYS A 66 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'B' and resid 53 through 59 removed outlier: 3.577A pdb=" N GLU B 74 " --> pdb=" O ILE B 56 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.824A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'B' and resid 179 through 184 removed outlier: 5.033A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'B' and resid 286 through 290 removed outlier: 4.068A pdb=" N PHE B 330 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'B' and resid 76 through 80 No H-bonds generated for sheet with id= 17 Processing sheet with id= 18, first strand: chain 'B' and resid 88 through 93 removed outlier: 3.568A pdb=" N VAL B 159 " --> pdb=" O TYR B 92 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'B' and resid 214 through 218 removed outlier: 4.308A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'D' and resid 6 through 10 removed outlier: 4.922A pdb=" N LYS D 20 " --> pdb=" O VAL D 10 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'D' and resid 226 through 232 removed outlier: 6.224A pdb=" N TYR D 211 " --> pdb=" O LEU D 230 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N PHE D 249 " --> pdb=" O GLY D 206 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'E' and resid 26 through 29 removed outlier: 6.423A pdb=" N LYS E 26 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N GLY E 70 " --> pdb=" O LYS E 44 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN E 50 " --> pdb=" O TYR E 74 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 19 through 24 removed outlier: 5.401A pdb=" N LYS F 19 " --> pdb=" O THR F 35 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 180 through 185 removed outlier: 3.540A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 5 through 11 removed outlier: 6.098A pdb=" N SER I 6 " --> pdb=" O LYS I 59 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N ARG I 54 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU I 44 " --> pdb=" O ASP I 58 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 17 through 20 removed outlier: 3.544A pdb=" N LYS I 28 " --> pdb=" O ASP I 17 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE I 26 " --> pdb=" O THR I 19 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 102 through 106 removed outlier: 6.434A pdb=" N ASN I 102 " --> pdb=" O ARG I 115 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN I 106 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N SER I 110 " --> pdb=" O MET I 128 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'I' and resid 132 through 137 removed outlier: 6.799A pdb=" N GLU I 143 " --> pdb=" O SER I 137 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP I 142 " --> pdb=" O SER I 94 " (cutoff:3.500A) removed outlier: 7.314A pdb=" N LYS I 91 " --> pdb=" O SER I 182 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'I' and resid 87 through 90 removed outlier: 4.495A pdb=" N GLY I 87 " --> pdb=" O VAL I 187 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'L' and resid 122 through 127 Processing sheet with id= 31, first strand: chain 'M' and resid 26 through 29 removed outlier: 7.605A pdb=" N ALA M 26 " --> pdb=" O GLY M 35 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N THR M 33 " --> pdb=" O HIS M 28 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'N' and resid 68 through 75 removed outlier: 5.589A pdb=" N ILE N 68 " --> pdb=" O VAL N 26 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL N 74 " --> pdb=" O LEU N 20 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS N 19 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N CYS N 21 " --> pdb=" O TYR N 131 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR N 131 " --> pdb=" O CYS N 21 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N CYS N 25 " --> pdb=" O GLY N 127 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N GLY N 127 " --> pdb=" O CYS N 25 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 2 through 5 removed outlier: 3.986A pdb=" N ARG O 3 " --> pdb=" O LEU O 42 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N VAL O 46 " --> pdb=" O ILE O 5 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER O 22 " --> pdb=" O ARG O 37 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LYS O 27 " --> pdb=" O LEU O 69 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 11 through 16 removed outlier: 4.342A pdb=" N ARG S 11 " --> pdb=" O ILE S 27 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS S 23 " --> pdb=" O VAL S 15 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU S 37 " --> pdb=" O VAL S 28 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N GLY S 40 " --> pdb=" O ARG S 46 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ARG S 46 " --> pdb=" O GLY S 40 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 102 through 109 removed outlier: 4.022A pdb=" N VAL T 21 " --> pdb=" O ARG T 90 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N THR T 22 " --> pdb=" O VAL T 122 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 35 through 39 removed outlier: 6.318A pdb=" N ALA U 35 " --> pdb=" O ARG U 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG U 65 " --> pdb=" O ALA U 35 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ILE U 61 " --> pdb=" O ALA U 39 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE U 133 " --> pdb=" O LEU U 116 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 117 through 121 removed outlier: 3.772A pdb=" N ASN U 117 " --> pdb=" O ILE U 133 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE U 129 " --> pdb=" O VAL U 121 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 6 through 10 Processing sheet with id= 39, first strand: chain 'W' and resid 7 through 10 removed outlier: 3.537A pdb=" N HIS W 21 " --> pdb=" O ARG W 8 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N VAL W 67 " --> pdb=" O TYR W 26 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 53 through 58 removed outlier: 4.993A pdb=" N GLY X 53 " --> pdb=" O GLY X 66 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'Y' and resid 16 through 20 Processing sheet with id= 42, first strand: chain 'Y' and resid 124 through 131 No H-bonds generated for sheet with id= 42 Processing sheet with id= 43, first strand: chain 'Z' and resid 99 through 102 removed outlier: 4.842A pdb=" N LYS Z 99 " --> pdb=" O LYS Z 78 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 27 through 33 removed outlier: 6.605A pdb=" N VAL b 13 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU b 17 " --> pdb=" O SER b 58 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N SER b 58 " --> pdb=" O LEU b 17 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 91 through 99 removed outlier: 4.316A pdb=" N ASN b 77 " --> pdb=" O ILE b 132 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 9 through 13 removed outlier: 4.665A pdb=" N GLU b 9 " --> pdb=" O VAL b 67 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 38 through 42 removed outlier: 4.561A pdb=" N ASP c 38 " --> pdb=" O VAL c 64 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS c 60 " --> pdb=" O ILE c 42 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 61 through 65 removed outlier: 5.682A pdb=" N PHE d 21 " --> pdb=" O VAL d 72 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR d 110 " --> pdb=" O THR d 22 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU d 112 " --> pdb=" O ASP d 24 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 24 through 28 removed outlier: 4.747A pdb=" N ALA e 24 " --> pdb=" O ILE e 39 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N LYS e 35 " --> pdb=" O CYS e 28 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N MET e 62 " --> pdb=" O ILE e 40 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N ASP e 100 " --> pdb=" O ARG e 85 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG e 85 " --> pdb=" O ASP e 100 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG e 83 " --> pdb=" O ALA e 102 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 87 through 90 removed outlier: 5.098A pdb=" N VAL e 94 " --> pdb=" O ARG e 90 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 18 through 22 Processing sheet with id= 52, first strand: chain 'g' and resid 95 through 100 removed outlier: 3.927A pdb=" N LYS g 134 " --> pdb=" O VAL g 100 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N GLU g 133 " --> pdb=" O ARG g 129 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 53 through 56 removed outlier: 4.989A pdb=" N ASP h 53 " --> pdb=" O VAL h 70 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 71 through 75 Processing sheet with id= 55, first strand: chain 'h' and resid 86 through 89 removed outlier: 4.835A pdb=" N THR h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 9 through 13 removed outlier: 4.306A pdb=" N LYS i 9 " --> pdb=" O ILE i 25 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ARG i 21 " --> pdb=" O VAL i 13 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU i 42 " --> pdb=" O VAL i 26 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N HIS i 40 " --> pdb=" O ILE i 29 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 42 through 45 Processing sheet with id= 58, first strand: chain 'l' and resid 48 through 53 removed outlier: 4.787A pdb=" N THR l 48 " --> pdb=" O LYS l 65 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N SER l 76 " --> pdb=" O ARG l 66 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 47 through 50 removed outlier: 3.867A pdb=" N ASP m 47 " --> pdb=" O LYS m 60 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS m 60 " --> pdb=" O LYS m 46 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 111 through 114 removed outlier: 4.202A pdb=" N THR m 111 " --> pdb=" O VAL m 136 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL m 136 " --> pdb=" O THR m 111 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARG m 147 " --> pdb=" O ILE m 137 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS m 145 " --> pdb=" O ASN m 140 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N SER m 138 " --> pdb=" O ARG m 147 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'm' and resid 58 through 65 No H-bonds generated for sheet with id= 61 Processing sheet with id= 62, first strand: chain 'm' and resid 146 through 150 removed outlier: 4.253A pdb=" N SER m 154 " --> pdb=" O LEU m 150 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'r' and resid 76 through 80 removed outlier: 3.977A pdb=" N CYS r 76 " --> pdb=" O ILE r 64 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE r 60 " --> pdb=" O ALA r 80 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 74 through 80 Processing sheet with id= 65, first strand: chain 'u' and resid 56 through 60 No H-bonds generated for sheet with id= 65 Processing sheet with id= 66, first strand: chain 'u' and resid 67 through 75 removed outlier: 4.370A pdb=" N LYS u 45 " --> pdb=" O VAL u 74 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ARG u 46 " --> pdb=" O MET u 104 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N VAL u 50 " --> pdb=" O ARG u 100 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ARG u 100 " --> pdb=" O VAL u 50 " (cutoff:3.500A) removed outlier: 14.049A pdb=" N LYS u 52 " --> pdb=" O GLY u 98 " (cutoff:3.500A) removed outlier: 15.860A pdb=" N GLY u 98 " --> pdb=" O LYS u 52 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N HIS u 99 " --> pdb=" O PHE u 11 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N LEU u 27 " --> pdb=" O ALA u 12 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 148 through 153 removed outlier: 4.360A pdb=" N THR v 148 " --> pdb=" O PHE v 164 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS v 160 " --> pdb=" O ILE v 152 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY v 177 " --> pdb=" O PRO v 185 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'w' and resid 139 through 144 removed outlier: 7.118A pdb=" N TYR w 139 " --> pdb=" O ILE w 95 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N PHE w 118 " --> pdb=" O LEU w 213 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'z' and resid 78 through 82 removed outlier: 13.051A pdb=" N ILE z 118 " --> pdb=" O LEU z 324 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N LEU z 324 " --> pdb=" O ILE z 118 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASN z 120 " --> pdb=" O THR z 322 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR z 322 " --> pdb=" O ASN z 120 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLN z 318 " --> pdb=" O THR z 124 " (cutoff:3.500A) removed outlier: 9.587A pdb=" N VAL z 126 " --> pdb=" O VAL z 316 " (cutoff:3.500A) removed outlier: 13.498A pdb=" N VAL z 316 " --> pdb=" O VAL z 126 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N PHE z 315 " --> pdb=" O SER z 232 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N GLU z 222 " --> pdb=" O LEU z 325 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N VAL z 223 " --> pdb=" O LEU z 190 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS z 188 " --> pdb=" O ALA z 225 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N ASP z 227 " --> pdb=" O LEU z 186 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N LEU z 186 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N AMET z 185 " --> pdb=" O GLN z 203 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N LYS z 199 " --> pdb=" O GLN z 189 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'z' and resid 84 through 87 removed outlier: 6.023A pdb=" N ASN z 84 " --> pdb=" O GLU z 310 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU z 308 " --> pdb=" O VAL z 86 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 322 through 326 removed outlier: 6.377A pdb=" N THR z 322 " --> pdb=" O ILE z 333 " (cutoff:3.500A) 2054 hydrogen bonds defined for protein. 6078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2931 hydrogen bonds 4988 hydrogen bond angles 0 basepair planarities 1120 basepair parallelities 2032 stacking parallelities Total time for adding SS restraints: 328.18 Time building geometry restraints manager: 47.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.40: 57827 1.40 - 1.71: 93264 1.71 - 2.03: 450 2.03 - 2.35: 5 2.35 - 2.67: 1 Bond restraints: 151547 Sorted by residual: bond pdb=" C2 G 2 417 " pdb=" N2 G 2 417 " ideal model delta sigma weight residual 1.341 2.670 -1.329 2.00e-02 2.50e+03 4.42e+03 bond pdb=" N3 G 8 16 " pdb=" C4 G 8 16 " ideal model delta sigma weight residual 1.350 2.218 -0.868 2.00e-02 2.50e+03 1.88e+03 bond pdb=" C2 G 8 16 " pdb=" N3 G 8 16 " ideal model delta sigma weight residual 1.323 2.178 -0.855 2.00e-02 2.50e+03 1.83e+03 bond pdb=" C6 G 8 16 " pdb=" N1 G 8 16 " ideal model delta sigma weight residual 1.391 2.100 -0.709 2.00e-02 2.50e+03 1.26e+03 bond pdb=" N1 G 8 16 " pdb=" C2 G 8 16 " ideal model delta sigma weight residual 1.373 2.069 -0.696 2.00e-02 2.50e+03 1.21e+03 ... (remaining 151542 not shown) Histogram of bond angle deviations from ideal: 93.29 - 104.49: 16216 104.49 - 115.70: 107338 115.70 - 126.90: 89224 126.90 - 138.10: 9899 138.10 - 149.30: 9 Bond angle restraints: 222686 Sorted by residual: angle pdb=" C1' 1MA 21322 " pdb=" N9 1MA 21322 " pdb=" C4 1MA 21322 " ideal model delta sigma weight residual 158.43 119.84 38.59 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' 1MA 21322 " pdb=" N9 1MA 21322 " pdb=" C8 1MA 21322 " ideal model delta sigma weight residual 93.44 131.92 -38.48 3.00e+00 1.11e-01 1.65e+02 angle pdb=" C1' A2M 24523 " pdb=" N9 A2M 24523 " pdb=" C8 A2M 24523 " ideal model delta sigma weight residual 93.22 129.65 -36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" C1' A2M 23718 " pdb=" N9 A2M 23718 " pdb=" C8 A2M 23718 " ideal model delta sigma weight residual 93.22 128.02 -34.80 3.00e+00 1.11e-01 1.35e+02 angle pdb=" N GLY A 170 " pdb=" CA GLY A 170 " pdb=" C GLY A 170 " ideal model delta sigma weight residual 110.96 128.02 -17.06 1.49e+00 4.50e-01 1.31e+02 ... (remaining 222681 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.96: 78590 35.96 - 71.91: 3624 71.91 - 107.87: 248 107.87 - 143.82: 22 143.82 - 179.78: 38 Dihedral angle restraints: 82522 sinusoidal: 60998 harmonic: 21524 Sorted by residual: dihedral pdb=" CA LEU B 17 " pdb=" C LEU B 17 " pdb=" N PRO B 18 " pdb=" CA PRO B 18 " ideal model delta harmonic sigma weight residual 180.00 85.63 94.37 0 5.00e+00 4.00e-02 3.56e+02 dihedral pdb=" CA TYR u 106 " pdb=" C TYR u 106 " pdb=" N PRO u 107 " pdb=" CA PRO u 107 " ideal model delta harmonic sigma weight residual -180.00 -111.42 -68.58 0 5.00e+00 4.00e-02 1.88e+02 dihedral pdb=" CA CYS E 52 " pdb=" C CYS E 52 " pdb=" N PRO E 53 " pdb=" CA PRO E 53 " ideal model delta harmonic sigma weight residual -180.00 -126.98 -53.02 0 5.00e+00 4.00e-02 1.12e+02 ... (remaining 82519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.125: 25917 0.125 - 0.250: 1289 0.250 - 0.376: 58 0.376 - 0.501: 14 0.501 - 0.626: 3 Chirality restraints: 27281 Sorted by residual: chirality pdb=" CG LEU w 109 " pdb=" CB LEU w 109 " pdb=" CD1 LEU w 109 " pdb=" CD2 LEU w 109 " both_signs ideal model delta sigma weight residual False -2.59 -1.96 -0.63 2.00e-01 2.50e+01 9.80e+00 chirality pdb=" CA ALA 3 331 " pdb=" N ALA 3 331 " pdb=" C ALA 3 331 " pdb=" CB ALA 3 331 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.37e+00 chirality pdb=" C3' B9H 22786 " pdb=" C4' B9H 22786 " pdb=" O3' B9H 22786 " pdb=" C2' B9H 22786 " both_signs ideal model delta sigma weight residual False -2.48 -1.97 -0.51 2.00e-01 2.50e+01 6.48e+00 ... (remaining 27278 not shown) Planarity restraints: 14299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 24550 " -0.097 2.00e-02 2.50e+03 6.28e-01 8.87e+03 pdb=" C4' 7MG 24550 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 7MG 24550 " -0.625 2.00e-02 2.50e+03 pdb=" C3' 7MG 24550 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 7MG 24550 " 0.699 2.00e-02 2.50e+03 pdb=" C2' 7MG 24550 " 0.142 2.00e-02 2.50e+03 pdb=" O2' 7MG 24550 " -1.041 2.00e-02 2.50e+03 pdb=" C1' 7MG 24550 " -0.217 2.00e-02 2.50e+03 pdb=" N9 7MG 24550 " 0.978 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 2 729 " 0.914 2.00e-02 2.50e+03 6.23e-01 8.72e+03 pdb=" C4' 2MG 2 729 " -0.206 2.00e-02 2.50e+03 pdb=" O4' 2MG 2 729 " -0.690 2.00e-02 2.50e+03 pdb=" C3' 2MG 2 729 " 0.173 2.00e-02 2.50e+03 pdb=" O3' 2MG 2 729 " -1.023 2.00e-02 2.50e+03 pdb=" C2' 2MG 2 729 " 0.645 2.00e-02 2.50e+03 pdb=" O2' 2MG 2 729 " 0.680 2.00e-02 2.50e+03 pdb=" C1' 2MG 2 729 " -0.418 2.00e-02 2.50e+03 pdb=" N9 2MG 2 729 " -0.075 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 2 978 " 0.068 2.00e-02 2.50e+03 6.22e-01 8.72e+03 pdb=" C4' 2MG 2 978 " 0.447 2.00e-02 2.50e+03 pdb=" O4' 2MG 2 978 " 0.691 2.00e-02 2.50e+03 pdb=" C3' 2MG 2 978 " -0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG 2 978 " -0.661 2.00e-02 2.50e+03 pdb=" C2' 2MG 2 978 " -0.175 2.00e-02 2.50e+03 pdb=" O2' 2MG 2 978 " 1.000 2.00e-02 2.50e+03 pdb=" C1' 2MG 2 978 " 0.197 2.00e-02 2.50e+03 pdb=" N9 2MG 2 978 " -0.972 2.00e-02 2.50e+03 ... (remaining 14296 not shown) Histogram of nonbonded interaction distances: 1.26 - 1.98: 7 1.98 - 2.71: 13538 2.71 - 3.44: 166642 3.44 - 4.17: 441508 4.17 - 4.90: 637603 Nonbonded interactions: 1259298 Sorted by model distance: nonbonded pdb="MG MG 25257 " pdb="MG MG 25258 " model vdw 1.256 1.300 nonbonded pdb="MG MG 25191 " pdb="MG MG 25192 " model vdw 1.307 1.300 nonbonded pdb=" CG2 VAL A 32 " pdb=" O GLY A 170 " model vdw 1.317 3.460 nonbonded pdb=" O GLN 3 325 " pdb=" CG2 ILE 3 327 " model vdw 1.561 3.460 nonbonded pdb=" NH2 ARG z 243 " pdb=" CD ARG z 290 " model vdw 1.568 3.520 ... (remaining 1259293 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 Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 3754 5.49 5 Mg 246 5.21 5 S 281 5.16 5 C 73970 2.51 5 N 26419 2.21 5 O 36502 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.440 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: 0.080 Extract box with map and model: 30.910 Check model and map are aligned: 1.530 Convert atoms to be neutral: 0.900 Process input model: 586.060 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 632.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 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 : 0.014 1.329 151547 Z= 0.815 Angle : 1.210 38.589 222686 Z= 0.599 Chirality : 0.062 0.626 27281 Planarity : 0.030 0.628 14299 Dihedral : 17.041 179.778 68785 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.52 % Favored : 92.25 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 1.92 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.92 (0.08), residues: 7479 helix: -2.91 (0.08), residues: 2444 sheet: -1.74 (0.14), residues: 1080 loop : -2.67 (0.08), residues: 3955 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 889 time to evaluate : 7.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 49 residues processed: 954 average time/residue: 1.4485 time to fit residues: 2397.9951 Evaluate side-chains 742 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 693 time to evaluate : 7.198 Switching outliers to nearest non-outliers outliers start: 49 outliers final: 0 residues processed: 49 average time/residue: 1.1154 time to fit residues: 114.5589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 938 optimal weight: 0.8980 chunk 842 optimal weight: 1.9990 chunk 467 optimal weight: 4.9990 chunk 287 optimal weight: 5.9990 chunk 568 optimal weight: 0.9980 chunk 450 optimal weight: 7.9990 chunk 871 optimal weight: 1.9990 chunk 337 optimal weight: 1.9990 chunk 529 optimal weight: 2.9990 chunk 648 optimal weight: 2.9990 chunk 1009 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 233 GLN 0 446 GLN 0 474 GLN 3 270 GLN ** 3 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 364 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 391 ASN 6 106 ASN 6 118 HIS 6 145 GLN 6 157 GLN 6 162 HIS 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 72 GLN ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 200 ASN B 167 GLN B 204 GLN B 281 ASN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 19 ASN C 49 HIS C 60 ASN D 21 ASN D 50 GLN D 119 GLN D 178 ASN E 73 HIS G 159 HIS G 227 ASN H 101 ASN H 108 GLN I 39 ASN I 163 GLN L 85 GLN N 65 ASN N 97 ASN N 104 ASN O 58 GLN P 19 GLN S 78 GLN S 125 ASN T 116 ASN V 167 HIS W 18 HIS W 45 GLN X 56 HIS Y 21 ASN Y 34 GLN Y 75 GLN Y 80 GLN Y 116 HIS Z 44 ASN ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 7 GLN b 23 HIS b 77 ASN b 125 GLN ** d 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 77 HIS f 59 HIS g 93 ASN g 151 ASN i 78 ASN l 6 GLN m 132 ASN m 194 ASN r 81 HIS r 195 HIS t 107 ASN t 117 GLN u 20 ASN ** v 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 190 HIS v 211 HIS v 268 GLN w 63 GLN z 147 HIS A z 147 HIS B z 242 GLN z 254 GLN z 299 HIS Total number of N/Q/H flips: 76 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 151547 Z= 0.190 Angle : 0.799 19.303 222686 Z= 0.432 Chirality : 0.038 0.325 27281 Planarity : 0.009 0.463 14299 Dihedral : 16.575 179.641 53251 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer Outliers : 2.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.06 % 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: -2.70 (0.09), residues: 7479 helix: -1.30 (0.10), residues: 2465 sheet: -1.48 (0.15), residues: 1001 loop : -2.23 (0.08), residues: 4013 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 915 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 780 time to evaluate : 7.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 79 residues processed: 870 average time/residue: 1.2520 time to fit residues: 1925.2802 Evaluate side-chains 786 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 707 time to evaluate : 7.041 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 79 outliers final: 1 residues processed: 79 average time/residue: 1.0254 time to fit residues: 163.5235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 561 optimal weight: 6.9990 chunk 313 optimal weight: 8.9990 chunk 840 optimal weight: 5.9990 chunk 687 optimal weight: 6.9990 chunk 278 optimal weight: 8.9990 chunk 1011 optimal weight: 5.9990 chunk 1092 optimal weight: 0.7980 chunk 900 optimal weight: 3.9990 chunk 1003 optimal weight: 6.9990 chunk 344 optimal weight: 7.9990 chunk 811 optimal weight: 7.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS 3 253 ASN 3 358 GLN 6 145 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS B 302 ASN B 315 ASN D 38 ASN D 231 ASN G 208 ASN I 156 ASN N 104 ASN N 167 GLN P 19 GLN S 66 HIS T 28 ASN T 100 ASN W 18 HIS W 51 GLN ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN ** d 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 94 ASN ** h 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 28 ASN l 100 ASN ** v 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 227 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.1165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.120 151547 Z= 0.430 Angle : 0.900 18.534 222686 Z= 0.473 Chirality : 0.046 0.409 27281 Planarity : 0.010 0.371 14299 Dihedral : 16.678 179.821 53251 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.35 % Favored : 92.58 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.08 % 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: -2.40 (0.09), residues: 7479 helix: -0.90 (0.10), residues: 2463 sheet: -1.33 (0.15), residues: 1021 loop : -2.15 (0.09), residues: 3995 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 895 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 696 time to evaluate : 7.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 132 residues processed: 850 average time/residue: 1.2273 time to fit residues: 1871.4109 Evaluate side-chains 789 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 657 time to evaluate : 7.234 Switching outliers to nearest non-outliers outliers start: 132 outliers final: 0 residues processed: 132 average time/residue: 1.1091 time to fit residues: 287.9807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 999 optimal weight: 3.9990 chunk 760 optimal weight: 0.6980 chunk 525 optimal weight: 6.9990 chunk 111 optimal weight: 8.9990 chunk 482 optimal weight: 9.9990 chunk 679 optimal weight: 0.0370 chunk 1015 optimal weight: 3.9990 chunk 1074 optimal weight: 0.9980 chunk 530 optimal weight: 5.9990 chunk 962 optimal weight: 0.9980 chunk 289 optimal weight: 7.9990 overall best weight: 1.3460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 322 GLN 0 402 GLN ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 GLN ** A 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 19 GLN S 78 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 34 ASN b 125 GLN ** v 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.096 151547 Z= 0.170 Angle : 0.752 17.607 222686 Z= 0.413 Chirality : 0.036 0.331 27281 Planarity : 0.008 0.230 14299 Dihedral : 16.291 179.948 53251 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.74 % Favored : 94.23 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.06 % 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: -1.86 (0.09), residues: 7479 helix: -0.28 (0.11), residues: 2457 sheet: -1.15 (0.15), residues: 1025 loop : -1.91 (0.09), residues: 3997 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 731 time to evaluate : 7.330 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 43 residues processed: 801 average time/residue: 1.3183 time to fit residues: 1886.8131 Evaluate side-chains 712 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 669 time to evaluate : 7.236 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 1.0620 time to fit residues: 96.2692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 895 optimal weight: 0.4980 chunk 610 optimal weight: 5.9990 chunk 15 optimal weight: 9.9990 chunk 800 optimal weight: 2.9990 chunk 443 optimal weight: 10.0000 chunk 917 optimal weight: 0.9980 chunk 742 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 548 optimal weight: 5.9990 chunk 964 optimal weight: 0.5980 chunk 271 optimal weight: 10.0000 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 HIS ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 107 GLN Q 149 GLN S 78 GLN T 100 ASN U 196 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN d 44 GLN ** h 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.135 151547 Z= 0.204 Angle : 0.746 17.469 222686 Z= 0.409 Chirality : 0.037 0.331 27281 Planarity : 0.008 0.170 14299 Dihedral : 16.155 179.577 53251 Min Nonbonded Distance : 1.091 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.42 % Favored : 93.56 % Rotamer Outliers : 1.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.09), residues: 7479 helix: -0.02 (0.11), residues: 2454 sheet: -1.01 (0.16), residues: 1029 loop : -1.77 (0.09), residues: 3996 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 810 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 699 time to evaluate : 7.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 68 residues processed: 785 average time/residue: 1.2654 time to fit residues: 1768.9946 Evaluate side-chains 734 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 666 time to evaluate : 7.198 Switching outliers to nearest non-outliers outliers start: 68 outliers final: 0 residues processed: 68 average time/residue: 1.0209 time to fit residues: 142.4847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 361 optimal weight: 9.9990 chunk 967 optimal weight: 0.6980 chunk 212 optimal weight: 6.9990 chunk 631 optimal weight: 0.9990 chunk 265 optimal weight: 7.9990 chunk 1075 optimal weight: 0.9980 chunk 893 optimal weight: 5.9990 chunk 498 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 355 optimal weight: 8.9990 chunk 564 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN Q 149 GLN ** S 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 105 GLN b 125 GLN d 44 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.188 151547 Z= 0.253 Angle : 0.771 17.652 222686 Z= 0.419 Chirality : 0.038 0.331 27281 Planarity : 0.008 0.137 14299 Dihedral : 16.161 179.988 53251 Min Nonbonded Distance : 1.062 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.69 % Favored : 93.29 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.09), residues: 7479 helix: 0.07 (0.11), residues: 2450 sheet: -0.91 (0.16), residues: 1026 loop : -1.73 (0.09), residues: 4003 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 800 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 693 time to evaluate : 7.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 107 outliers final: 67 residues processed: 761 average time/residue: 1.2915 time to fit residues: 1754.1975 Evaluate side-chains 728 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 661 time to evaluate : 9.278 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 1.1088 time to fit residues: 148.5533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 1037 optimal weight: 7.9990 chunk 121 optimal weight: 20.0000 chunk 613 optimal weight: 0.0770 chunk 785 optimal weight: 9.9990 chunk 608 optimal weight: 0.9990 chunk 905 optimal weight: 9.9990 chunk 600 optimal weight: 0.6980 chunk 1071 optimal weight: 6.9990 chunk 670 optimal weight: 10.0000 chunk 653 optimal weight: 6.9990 chunk 494 optimal weight: 7.9990 overall best weight: 3.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 110 GLN Q 149 GLN S 78 GLN T 100 ASN U 29 GLN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN l 21 ASN z 254 GLN z 306 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.243 151547 Z= 0.302 Angle : 0.800 19.523 222686 Z= 0.431 Chirality : 0.040 0.329 27281 Planarity : 0.008 0.139 14299 Dihedral : 16.244 179.892 53251 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.21 % Favored : 92.76 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.06 % 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: -1.52 (0.09), residues: 7479 helix: 0.02 (0.11), residues: 2459 sheet: -0.92 (0.16), residues: 1025 loop : -1.73 (0.09), residues: 3995 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 776 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 690 time to evaluate : 7.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 53 residues processed: 753 average time/residue: 1.2667 time to fit residues: 1705.8942 Evaluate side-chains 713 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 660 time to evaluate : 7.284 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.0611 time to fit residues: 116.2870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 663 optimal weight: 3.9990 chunk 428 optimal weight: 10.0000 chunk 640 optimal weight: 3.9990 chunk 322 optimal weight: 10.0000 chunk 210 optimal weight: 7.9990 chunk 207 optimal weight: 7.9990 chunk 681 optimal weight: 9.9990 chunk 730 optimal weight: 6.9990 chunk 529 optimal weight: 1.9990 chunk 99 optimal weight: 20.0000 chunk 842 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 GLN Q 175 ASN T 93 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN z 306 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.575 151547 Z= 0.445 Angle : 0.864 73.894 222686 Z= 0.454 Chirality : 0.044 0.848 27281 Planarity : 0.008 0.141 14299 Dihedral : 16.251 179.928 53251 Min Nonbonded Distance : 1.036 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 7.27 % Favored : 92.70 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.06 % 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: -1.56 (0.09), residues: 7479 helix: -0.03 (0.11), residues: 2459 sheet: -0.91 (0.16), residues: 1038 loop : -1.75 (0.09), residues: 3982 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 736 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 664 time to evaluate : 7.187 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 72 outliers final: 53 residues processed: 709 average time/residue: 1.3534 time to fit residues: 1728.2888 Evaluate side-chains 704 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 651 time to evaluate : 7.257 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.1137 time to fit residues: 121.6926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 974 optimal weight: 0.8980 chunk 1026 optimal weight: 0.7980 chunk 936 optimal weight: 3.9990 chunk 998 optimal weight: 2.9990 chunk 601 optimal weight: 1.9990 chunk 435 optimal weight: 9.9990 chunk 784 optimal weight: 7.9990 chunk 306 optimal weight: 20.0000 chunk 902 optimal weight: 8.9990 chunk 944 optimal weight: 0.7980 chunk 995 optimal weight: 7.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 GLN Q 175 ASN T 100 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 ASN b 125 GLN w 131 ASN z 306 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.582 151547 Z= 0.208 Angle : 0.783 63.009 222686 Z= 0.423 Chirality : 0.037 0.320 27281 Planarity : 0.008 0.196 14299 Dihedral : 16.214 179.375 53251 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.01 % Favored : 92.97 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.06 % 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: -1.42 (0.09), residues: 7479 helix: 0.15 (0.11), residues: 2446 sheet: -0.92 (0.16), residues: 1036 loop : -1.67 (0.09), residues: 3997 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 688 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 666 time to evaluate : 7.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 10 residues processed: 682 average time/residue: 1.2643 time to fit residues: 1541.9450 Evaluate side-chains 665 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 655 time to evaluate : 7.278 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 1.0628 time to fit residues: 29.2635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 655 optimal weight: 0.8980 chunk 1056 optimal weight: 0.9990 chunk 644 optimal weight: 0.4980 chunk 501 optimal weight: 0.9980 chunk 734 optimal weight: 5.9990 chunk 1107 optimal weight: 40.0000 chunk 1019 optimal weight: 0.7980 chunk 882 optimal weight: 1.9990 chunk 91 optimal weight: 20.0000 chunk 681 optimal weight: 10.0000 chunk 540 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN ** 6 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 GLN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN ** g 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 30 ASN z 306 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.768 151547 Z= 0.327 Angle : 0.838 106.034 222686 Z= 0.447 Chirality : 0.037 1.068 27281 Planarity : 0.008 0.192 14299 Dihedral : 16.212 179.364 53251 Min Nonbonded Distance : 1.074 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 7.03 % Favored : 92.96 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.06 % 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: -1.41 (0.09), residues: 7479 helix: 0.16 (0.11), residues: 2446 sheet: -0.89 (0.16), residues: 1030 loop : -1.67 (0.09), residues: 4003 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14958 Ramachandran restraints generated. 7479 Oldfield, 0 Emsley, 7479 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 657 time to evaluate : 7.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 661 average time/residue: 1.3240 time to fit residues: 1566.4104 Evaluate side-chains 662 residues out of total 6542 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 655 time to evaluate : 7.281 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 1.1066 time to fit residues: 23.1125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1112 random chunks: chunk 700 optimal weight: 0.0870 chunk 939 optimal weight: 2.9990 chunk 270 optimal weight: 10.0000 chunk 813 optimal weight: 0.9990 chunk 130 optimal weight: 10.0000 chunk 245 optimal weight: 10.0000 chunk 883 optimal weight: 0.0980 chunk 369 optimal weight: 9.9990 chunk 907 optimal weight: 1.9990 chunk 111 optimal weight: 10.0000 chunk 162 optimal weight: 7.9990 overall best weight: 1.2364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 324 HIS ** 3 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 145 GLN 6 157 GLN 6 170 GLN ** 6 187 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 GLN ** Q 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 100 ASN ** W 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 125 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.124596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.108477 restraints weight = 380607.194| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 0.94 r_work: 0.3375 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work: 0.3252 rms_B_bonded: 3.95 restraints_weight: 0.1250 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.125 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 16 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.673 151547 Z= 0.274 Angle : 0.793 76.464 222686 Z= 0.430 Chirality : 0.036 0.318 27281 Planarity : 0.008 0.134 14299 Dihedral : 16.151 179.484 53251 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.60 % Favored : 93.39 % Rotamer Outliers : 0.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.28 % Cis-general : 0.07 % Twisted Proline : 0.96 % Twisted General : 0.07 % 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: -1.30 (0.10), residues: 7479 helix: 0.25 (0.11), residues: 2454 sheet: -0.85 (0.16), residues: 1025 loop : -1.61 (0.09), residues: 4000 =============================================================================== Job complete usr+sys time: 27773.20 seconds wall clock time: 485 minutes 5.98 seconds (29105.98 seconds total)