Starting phenix.real_space_refine (version: 1.19rc7) on Thu Jan 14 13:06:38 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q97_4476/01_2021/6q97_4476_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.013 Set model interpretation parameters Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 "B TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.19rc7-4070/modules/chem_data/mon_lib" Total number of atoms: 156609 Number of models: 1 Model: "" Number of chains: 72 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna3p': 18, 'rna2p': 4, 'rna3p_pur': 1378, 'rna3p_pyr': 1049, 'rna2p_pur': 288, 'rna2p_pyr': 165} Link IDs: {'rna3p': 2446, 'rna2p': 456} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 751, 'rna3p_pyr': 563, 'rna2p_pur': 118, 'rna2p_pyr': 90} Link IDs: {'rna3p': 1325, 'rna2p': 208} Chain breaks: 2 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 8} Link IDs: {'rna3p': 105, 'rna2p': 14} Chain: "5" Number of atoms: 1170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1170 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 2, 'TRANS': 142} Chain: "6" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 140 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Chain: "8" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1638 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 29, 'rna2p_pur': 8, 'rna3p_pur': 31, 'rna2p_pyr': 9} Link IDs: {'rna3p': 60, 'rna2p': 16} Chain: "9" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 128 Classifications: {'RNA': 6} Modifications used: {'rna3p_pyr': 3, 'rna3p_pur': 3} Link IDs: {'rna3p': 5} Chain: "B" Number of atoms: 2078 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2078 Classifications: {'peptide': 270} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 252} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1121 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'TRANS': 101, 'PCIS': 1} Chain: "S" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 840 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "u" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "x" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 7134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 7134 Classifications: {'RNA': 334} Modifications used: {'rna3p_pyr': 139, 'rna2p_pur': 22, 'rna3p_pur': 156, 'rna2p_pyr': 17} Link IDs: {'rna3p': 294, 'rna2p': 39} Chain breaks: 1 Chain: "7" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1644 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 30, 'rna2p_pur': 7, 'rna3p_pur': 32, 'rna2p_pyr': 8} Link IDs: {'rna3p': 62, 'rna2p': 14} Chain: "1" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 294 Unusual residues: {' MG': 294} Classifications: {'undetermined': 294} Link IDs: {None: 293} Chain: "2" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Unusual residues: {' MG': 128} Classifications: {'undetermined': 128} Link IDs: {None: 127} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "8" 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: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" 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: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "7" 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: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0LUX SG CYS f 27 187.386 132.299 122.471 1.00 70.81 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13144 " occ=0.50 Time building chain proxies: 59.77, per 1000 atoms: 0.38 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Number of scatterers: 156609 At special positions: 0 Unit cell: (248.24, 310.3, 278.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 160 16.00 P 5051 15.00 Mg 439 11.99 O 43622 8.00 N 29030 7.00 C 78305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 54.59 Conformation dependent library (CDL) restraints added in 5.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11264 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: 178 helices and 72 sheets defined 38.0% alpha, 17.6% beta 807 base pairs and 2097 stacking pairs defined. Time for finding SS restraints: 55.31 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 3.824A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N HIS 5 22 " --> pdb=" O LYS 5 18 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU 5 23 " --> pdb=" O ARG 5 19 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR 5 24 " --> pdb=" O ALA 5 20 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 17 through 24' Processing helix chain '5' and resid 37 through 45 removed outlier: 4.320A pdb=" N VAL 5 41 " --> pdb=" O GLN 5 37 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LYS 5 42 " --> pdb=" O GLY 5 38 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER 5 43 " --> pdb=" O TRP 5 39 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 107 removed outlier: 3.515A pdb=" N TYR 5 101 " --> pdb=" O LEU 5 97 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ARG 5 106 " --> pdb=" O GLY 5 102 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU 5 107 " --> pdb=" O ARG 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 157 removed outlier: 4.887A pdb=" N ILE 5 142 " --> pdb=" O LYS 5 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 removed outlier: 3.749A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 15' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.712A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.484A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG B 212 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.459A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.606A pdb=" N GLY C 66 " --> pdb=" O LYS C 62 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 20 removed outlier: 4.214A pdb=" N PHE D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.997A pdb=" N VAL D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY D 38 " --> pdb=" O ALA D 34 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ALA D 39 " --> pdb=" O TYR D 35 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 4.239A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU D 111 " --> pdb=" O SER D 107 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 4.054A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 162 removed outlier: 4.120A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA D 161 " --> pdb=" O LEU D 157 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 4.671A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 4.777A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N MET D 199 " --> pdb=" O GLN D 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 3.603A pdb=" N LYS E 9 " --> pdb=" O HIS E 5 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LYS E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N PHE E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ASN E 21 " --> pdb=" O MET E 17 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.965A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LEU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ILE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER E 61 " --> pdb=" O LEU E 57 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.708A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 172 removed outlier: 3.954A pdb=" N ARG E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N ALA E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N LEU E 169 " --> pdb=" O GLU E 165 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LEU E 170 " --> pdb=" O GLY E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.652A pdb=" N GLN E 27 " --> pdb=" O SER E 24 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N VAL E 28 " --> pdb=" O VAL E 25 " (cutoff:3.500A) Proline residue: E 29 - end of helix No H-bonds generated for 'chain 'E' and resid 24 through 29' Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.518A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.666A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA F 65 " --> pdb=" O GLY F 61 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLY F 66 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL F 76 " --> pdb=" O LEU F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 151 removed outlier: 3.634A pdb=" N GLN F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA F 145 " --> pdb=" O ILE F 141 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 29 removed outlier: 4.138A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 51 removed outlier: 4.265A pdb=" N ALA G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 74 removed outlier: 5.461A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 4.271A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ALA G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N GLY G 107 " --> pdb=" O VAL G 103 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 116 removed outlier: 3.737A pdb=" N VAL G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ARG G 116 " --> pdb=" O LYS G 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 111 through 116' Processing helix chain 'H' and resid 3 through 21 removed outlier: 4.183A pdb=" N GLN H 9 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N GLY H 21 " --> pdb=" O GLU H 17 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 49 removed outlier: 3.831A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLU H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N LYS H 43 " --> pdb=" O THR H 39 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLY H 49 " --> pdb=" O GLY H 45 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 66 removed outlier: 4.407A pdb=" N ALA H 63 " --> pdb=" O LEU H 59 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N VAL H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N GLU H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLY H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 59 through 66' Processing helix chain 'H' and resid 93 through 106 removed outlier: 4.672A pdb=" N LYS H 97 " --> pdb=" O ALA H 93 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 71 through 76 removed outlier: 3.761A pdb=" N ASP H 74 " --> pdb=" O CYS H 71 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N ALA H 75 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N PHE H 76 " --> pdb=" O LYS H 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 71 through 76' Processing helix chain 'I' and resid 33 through 49 removed outlier: 3.595A pdb=" N LYS I 39 " --> pdb=" O MET I 35 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA I 43 " --> pdb=" O LYS I 39 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N SER I 47 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE I 48 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N GLU I 49 " --> pdb=" O THR I 45 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.642A pdb=" N LEU I 79 " --> pdb=" O ALA I 75 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 113 removed outlier: 4.742A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 3.831A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 12 removed outlier: 3.556A pdb=" N VAL J 11 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N LYS J 12 " --> pdb=" O PRO J 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 7 through 12' Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.034A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU J 36 " --> pdb=" O LEU J 32 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.782A pdb=" N LYS J 72 " --> pdb=" O LYS J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.767A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.163A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 4.510A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA K 119 " --> pdb=" O ILE K 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 112 through 119' Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.775A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 74 removed outlier: 4.969A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.067A pdb=" N LEU L 95 " --> pdb=" O ASP L 91 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.658A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ILE L 135 " --> pdb=" O ALA L 131 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 84 removed outlier: 3.726A pdb=" N LEU L 82 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N ALA L 83 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 5.886A pdb=" N LYS L 84 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 84' Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.137A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 125 removed outlier: 4.357A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 4.621A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N PHE N 21 " --> pdb=" O ARG N 17 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N VAL N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.686A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.529A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 4.663A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG N 64 " --> pdb=" O VAL N 60 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE N 67 " --> pdb=" O ARG N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.584A pdb=" N ALA N 77 " --> pdb=" O ASN N 73 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 4.043A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 22 removed outlier: 4.572A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ILE O 8 " --> pdb=" O LYS O 4 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG O 16 " --> pdb=" O THR O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.771A pdb=" N ALA O 59 " --> pdb=" O GLU O 55 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.823A pdb=" N ALA O 72 " --> pdb=" O LYS O 68 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG O 81 " --> pdb=" O ALA O 77 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 4.191A pdb=" N ASP O 108 " --> pdb=" O GLN O 104 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA O 110 " --> pdb=" O LEU O 106 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N ARG O 111 " --> pdb=" O ALA O 107 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.844A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LEU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 5.458A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 4.013A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LYS Q 15 " --> pdb=" O ARG Q 11 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 5.028A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 40 through 72 removed outlier: 3.907A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ILE Q 62 " --> pdb=" O ARG Q 58 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA Q 63 " --> pdb=" O GLN Q 59 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE Q 65 " --> pdb=" O TRP Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.908A pdb=" N PHE Q 79 " --> pdb=" O SER Q 75 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASN Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.745A pdb=" N ALA Q 99 " --> pdb=" O LEU Q 95 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N PHE Q 101 " --> pdb=" O ASP Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.860A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 5.698A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ALA S 21 " --> pdb=" O VAL S 17 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ASP S 22 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 4.142A pdb=" N LEU S 33 " --> pdb=" O VAL S 29 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.710A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE S 55 " --> pdb=" O LEU S 51 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN S 57 " --> pdb=" O SER S 53 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N HIS S 60 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ASN S 61 " --> pdb=" O ASN S 57 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 5.023A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 3.903A pdb=" N THR T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA T 23 " --> pdb=" O LYS T 19 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 3.717A pdb=" N LYS T 44 " --> pdb=" O LYS T 40 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.877A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 14 through 24 removed outlier: 3.677A pdb=" N ARG V 19 " --> pdb=" O GLY V 15 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.854A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.417A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 removed outlier: 3.828A pdb=" N MET X 56 " --> pdb=" O SER X 52 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ASP X 60 " --> pdb=" O MET X 56 " (cutoff:3.500A) Processing helix chain 'X' and resid 64 through 75 removed outlier: 3.631A pdb=" N ALA X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 3 through 9 removed outlier: 4.469A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 35 removed outlier: 4.027A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG Y 23 " --> pdb=" O LEU Y 19 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 60 removed outlier: 3.549A pdb=" N ARG Y 48 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N LEU Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N GLU Y 59 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 4.148A pdb=" N ALA Z 22 " --> pdb=" O PRO Z 18 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N THR Z 23 " --> pdb=" O LYS Z 19 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LEU Z 24 " --> pdb=" O HIS Z 20 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LEU Z 25 " --> pdb=" O LYS Z 21 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY Z 26 " --> pdb=" O ALA Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.587A pdb=" N ARG Z 45 " --> pdb=" O THR Z 41 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 46 removed outlier: 4.359A pdb=" N THR a 45 " --> pdb=" O HIS a 41 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY a 46 " --> pdb=" O PRO a 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 41 through 46' Processing helix chain 'a' and resid 55 through 64 removed outlier: 4.274A pdb=" N ARG a 63 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) Processing helix chain 'a' and resid 47 through 52 removed outlier: 4.486A pdb=" N ASP a 50 " --> pdb=" O LYS a 47 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL a 51 " --> pdb=" O GLN a 48 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ALA a 52 " --> pdb=" O ARG a 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 47 through 52' Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.120A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 4.019A pdb=" N ARG d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.341A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 removed outlier: 4.000A pdb=" N VAL d 30 " --> pdb=" O ASN d 26 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.704A pdb=" N PHE e 14 " --> pdb=" O ALA e 10 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 4.060A pdb=" N LYS e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG e 45 " --> pdb=" O LYS e 41 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 54 through 63 removed outlier: 3.692A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 4.508A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.822A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 4.518A pdb=" N LEU g 54 " --> pdb=" O PHE g 50 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS g 59 " --> pdb=" O ALA g 55 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ALA g 61 " --> pdb=" O LEU g 57 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N SER g 62 " --> pdb=" O ASN g 58 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.262A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 7.043A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA g 84 " --> pdb=" O VAL g 80 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N LEU g 85 " --> pdb=" O LYS g 81 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N SER g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 5.673A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N LEU g 114 " --> pdb=" O SER g 110 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N LYS g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N ASP g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.734A pdb=" N ALA g 134 " --> pdb=" O THR g 130 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU g 135 " --> pdb=" O LYS g 131 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN g 146 " --> pdb=" O GLU g 142 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 149 through 155 removed outlier: 7.003A pdb=" N ASP g 153 " --> pdb=" O GLY g 149 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N MET g 154 " --> pdb=" O GLY g 150 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY g 155 " --> pdb=" O ILE g 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 149 through 155' Processing helix chain 'g' and resid 169 through 180 removed outlier: 3.707A pdb=" N ILE g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ASN g 177 " --> pdb=" O ILE g 173 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ASN g 178 " --> pdb=" O LYS g 174 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.660A pdb=" N LEU g 212 " --> pdb=" O ARG g 208 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR g 213 " --> pdb=" O ALA g 209 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA g 216 " --> pdb=" O LEU g 212 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.637A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 6 through 12' Processing helix chain 'h' and resid 26 through 48 removed outlier: 4.125A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASP h 34 " --> pdb=" O ALA h 30 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N PHE h 37 " --> pdb=" O LEU h 33 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL h 39 " --> pdb=" O SER h 35 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR h 42 " --> pdb=" O LYS h 38 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 82 through 96 removed outlier: 4.289A pdb=" N LYS h 89 " --> pdb=" O GLU h 85 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP h 93 " --> pdb=" O LYS h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.207A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 removed outlier: 3.570A pdb=" N GLU h 125 " --> pdb=" O THR h 121 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.728A pdb=" N LYS h 135 " --> pdb=" O ARG h 131 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU h 144 " --> pdb=" O ASN h 140 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.344A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 4.142A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N CYS i 32 " --> pdb=" O ILE i 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 27 through 32' Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.635A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU i 57 " --> pdb=" O VAL i 53 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LYS i 60 " --> pdb=" O ARG i 56 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N TYR i 65 " --> pdb=" O VAL i 61 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.574A pdb=" N ASN i 74 " --> pdb=" O ARG i 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA i 79 " --> pdb=" O TYR i 75 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 4.217A pdb=" N ASN i 89 " --> pdb=" O ASN i 85 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ALA i 92 " --> pdb=" O GLU i 88 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N LEU i 93 " --> pdb=" O ASN i 89 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU i 94 " --> pdb=" O LEU i 90 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU i 95 " --> pdb=" O LEU i 91 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 4.754A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET i 105 " --> pdb=" O VAL i 101 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.753A pdb=" N ALA i 114 " --> pdb=" O THR i 110 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ARG i 115 " --> pdb=" O ARG i 111 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.621A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.958A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.329A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 197 through 206 removed outlier: 4.411A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LEU i 203 " --> pdb=" O LEU i 199 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR i 204 " --> pdb=" O ILE i 200 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.581A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.828A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ALA j 118 " --> pdb=" O VAL j 114 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.771A pdb=" N VAL j 136 " --> pdb=" O ASN j 132 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ILE j 141 " --> pdb=" O VAL j 137 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU j 144 " --> pdb=" O THR j 140 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ASN j 146 " --> pdb=" O ASP j 142 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 removed outlier: 4.257A pdb=" N ALA j 154 " --> pdb=" O PRO j 150 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA j 155 " --> pdb=" O GLU j 151 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG j 157 " --> pdb=" O VAL j 153 " (cutoff:3.500A) Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 17 through 33 removed outlier: 4.682A pdb=" N ALA k 27 " --> pdb=" O GLU k 23 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA k 28 " --> pdb=" O ARG k 24 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 4.001A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP k 72 " --> pdb=" O GLN k 68 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU k 75 " --> pdb=" O ILE k 71 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N THR k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N THR k 77 " --> pdb=" O GLU k 73 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE k 78 " --> pdb=" O LEU k 74 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 4.215A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N LYS l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N PHE l 26 " --> pdb=" O LEU l 22 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU l 30 " --> pdb=" O PHE l 26 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N MET l 31 " --> pdb=" O VAL l 27 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.836A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL l 43 " --> pdb=" O ALA l 39 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR l 44 " --> pdb=" O GLU l 40 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N GLU l 48 " --> pdb=" O TYR l 44 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ALA l 51 " --> pdb=" O LEU l 47 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY l 55 " --> pdb=" O ALA l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 4.665A pdb=" N PHE l 62 " --> pdb=" O GLU l 58 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 4.170A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG l 102 " --> pdb=" O ALA l 98 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE l 104 " --> pdb=" O ALA l 100 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL l 105 " --> pdb=" O MET l 101 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG l 109 " --> pdb=" O VAL l 105 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.615A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA l 127 " --> pdb=" O GLU l 123 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.718A pdb=" N LYS l 137 " --> pdb=" O THR l 133 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ALA l 145 " --> pdb=" O VAL l 141 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 4.453A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N THR m 12 " --> pdb=" O ALA m 8 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ALA m 20 " --> pdb=" O ASN m 16 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ASN m 21 " --> pdb=" O GLY m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 4.275A pdb=" N VAL m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ALA m 35 " --> pdb=" O LYS m 31 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N ALA m 37 " --> pdb=" O LYS m 33 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL m 39 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LYS m 41 " --> pdb=" O ALA m 37 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLU m 42 " --> pdb=" O ASN m 38 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 removed outlier: 4.524A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N GLY m 120 " --> pdb=" O ALA m 116 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 40 removed outlier: 3.604A pdb=" N TYR n 38 " --> pdb=" O SER n 34 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 34 through 40' Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.730A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.673A pdb=" N VAL n 55 " --> pdb=" O PRO n 51 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 removed outlier: 3.913A pdb=" N ALA n 76 " --> pdb=" O ILE n 72 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE n 79 " --> pdb=" O GLN n 75 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N MET n 88 " --> pdb=" O THR n 84 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLU n 89 " --> pdb=" O ARG n 85 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR n 90 " --> pdb=" O ALA n 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 92 through 102 removed outlier: 5.019A pdb=" N SER n 96 " --> pdb=" O GLU n 92 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 4.668A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ALA o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE o 25 " --> pdb=" O ALA o 21 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ARG o 31 " --> pdb=" O GLU o 27 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.624A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.981A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 59 through 75 removed outlier: 3.560A pdb=" N ALA p 63 " --> pdb=" O THR p 59 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLN p 64 " --> pdb=" O PRO p 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA p 66 " --> pdb=" O ALA p 62 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLU p 68 " --> pdb=" O GLN p 64 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG p 69 " --> pdb=" O VAL p 65 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA p 71 " --> pdb=" O ALA p 67 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 4.110A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN p 101 " --> pdb=" O ILE p 97 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 4.172A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.923A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 4.661A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N LEU r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N GLY r 38 " --> pdb=" O LEU r 34 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 63 removed outlier: 4.162A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP r 58 " --> pdb=" O ASP r 54 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA r 61 " --> pdb=" O ARG r 57 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.665A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LYS r 78 " --> pdb=" O SER r 74 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU r 83 " --> pdb=" O ARG r 79 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY r 84 " --> pdb=" O LEU r 80 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.642A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 22 removed outlier: 4.288A pdb=" N LYS s 7 " --> pdb=" O LYS s 3 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA s 8 " --> pdb=" O GLN s 4 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA s 15 " --> pdb=" O VAL s 11 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU s 16 " --> pdb=" O LYS s 12 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ALA s 22 " --> pdb=" O ASP s 18 " (cutoff:3.500A) Processing helix chain 's' and resid 23 through 33 removed outlier: 4.925A pdb=" N LYS s 28 " --> pdb=" O ARG s 24 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 4.604A pdb=" N TRP s 42 " --> pdb=" O ASP s 38 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ASN s 43 " --> pdb=" O GLU s 39 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL s 45 " --> pdb=" O ARG s 41 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU s 46 " --> pdb=" O TRP s 42 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.641A pdb=" N VAL s 84 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ALA s 87 " --> pdb=" O LYS s 83 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 3.842A pdb=" N LYS t 10 " --> pdb=" O GLU t 6 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N ILE t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N SER t 13 " --> pdb=" O ALA t 9 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 44 removed outlier: 4.354A pdb=" N LEU t 32 " --> pdb=" O GLN t 28 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLN t 35 " --> pdb=" O LEU t 31 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N HIS t 38 " --> pdb=" O ALA t 34 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N PHE t 43 " --> pdb=" O LEU t 39 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA t 44 " --> pdb=" O GLN t 40 " (cutoff:3.500A) Processing helix chain 't' and resid 50 through 74 removed outlier: 5.235A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU t 56 " --> pdb=" O SER t 52 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LYS t 65 " --> pdb=" O SER t 61 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LEU t 70 " --> pdb=" O LEU t 66 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ARG t 72 " --> pdb=" O ASP t 68 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.919A pdb=" N THR t 79 " --> pdb=" O VAL t 75 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 4.101A pdb=" N ALA u 58 " --> pdb=" O LEU u 54 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N VAL u 61 " --> pdb=" O ILE u 57 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN u 63 " --> pdb=" O HIS u 59 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY u 64 " --> pdb=" O TRP u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 81 removed outlier: 3.920A pdb=" N LYS u 80 " --> pdb=" O LYS u 76 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.941A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.550A pdb=" N LEU w 29 " --> pdb=" O ASP w 25 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 5.154A pdb=" N ARG w 53 " --> pdb=" O ALA w 49 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS w 60 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ALA w 62 " --> pdb=" O ALA w 58 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N TYR w 64 " --> pdb=" O LYS w 60 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 4.124A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 71 through 76 removed outlier: 4.520A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 71 through 76' Processing helix chain 'y' and resid 4 through 42 removed outlier: 4.060A pdb=" N ARG y 10 " --> pdb=" O SER y 6 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N SER y 14 " --> pdb=" O ARG y 10 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS y 16 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA y 17 " --> pdb=" O GLN y 13 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N HIS y 20 " --> pdb=" O LYS y 16 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N ARG y 25 " --> pdb=" O ASN y 21 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N MET y 28 " --> pdb=" O ARG y 24 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE y 39 " --> pdb=" O VAL y 35 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU y 40 " --> pdb=" O TYR y 36 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY y 42 " --> pdb=" O ALA y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.881A pdb=" N GLN y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LYS y 49 " --> pdb=" O ALA y 45 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA y 50 " --> pdb=" O ALA y 46 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 4.748A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 86 removed outlier: 3.821A pdb=" N HIS y 75 " --> pdb=" O LYS y 71 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N LYS y 76 " --> pdb=" O ALA y 72 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ALA y 77 " --> pdb=" O ALA y 73 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR y 80 " --> pdb=" O LYS y 76 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA y 81 " --> pdb=" O ALA y 77 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 4.360A pdb=" N PHE z 19 " --> pdb=" O ALA z 15 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ALA z 26 " --> pdb=" O SER z 22 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 4.017A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N GLU z 36 " --> pdb=" O VAL z 32 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.800A pdb=" N ARG z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ALA z 52 " --> pdb=" O ALA z 48 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS z 54 " --> pdb=" O ALA z 50 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N ARG z 55 " --> pdb=" O SER z 51 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 27 through 33 removed outlier: 3.881A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ILE 5 127 " --> pdb=" O PHE 5 30 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '5' and resid 63 through 66 removed outlier: 6.184A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 90 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG 5 88 " --> pdb=" O LEU 5 65 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '5' and resid 115 through 119 removed outlier: 4.323A pdb=" N SER 5 115 " --> pdb=" O LYS 5 126 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS 5 126 " --> pdb=" O SER 5 115 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 33 through 36 removed outlier: 7.030A pdb=" N LEU B 33 " --> pdb=" O ILE B 64 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 35 " --> pdb=" O TYR B 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR B 62 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 100 through 105 removed outlier: 4.789A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.724A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE B 164 " --> pdb=" O SER B 139 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 171 through 176 removed outlier: 3.797A pdb=" N ARG B 182 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 3 through 7 removed outlier: 7.948A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.570A pdb=" N THR C 16 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N LEU C 186 " --> pdb=" O ASP C 181 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 36 through 39 removed outlier: 3.871A pdb=" N LYS C 38 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 47 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N THR C 52 " --> pdb=" O GLY C 78 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N GLY C 78 " --> pdb=" O THR C 52 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ALA C 54 " --> pdb=" O GLY C 76 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N GLY C 76 " --> pdb=" O ALA C 54 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 118 through 121 removed outlier: 4.328A pdb=" N GLY C 163 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR C 121 " --> pdb=" O MET C 161 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N MET C 161 " --> pdb=" O THR C 121 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 2 through 6 removed outlier: 4.617A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.812A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N ILE D 149 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASP D 168 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 86 through 92 removed outlier: 3.755A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL E 132 " --> pdb=" O LEU E 152 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE E 156 " --> pdb=" O TYR E 128 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 16, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.532A pdb=" N GLY F 53 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LYS F 44 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 95 through 98 removed outlier: 4.337A pdb=" N ARG F 95 " --> pdb=" O SER F 106 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 121 through 125 removed outlier: 4.070A pdb=" N THR F 122 " --> pdb=" O LYS F 134 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 2 through 5 removed outlier: 5.177A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA G 39 " --> pdb=" O GLN G 2 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 76 through 82 removed outlier: 5.866A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N VAL G 147 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL G 142 " --> pdb=" O VAL G 130 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 23 through 26 removed outlier: 7.471A pdb=" N LEU H 23 " --> pdb=" O MET H 86 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N MET H 86 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA H 25 " --> pdb=" O TYR H 84 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.051A pdb=" N TYR J 53 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 74 through 77 removed outlier: 3.550A pdb=" N ALA J 87 " --> pdb=" O TYR J 74 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N HIS J 76 " --> pdb=" O LYS J 85 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 17 through 21 removed outlier: 5.946A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.975A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.875A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 75 through 78 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 75 through 78 current: chain 'L' and resid 108 through 111 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.766A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 4.277A pdb=" N LYS M 62 " --> pdb=" O ASP M 106 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 36 removed outlier: 4.171A pdb=" N ALA N 108 " --> pdb=" O ARG N 103 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N MET N 110 " --> pdb=" O GLY N 101 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLY N 101 " --> pdb=" O MET N 110 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.539A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL O 39 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N HIS O 34 " --> pdb=" O THR O 31 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR O 31 " --> pdb=" O HIS O 34 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N TYR O 36 " --> pdb=" O HIS O 29 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.691A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 53 removed outlier: 4.153A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N PHE P 59 " --> pdb=" O PHE P 74 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 34, first strand: chain 'R' and resid 19 through 23 removed outlier: 6.521A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS R 97 " --> pdb=" O VAL R 63 " (cutoff:3.500A) removed outlier: 5.534A pdb=" N VAL R 63 " --> pdb=" O LYS R 97 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N THR R 99 " --> pdb=" O ALA R 61 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N ALA R 61 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE R 59 " --> pdb=" O PHE R 35 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 57 through 60 removed outlier: 6.426A pdb=" N ALA R 103 " --> pdb=" O GLY R 57 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ILE R 59 " --> pdb=" O ILE R 101 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE R 101 " --> pdb=" O ILE R 59 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.748A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 74 through 85 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'T' and resid 28 through 33 removed outlier: 5.812A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 10 through 13 removed outlier: 4.334A pdb=" N LYS U 21 " --> pdb=" O VAL U 13 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.149A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 42, first strand: chain 'V' and resid 2 through 5 removed outlier: 5.084A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR V 62 " --> pdb=" O PHE V 2 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 37 through 43 removed outlier: 3.886A pdb=" N ILE V 40 " --> pdb=" O ALA V 28 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 50 through 54 removed outlier: 8.962A pdb=" N ASN W 50 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.689A pdb=" N VAL X 13 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Z' and resid 6 through 10 removed outlier: 3.913A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'a' and resid 11 through 15 removed outlier: 3.649A pdb=" N MET a 22 " --> pdb=" O ALA a 14 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 19 through 24 removed outlier: 5.891A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU c 36 " --> pdb=" O TYR c 49 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'f' and resid 14 through 19 removed outlier: 3.522A pdb=" N ILE f 26 " --> pdb=" O LYS f 15 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN f 37 " --> pdb=" O ILE f 23 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N VAL f 25 " --> pdb=" O GLN f 35 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.844A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 89 through 92 Processing sheet with id= 52, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.595A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 58 " --> pdb=" O ARG h 65 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE h 64 " --> pdb=" O PRO h 98 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN h 100 " --> pdb=" O ILE h 64 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE h 68 " --> pdb=" O ASN h 102 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.934A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA h 189 " --> pdb=" O ILE h 196 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS h 204 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 171 through 175 removed outlier: 3.651A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.759A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.674A pdb=" N ARG j 93 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 32 through 40 removed outlier: 3.721A pdb=" N ALA j 35 " --> pdb=" O GLY j 51 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLY j 51 " --> pdb=" O ALA j 35 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 38 through 43 removed outlier: 5.636A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR k 92 " --> pdb=" O HIS k 3 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 44 through 47 removed outlier: 7.808A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 73 through 79 removed outlier: 5.894A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.429A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N VAL m 25 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLU m 60 " --> pdb=" O LYS m 50 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR m 62 " --> pdb=" O ASP m 48 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 74 through 77 removed outlier: 4.668A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.645A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS n 68 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'o' and resid 35 through 38 removed outlier: 8.164A pdb=" N GLN o 35 " --> pdb=" O VAL o 77 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP o 75 " --> pdb=" O ARG o 37 " (cutoff:3.500A) removed outlier: 7.335A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG o 9 " --> pdb=" O GLN o 99 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLN o 99 " --> pdb=" O ARG o 9 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 42 through 52 removed outlier: 4.346A pdb=" N LEU o 71 " --> pdb=" O PRO o 43 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ARG o 45 " --> pdb=" O THR o 69 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'p' and resid 29 through 36 removed outlier: 3.577A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N SER p 26 " --> pdb=" O ASN p 29 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ILE p 23 " --> pdb=" O MET p 85 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS p 87 " --> pdb=" O ILE p 23 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 29 through 33 removed outlier: 5.397A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 36 through 41 removed outlier: 3.682A pdb=" N ARG q 36 " --> pdb=" O ARG q 54 " (cutoff:3.500A) removed outlier: 4.997A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE q 67 " --> pdb=" O LYS q 51 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.364A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.984A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 20 through 31 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'x' and resid 30 through 33 removed outlier: 3.708A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) 1422 hydrogen bonds defined for protein. 4227 hydrogen bond angles defined for protein. NA hbond rejected: pdb=" O2 C 2 386 " pdb=" N2 G 2 378 " distance=3.54 NA hbond rejected: pdb=" O2 C 12540 " pdb=" N2 G 12524 " distance=3.92 NA hbond rejected: pdb=" N4 C 11007 " pdb=" O6 G 11137 " distance=3.50 NA hbond rejected: pdb=" N4 C 4 5 " pdb=" O6 G 4 355 " distance=3.52 NA hbond rejected: pdb=" O2 C 2 582 " pdb=" N2 G 2 760 " distance=3.85 NA hbond rejected: pdb=" N4 C 12427 " pdb=" O6 G 12282 " distance=3.45 NA hbond rejected: pdb=" O2 C 1 69 " pdb=" N2 G 1 58 " distance=3.60 NA hbond rejected: pdb=" O2 C 12403 " pdb=" N2 G 12415 " distance=3.47 NA hbond rejected: pdb=" O2 C 2 580 " pdb=" N2 G 2 761 " distance=3.56 NA hbond rejected: pdb=" O2 C 4 109 " pdb=" N2 G 4 136 " distance=3.75 NA hbond rejected: pdb=" N4 C 2 613 " pdb=" O6 G 2 628 " distance=3.65 NA hbond rejected: pdb=" O2 C 2 207 " pdb=" N2 G 2 213 " distance=3.86 NA hbond rejected: pdb=" N4 C 12045 " pdb=" O6 G 12624 " distance=3.58 NA hbond rejected: pdb=" O2 C 2 866 " pdb=" N2 G 2 570 " distance=4.29 Restraints generated for nucleic acids: 2057 hydrogen bonds 3332 hydrogen bond angles 0 basepair planarities 807 basepair parallelities 2097 stacking parallelities Total time for adding SS restraints: 198.08 Time building geometry restraints manager: 60.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.65: 169505 1.65 - 2.15: 291 2.15 - 2.65: 0 2.65 - 3.15: 0 3.15 - 3.64: 1 Bond restraints: 169797 Sorted by residual: bond pdb=" P G 1 388 " pdb=" O5' G 1 388 " ideal model delta sigma weight residual 1.593 3.645 -2.052 2.00e-02 2.50e+03 1.05e+04 bond pdb=" N9 A 8 77 " pdb=" C4 A 8 77 " ideal model delta sigma weight residual 1.374 2.058 -0.684 2.00e-02 2.50e+03 1.17e+03 bond pdb=" N9 A 8 77 " pdb=" C8 A 8 77 " ideal model delta sigma weight residual 1.373 2.054 -0.681 2.00e-02 2.50e+03 1.16e+03 bond pdb=" C8 A 8 77 " pdb=" N7 A 8 77 " ideal model delta sigma weight residual 1.311 1.961 -0.650 2.00e-02 2.50e+03 1.06e+03 bond pdb=" N7 A 8 77 " pdb=" C5 A 8 77 " ideal model delta sigma weight residual 1.388 2.025 -0.637 2.00e-02 2.50e+03 1.01e+03 ... (remaining 169792 not shown) Histogram of bond angle deviations from ideal: 62.15 - 81.08: 1 81.08 - 100.01: 95 100.01 - 118.94: 169995 118.94 - 137.87: 84165 137.87 - 156.80: 5 Bond angle restraints: 254261 Sorted by residual: angle pdb=" O3' G 7 72 " pdb=" P C 7 73 " pdb=" OP1 C 7 73 " ideal model delta sigma weight residual 108.00 62.15 45.85 3.00e+00 1.11e-01 2.34e+02 angle pdb=" P G 1 388 " pdb=" O5' G 1 388 " pdb=" C5' G 1 388 " ideal model delta sigma weight residual 120.90 156.80 -35.90 3.00e+00 1.11e-01 1.43e+02 angle pdb=" O4' 1MG 1 745 " pdb=" C1' 1MG 1 745 " pdb=" N9 1MG 1 745 " ideal model delta sigma weight residual 108.50 124.55 -16.05 1.50e+00 4.44e-01 1.15e+02 angle pdb=" O3' C 4 48 " pdb=" P C 4 49 " pdb=" O5' C 4 49 " ideal model delta sigma weight residual 104.00 119.23 -15.23 1.50e+00 4.44e-01 1.03e+02 angle pdb=" C1' 6MZ 11618 " pdb=" N9 6MZ 11618 " pdb=" C4 6MZ 11618 " ideal model delta sigma weight residual 100.91 130.79 -29.88 3.00e+00 1.11e-01 9.92e+01 ... (remaining 254256 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.64: 84507 35.64 - 71.28: 5428 71.28 - 106.93: 434 106.93 - 142.57: 52 142.57 - 178.21: 70 Dihedral angle restraints: 90491 sinusoidal: 73037 harmonic: 17454 Sorted by residual: dihedral pdb=" C5* PSU 2 516 " pdb=" C4* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" O3* PSU 2 516 " ideal model delta sinusoidal sigma weight residual 82.00 -88.63 170.63 1 8.00e+00 1.56e-02 2.98e+02 dihedral pdb=" C5* PSU 12605 " pdb=" C4* PSU 12605 " pdb=" C3* PSU 12605 " pdb=" O3* PSU 12605 " ideal model delta sinusoidal sigma weight residual 82.00 -86.13 168.13 1 8.00e+00 1.56e-02 2.97e+02 dihedral pdb=" C5* PSU 12504 " pdb=" C4* PSU 12504 " pdb=" C3* PSU 12504 " pdb=" O3* PSU 12504 " ideal model delta sinusoidal sigma weight residual 82.00 -79.84 161.84 1 8.00e+00 1.56e-02 2.93e+02 ... (remaining 90488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.096: 32436 1.096 - 2.193: 3 2.193 - 3.289: 1 3.289 - 4.385: 1 4.385 - 5.481: 30 Chirality restraints: 32471 Sorted by residual: chirality pdb=" C2' 6MZ 12030 " pdb=" C3' 6MZ 12030 " pdb=" O2' 6MZ 12030 " pdb=" C1' 6MZ 12030 " both_signs ideal model delta sigma weight residual False -2.75 2.73 -5.48 2.00e-01 2.50e+01 7.51e+02 chirality pdb=" C2' G7M 12069 " pdb=" C3' G7M 12069 " pdb=" O2' G7M 12069 " pdb=" C1' G7M 12069 " both_signs ideal model delta sigma weight residual False -2.75 2.73 -5.48 2.00e-01 2.50e+01 7.50e+02 chirality pdb=" C3' 6MZ 11618 " pdb=" C4' 6MZ 11618 " pdb=" O3' 6MZ 11618 " pdb=" C2' 6MZ 11618 " both_signs ideal model delta sigma weight residual False -2.74 2.67 -5.42 2.00e-01 2.50e+01 7.33e+02 ... (remaining 32468 not shown) Planarity restraints: 13456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.458 2.00e-02 2.50e+03 6.03e-01 8.17e+03 pdb=" C4' OMC 12498 " 0.228 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.622 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.775 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.582 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.119 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -1.029 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.311 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.715 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " -0.047 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 2MG 21207 " -0.435 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " -0.670 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " 0.600 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " 0.617 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " 0.190 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " -0.962 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " -0.213 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " 0.921 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.007 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 2MG 12445 " -0.458 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.838 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.581 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.503 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.276 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.798 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.198 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.925 2.00e-02 2.50e+03 ... (remaining 13453 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 20 2.04 - 2.75: 28112 2.75 - 3.47: 197857 3.47 - 4.18: 457251 4.18 - 4.90: 643614 Nonbonded interactions: 1326854 Sorted by model distance: nonbonded pdb="MG MG 13235 " pdb="MG MG 13252 " model vdw 1.320 1.420 nonbonded pdb="MG MG 13285 " pdb="MG MG 13286 " model vdw 1.956 1.420 nonbonded pdb=" OP1 A 2 174 " pdb="MG MG 21650 " model vdw 1.998 2.230 nonbonded pdb=" O5' U 2 531 " pdb="MG MG 21613 " model vdw 2.005 2.230 nonbonded pdb=" OP2 G 2 588 " pdb="MG MG 21695 " model vdw 2.008 2.230 ... (remaining 1326849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Set up NCS constraints 0 156609 True True No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 5051 5.49 5 Mg 439 5.21 5 S 160 5.16 5 C 78305 2.51 5 N 29030 2.21 5 O 43622 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 Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set model interpretation parameters: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 22.570 Check model and map are aligned: 0.000 Convert atoms to be neutral: 0.510 Process input model: 523.640 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:1.900 Internal consistency checks: 0.000 Total: 552.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0112 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.011 2.052 169797 Angle : 1.217 45.853 254261 Chirality : 0.164 5.481 32471 Planarity : 0.018 0.603 13456 Dihedral : 18.910 178.211 79224 Min Nonbonded Distance : 1.320 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.09 % Favored : 89.79 % Rotamer Outliers : 0.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.49 % Twisted General : 0.14 % 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: -5.34 (0.08), residues: 6015 helix: -4.01 (0.07), residues: 1761 sheet: -3.01 (0.14), residues: 1056 loop : -3.51 (0.08), residues: 3198 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 19 poor density : 443 time to evaluate : 6.613 Fit side-chains outliers start: 19 outliers final: 4 residues processed: 461 average time/residue: 1.7499 time to fit residues: 817.3895 Evaluate side-chains 265 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 261 time to evaluate : 6.343 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.1918 time to fit residues: 11.8746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 919 optimal weight: 5.9990 chunk 825 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 chunk 281 optimal weight: 30.0000 chunk 556 optimal weight: 8.9990 chunk 440 optimal weight: 0.7980 chunk 853 optimal weight: 3.9990 chunk 330 optimal weight: 20.0000 chunk 519 optimal weight: 1.9990 chunk 635 optimal weight: 0.5980 chunk 988 optimal weight: 7.9990 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 50 ASN B 86 ASN B 90 ASN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN B 239 ASN ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS C 130 GLN C 150 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN F 48 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 43 ASN ** G 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN H 4 ASN H 103 ASN I 29 GLN I 30 GLN I 110 GLN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 35 HIS M 22 GLN N 81 ASN O 104 GLN Q 37 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN R 87 GLN S 60 HIS S 61 ASN T 15 HIS T 28 ASN T 91 GLN U 45 HIS U 66 GLN V 5 ASN V 44 HIS V 75 GLN X 20 HIS X 36 HIS ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN Y 36 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 HIS a 20 ASN c 46 HIS d 16 HIS f 33 HIS f 37 GLN g 39 HIS g 109 GLN h 185 ASN i 126 ASN ** j 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 GLN k 63 ASN l 97 ASN m 18 GLN m 21 ASN n 31 ASN n 75 GLN ** n 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 64 GLN p 22 HIS ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN t 40 GLN t 50 HIS u 29 ASN v 45 HIS x 57 HIS y 61 GLN y 70 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1030 moved from start: 0.5109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.886 169797 Angle : 0.826 40.132 254261 Chirality : 0.042 2.113 32471 Planarity : 0.007 0.124 13456 Dihedral : 18.086 179.981 67257 Min Nonbonded Distance : 1.113 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.45 % Favored : 92.47 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.09), residues: 6017 helix: -2.81 (0.10), residues: 1801 sheet: -2.44 (0.15), residues: 1025 loop : -3.08 (0.09), residues: 3191 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12034 Ramachandran restraints generated. 6017 Oldfield and 0 Emsley and 6017 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12034 Ramachandran restraints generated. 6017 Oldfield and 0 Emsley and 6017 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 25 poor density : 283 time to evaluate : 6.833 Fit side-chains outliers start: 25 outliers final: 12 residues processed: 304 average time/residue: 1.5826 time to fit residues: 492.1037 Evaluate side-chains 231 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 219 time to evaluate : 6.734 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 1.4928 time to fit residues: 25.4755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 549 optimal weight: 3.9990 chunk 306 optimal weight: 20.0000 chunk 823 optimal weight: 50.0000 chunk 673 optimal weight: 8.9990 chunk 272 optimal weight: 30.0000 chunk 990 optimal weight: 3.9990 chunk 1070 optimal weight: 70.0000 chunk 882 optimal weight: 20.0000 chunk 982 optimal weight: 0.7980 chunk 337 optimal weight: 50.0000 chunk 794 optimal weight: 0.6980 overall best weight: 3.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 50 ASN ** 5 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 ASN B 86 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 ASN I 93 ASN J 136 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 59 GLN R 12 HIS R 82 HIS R 87 GLN S 9 HIS T 15 HIS U 40 ASN U 74 ASN U 99 ASN X 20 HIS X 36 HIS Y 20 ASN Y 41 HIS a 41 HIS c 19 HIS d 16 HIS e 26 HIS h 69 HIS ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 120 HIS i 198 HIS j 132 ASN l 68 ASN n 5 GLN ** o 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 64 GLN ** p 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1541 moved from start: 0.8407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.900 169797 Angle : 0.871 39.220 254261 Chirality : 0.044 1.975 32471 Planarity : 0.007 0.128 13456 Dihedral : 18.678 179.864 67257 Min Nonbonded Distance : 1.218 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.90 % Favored : 92.05 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.00 (0.09), residues: 6015 helix: -2.44 (0.11), residues: 1738 sheet: -2.22 (0.15), residues: 959 loop : -2.99 (0.09), residues: 3318 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 18 poor density : 293 time to evaluate : 6.250 Fit side-chains outliers start: 18 outliers final: 4 residues processed: 308 average time/residue: 1.5296 time to fit residues: 481.2421 Evaluate side-chains 227 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 4 poor density : 223 time to evaluate : 6.727 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 1.4180 time to fit residues: 12.8438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 978 optimal weight: 0.0980 chunk 744 optimal weight: 5.9990 chunk 514 optimal weight: 10.0000 chunk 109 optimal weight: 40.0000 chunk 472 optimal weight: 30.0000 chunk 665 optimal weight: 1.9990 chunk 994 optimal weight: 1.9990 chunk 1052 optimal weight: 20.0000 chunk 519 optimal weight: 0.9990 chunk 942 optimal weight: 0.0040 chunk 283 optimal weight: 50.0000 overall best weight: 1.0198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS 5 50 ASN B 60 GLN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 104 GLN L 54 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 29 HIS P 41 GLN Q 37 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN d 16 HIS ** g 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN i 120 HIS n 5 GLN o 20 GLN o 58 ASN o 64 GLN p 22 HIS p 28 ASN p 118 HIS y 13 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1286 moved from start: 0.8667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.905 169797 Angle : 0.591 38.737 254261 Chirality : 0.032 1.991 32471 Planarity : 0.006 0.116 13456 Dihedral : 17.540 179.358 67257 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.17 % Favored : 94.81 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.35 (0.10), residues: 6015 helix: -1.81 (0.11), residues: 1775 sheet: -1.83 (0.16), residues: 982 loop : -2.64 (0.09), residues: 3258 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 282 time to evaluate : 6.764 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 282 average time/residue: 1.5113 time to fit residues: 436.6622 Evaluate side-chains 228 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 228 time to evaluate : 6.654 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 876 optimal weight: 20.0000 chunk 597 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 783 optimal weight: 8.9990 chunk 434 optimal weight: 10.0000 chunk 898 optimal weight: 0.0870 chunk 727 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 537 optimal weight: 0.6980 chunk 944 optimal weight: 6.9990 chunk 265 optimal weight: 90.0000 overall best weight: 3.5562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 21 ASN ** B 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 128 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN H 4 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN h 3 GLN ** h 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 GLN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN l 68 ASN m 16 ASN o 20 GLN v 45 HIS ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1767 moved from start: 1.0844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.005 0.901 169797 Angle : 0.827 39.257 254261 Chirality : 0.042 1.993 32471 Planarity : 0.007 0.119 13456 Dihedral : 18.758 179.849 67257 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 19.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.26 % Favored : 91.72 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % 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: -3.33 (0.10), residues: 6015 helix: -1.79 (0.12), residues: 1753 sheet: -1.79 (0.16), residues: 991 loop : -2.64 (0.09), residues: 3271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 260 time to evaluate : 6.687 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 262 average time/residue: 1.5494 time to fit residues: 416.5561 Evaluate side-chains 227 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 225 time to evaluate : 6.688 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.1709 time to fit residues: 9.5835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 354 optimal weight: 60.0000 chunk 947 optimal weight: 8.9990 chunk 208 optimal weight: 10.0000 chunk 618 optimal weight: 20.0000 chunk 259 optimal weight: 10.0000 chunk 1053 optimal weight: 50.0000 chunk 874 optimal weight: 40.0000 chunk 487 optimal weight: 30.0000 chunk 87 optimal weight: 50.0000 chunk 348 optimal weight: 9.9990 chunk 553 optimal weight: 0.0670 overall best weight: 7.8130 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 GLN B 90 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN H 88 HIS ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 ASN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 6 GLN R 87 GLN V 44 HIS Y 25 GLN ** Z 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 30 HIS ** b 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 ASN j 122 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2264 moved from start: 1.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.007 0.902 169797 Angle : 1.257 39.743 254261 Chirality : 0.059 2.008 32471 Planarity : 0.010 0.144 13456 Dihedral : 20.928 179.534 67257 Min Nonbonded Distance : 1.002 Molprobity Statistics. All-atom Clashscore : 30.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.97 % Favored : 88.94 % Rotamer Outliers : 0.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.99 % Twisted General : 0.49 % 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: -3.79 (0.09), residues: 6015 helix: -2.17 (0.11), residues: 1651 sheet: -1.77 (0.17), residues: 855 loop : -3.01 (0.09), residues: 3509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 12 poor density : 273 time to evaluate : 7.923 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 285 average time/residue: 1.5861 time to fit residues: 462.6796 Evaluate side-chains 235 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 10 poor density : 225 time to evaluate : 6.652 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 1.2418 time to fit residues: 19.6213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 1015 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 chunk 600 optimal weight: 0.2980 chunk 769 optimal weight: 3.9990 chunk 596 optimal weight: 40.0000 chunk 886 optimal weight: 0.0050 chunk 588 optimal weight: 0.7980 chunk 1049 optimal weight: 30.0000 chunk 656 optimal weight: 2.9990 chunk 639 optimal weight: 2.9990 chunk 484 optimal weight: 1.9990 overall best weight: 1.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 79 HIS ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 HIS B 90 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 167 ASN D 92 HIS ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 11 ASN G 119 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 81 ASN T 15 HIS Y 25 GLN Z 49 ASN a 20 ASN e 43 HIS h 140 ASN i 54 GLN i 71 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 89 HIS ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 77 HIS r 91 HIS ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1874 moved from start: 1.3706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.904 169797 Angle : 0.710 38.949 254261 Chirality : 0.038 2.026 32471 Planarity : 0.006 0.118 13456 Dihedral : 19.370 179.860 67257 Min Nonbonded Distance : 1.180 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.68 % Favored : 93.28 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -3.19 (0.10), residues: 6015 helix: -1.55 (0.12), residues: 1688 sheet: -1.65 (0.17), residues: 949 loop : -2.64 (0.09), residues: 3378 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 272 time to evaluate : 6.732 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 273 average time/residue: 1.5609 time to fit residues: 436.8869 Evaluate side-chains 222 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 221 time to evaluate : 6.672 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3247 time to fit residues: 8.5035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 649 optimal weight: 9.9990 chunk 419 optimal weight: 10.0000 chunk 626 optimal weight: 6.9990 chunk 316 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 667 optimal weight: 3.9990 chunk 715 optimal weight: 9.9990 chunk 518 optimal weight: 9.9990 chunk 97 optimal weight: 30.0000 chunk 825 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 50 ASN ** B 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 4 GLN b 6 ASN ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 116 GLN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN l 86 GLN n 126 GLN ** p 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 119 ASN ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN t 38 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2403 moved from start: 1.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.008 0.902 169797 Angle : 1.284 39.901 254261 Chirality : 0.061 1.931 32471 Planarity : 0.010 0.140 13456 Dihedral : 21.157 179.976 67257 Min Nonbonded Distance : 0.990 Molprobity Statistics. All-atom Clashscore : 30.97 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.54 % Favored : 87.22 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.99 % Twisted General : 0.60 % 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: -3.75 (0.09), residues: 6015 helix: -2.03 (0.12), residues: 1662 sheet: -1.75 (0.18), residues: 783 loop : -3.04 (0.09), residues: 3570 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 246 time to evaluate : 7.003 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 249 average time/residue: 1.5338 time to fit residues: 392.8714 Evaluate side-chains 211 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 0 poor density : 211 time to evaluate : 6.806 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.3754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 954 optimal weight: 7.9990 chunk 1005 optimal weight: 0.3980 chunk 917 optimal weight: 0.0870 chunk 978 optimal weight: 4.9990 chunk 588 optimal weight: 2.9990 chunk 426 optimal weight: 10.0000 chunk 768 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 883 optimal weight: 7.9990 chunk 925 optimal weight: 20.0000 chunk 974 optimal weight: 1.9990 overall best weight: 2.0964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS B 53 HIS B 134 ASN ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN E 127 ASN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 54 GLN ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN R 87 GLN U 99 ASN j 135 ASN ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 105 ASN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 55 GLN y 61 GLN ** y 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2054 moved from start: 1.5497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.904 169797 Angle : 0.751 39.141 254261 Chirality : 0.039 2.028 32471 Planarity : 0.006 0.118 13456 Dihedral : 19.873 179.701 67257 Min Nonbonded Distance : 1.135 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.02 % Allowed : 7.08 % Favored : 92.90 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.50 % Twisted General : 0.10 % 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: -3.22 (0.10), residues: 6015 helix: -1.46 (0.12), residues: 1694 sheet: -1.64 (0.17), residues: 892 loop : -2.73 (0.09), residues: 3429 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 2 poor density : 243 time to evaluate : 6.593 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 1.5526 time to fit residues: 389.7888 Evaluate side-chains 218 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 217 time to evaluate : 7.061 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.4692 time to fit residues: 9.2876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 642 optimal weight: 7.9990 chunk 1034 optimal weight: 0.9980 chunk 631 optimal weight: 0.6980 chunk 490 optimal weight: 0.8980 chunk 719 optimal weight: 0.4980 chunk 1084 optimal weight: 20.0000 chunk 998 optimal weight: 1.9990 chunk 863 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 chunk 667 optimal weight: 4.9990 chunk 529 optimal weight: 9.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 HIS ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 135 GLN F 64 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 99 ASN ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 176 HIS ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN n 75 GLN q 5 ASN ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 96 HIS s 49 GLN u 26 ASN y 21 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1765 moved from start: 1.5516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.004 0.903 169797 Angle : 0.628 39.378 254261 Chirality : 0.033 1.994 32471 Planarity : 0.006 0.118 13456 Dihedral : 18.991 179.858 67257 Min Nonbonded Distance : 1.199 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.02 % Allowed : 6.45 % Favored : 93.53 % Rotamer Outliers : 0.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -2.66 (0.10), residues: 6015 helix: -0.92 (0.12), residues: 1728 sheet: -1.41 (0.17), residues: 911 loop : -2.40 (0.10), residues: 3376 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12030 Ramachandran restraints generated. 6015 Oldfield and 0 Emsley and 6015 emsley8k. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 3 poor density : 263 time to evaluate : 6.879 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 266 average time/residue: 1.5584 time to fit residues: 425.2846 Evaluate side-chains 226 residues out of total 4981 (non-ALA, GLY, PRO) need a fit. rotamer outliers: 1 poor density : 225 time to evaluate : 6.674 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.3458 time to fit residues: 8.5488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1089 random chunks: chunk 686 optimal weight: 0.0370 chunk 920 optimal weight: 7.9990 chunk 264 optimal weight: 40.0000 chunk 796 optimal weight: 10.0000 chunk 127 optimal weight: 9.9990 chunk 240 optimal weight: 20.0000 chunk 865 optimal weight: 20.0000 chunk 362 optimal weight: 7.9990 chunk 888 optimal weight: 2.9990 chunk 109 optimal weight: 40.0000 chunk 159 optimal weight: 20.0000 overall best weight: 5.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 49 GLN ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN G 119 ASN K 3 GLN K 9 ASN K 29 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN a 6 HIS ** d 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 99 GLN ** q 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 42 HIS x 56 GLN y 61 GLN ** y 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Group ADP refinement ******************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.316300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 2)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.316300 restraints weight = 0.000 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 2)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.316300 restraints weight = 0.000 | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 2)-----------------| | r_work = 0.5353 r_free = 0.5353 target = 0.316300 restraints weight = 0.000 | |-----------------------------------------------------------------------------| GEOMETRY RESTRAINTS LIBRARY: GEOSTD + MONOMER LIBRARY + CDL V1.2 DEVIATIONS FROM IDEAL VALUES. BOND : 0.006 0.902 169797 ANGLE : 1.028 40.165 254261 CHIRALITY : 0.050 1.960 32471 PLANARITY : 0.008 0.120 13456 DIHEDRAL : 20.347 179.867 67257 MIN NONBONDED DISTANCE : 1.084 MOLPROBITY STATISTICS. ALL-ATOM CLASHSCORE : 24.36 RAMACHANDRAN PLOT: OUTLIERS : 0.08 % ALLOWED : 11.04 % FAVORED : 88.88 % ROTAMER OUTLIERS : 0.00 % CBETA DEVIATIONS : 0.00 % PEPTIDE PLANE: CIS-PROLINE : 1.49 % CIS-GENERAL : 0.00 % TWISTED PROLINE : 1.00 % TWISTED GENERAL : 0.34 % 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: -3.14 (0.10), RESIDUES: 6015 HELIX: -1.39 (0.12), RESIDUES: 1691 SHEET: -1.48 (0.18), RESIDUES: 870 LOOP : -2.72 (0.09), RESIDUES: 3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2308 moved from start: 1.6841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values. Bond : 0.006 0.902 169797 Angle : 1.028 40.165 254261 Chirality : 0.050 1.960 32471 Planarity : 0.008 0.120 13456 Dihedral : 20.347 179.867 67257 Min Nonbonded Distance : 1.084 Molprobity Statistics. All-atom Clashscore : 24.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 11.04 % Favored : 88.88 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.49 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.34 % 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: -3.14 (0.10), residues: 6015 helix: -1.39 (0.12), residues: 1691 sheet: -1.48 (0.18), residues: 870 loop : -2.72 (0.09), residues: 3454 =============================================================================== Job complete usr+sys time: 13524.43 seconds wall clock time: 253 minutes 58.02 seconds (15238.02 seconds total)