Starting phenix.real_space_refine (version: dev) on Mon May 23 01:23:18 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/05_2022/7acr_11718_updated.pdb" } resolution = 3.44 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 151668 Number of models: 1 Model: "" Number of chains: 66 Chain: "1" Number of atoms: 62335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62335 Classifications: {'RNA': 2903} Modifications used: {'rna3p': 16, 'rna2p': 6, 'rna3p_pur': 1366, 'rna3p_pyr': 1050, 'rna2p_pur': 301, 'rna2p_pyr': 164} Link IDs: {'rna3p': 2432, 'rna2p': 470} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 32927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32927 Classifications: {'RNA': 1534} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 748, 'rna3p_pyr': 555, 'rna2p_pur': 121, 'rna2p_pyr': 98} Link IDs: {'rna3p': 1313, 'rna2p': 220} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 49, 'rna2p_pur': 8, 'rna3p_pur': 56, 'rna2p_pyr': 7} Link IDs: {'rna3p': 105, 'rna2p': 14} Chain: "4" Number of atoms: 7755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7755 Classifications: {'RNA': 363} Modifications used: {'5*END': 1, 'rna3p': 3, 'rna2p_pyr': 30, 'rna3p_pur': 160, 'rna3p_pyr': 132, 'rna2p_pur': 38} Link IDs: {'rna3p': 295, 'rna2p': 67} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "5" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Chain: "A" 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: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} 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: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} 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: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} 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: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 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: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} 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: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} 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: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} 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: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} 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: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1658 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} 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: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} 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: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 6, 'TRANS': 114, '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: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} 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: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 553 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} 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: "1" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Unusual residues: {' MG': 172} Classifications: {'undetermined': 172} Link IDs: {None: 171} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Unusual residues: {' MG': 31} Classifications: {'undetermined': 31} Link IDs: {None: 30} Chain: "3" 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: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0N5B SG CYS a 16 126.811 95.456 37.757 1.00237.03 S ATOM A0N9L SG CYS a 37 129.296 97.891 38.776 1.00222.56 S ATOM A0NA6 SG CYS a 40 125.960 99.295 38.959 1.00226.25 S ATOM A0OUZ SG CYS f 11 179.228 183.683 89.100 1.00 99.87 S ATOM A0OVO SG CYS f 14 182.411 182.310 90.622 1.00103.32 S ATOM A0OYJ SG CYS f 27 180.788 185.488 92.084 1.00105.74 S Time building chain proxies: 58.63, per 1000 atoms: 0.39 Number of scatterers: 151668 At special positions: 0 Unit cell: (298.48, 266.24, 245.44, 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 153 16.00 P 4916 15.00 Mg 212 11.99 O 42324 8.00 N 28215 7.00 C 75846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 91769 O5' U 21372 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.39 Conformation dependent library (CDL) restraints added in 5.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10766 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: 170 helices and 73 sheets defined 37.7% alpha, 19.2% beta 1449 base pairs and 2379 stacking pairs defined. Time for finding SS restraints: 60.17 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 4.264A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS 5 22 " --> pdb=" O LYS 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 47 removed outlier: 4.016A pdb=" N VAL 5 41 " --> pdb=" O GLN 5 37 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS 5 42 " --> pdb=" O GLY 5 38 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER 5 43 " --> pdb=" O TRP 5 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG 5 45 " --> pdb=" O VAL 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 103 removed outlier: 3.896A pdb=" N ASP 5 98 " --> pdb=" O GLN 5 94 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER 5 99 " --> pdb=" O ARG 5 95 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU 5 100 " --> pdb=" O GLU 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 160 removed outlier: 6.507A pdb=" N LYS 5 138 " --> pdb=" O LYS 5 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG 5 139 " --> pdb=" O GLN 5 135 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL 5 149 " --> pdb=" O ARG 5 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 removed outlier: 7.265A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.715A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.816A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.870A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.924A 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 Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.316A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.739A pdb=" N PHE D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.612A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.543A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.712A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.891A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 20 removed outlier: 4.090A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.006A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 47' Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 93 through 108 Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.849A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.268A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.990A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.849A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 removed outlier: 3.840A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 22 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 43 through 51 removed outlier: 3.512A pdb=" N PHE G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 63 removed outlier: 3.730A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 5.283A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 74' Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 98 through 107 removed outlier: 3.904A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.409A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 98 through 110 removed outlier: 4.961A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.276A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.781A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.325A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 83 removed outlier: 3.939A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.171A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.331A 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: 3.515A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.888A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.218A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.418A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 5.169A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.052A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 104 removed outlier: 4.727A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.687A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.262A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 72 removed outlier: 3.680A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN Q 59 " --> pdb=" O ARG Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.890A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.704A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.953A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.822A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 removed outlier: 4.130A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.868A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.738A 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 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.236A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.262A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 8 removed outlier: 4.107A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.804A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.830A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.867A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.045A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 15 removed outlier: 3.885A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE e 14 " --> pdb=" O ALA e 10 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS e 15 " --> pdb=" O ALA e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.536A 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 51 through 63 removed outlier: 4.030A pdb=" N LEU e 55 " --> pdb=" O SER e 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 4.423A 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 Processing helix chain 'g' and resid 27 through 32 removed outlier: 4.467A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 5.468A 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: 3.512A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 removed outlier: 3.740A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 124 removed outlier: 4.644A pdb=" N GLU g 118 " --> pdb=" O LEU g 114 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY g 124 " --> pdb=" O GLN g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 130 removed outlier: 4.717A pdb=" N LEU g 129 " --> pdb=" O THR g 125 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 125 through 130' Processing helix chain 'g' and resid 131 through 149 removed outlier: 3.509A pdb=" N LEU g 144 " --> pdb=" O GLU g 140 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 4.993A pdb=" N GLN g 227 " --> pdb=" O GLU g 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.802A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.299A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 5.295A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 5.342A pdb=" N SER h 119 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER h 122 " --> pdb=" O ASP h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.966A pdb=" N LEU h 144 " --> pdb=" O ASN h 140 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.764A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.001A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.888A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.502A pdb=" N GLN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 152 removed outlier: 4.157A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN i 152 " --> pdb=" O LYS i 148 " (cutoff:3.500A) Processing helix chain 'i' and resid 153 through 166 removed outlier: 3.829A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.581A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.770A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR i 204 " --> pdb=" O ILE i 200 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.578A pdb=" N GLU j 65 " --> pdb=" O GLN j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 119 removed outlier: 3.639A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.861A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.717A pdb=" N LEU j 165 " --> pdb=" O VAL j 161 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 33 removed outlier: 4.988A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix Processing helix chain 'k' and resid 67 through 81 Processing helix chain 'l' and resid 20 through 32 removed outlier: 6.116A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.569A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 Processing helix chain 'l' and resid 92 through 112 removed outlier: 5.071A pdb=" N GLY l 112 " --> pdb=" O ALA l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 4.429A pdb=" N GLU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 5.080A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET l 144 " --> pdb=" O ASP l 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.542A pdb=" N MET n 46 " --> pdb=" O GLU n 42 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.677A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 92 removed outlier: 4.811A pdb=" N GLY n 77 " --> pdb=" O SER n 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE n 79 " --> pdb=" O GLN n 75 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG n 80 " --> pdb=" O ALA n 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.515A pdb=" N GLY n 102 " --> pdb=" O LEU n 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.604A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 90 removed outlier: 3.891A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.139A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.598A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 76 removed outlier: 3.603A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 4.559A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 4.140A 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: 3.876A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.539A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.707A pdb=" N SER r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.667A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP r 54 " --> pdb=" O GLU r 50 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA r 61 " --> pdb=" O ARG r 57 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 84 Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.922A pdb=" N ARG r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 removed outlier: 4.102A pdb=" N GLY r 111 " --> pdb=" O ARG r 107 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 21 removed outlier: 3.629A pdb=" N ALA s 8 " --> pdb=" O GLN s 4 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG s 9 " --> pdb=" O SER s 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU s 10 " --> pdb=" O MET s 6 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL s 11 " --> pdb=" O LYS s 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA s 17 " --> pdb=" O ARG s 13 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS s 19 " --> pdb=" O ALA s 15 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR s 20 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 34 removed outlier: 5.190A pdb=" N VAL s 34 " --> pdb=" O ILE s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.716A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.601A pdb=" N GLU s 86 " --> pdb=" O ILE s 82 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 47 removed outlier: 4.437A pdb=" N VAL t 29 " --> pdb=" O THR t 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 50 through 74 removed outlier: 4.508A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU t 56 " --> pdb=" O SER t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 5.441A pdb=" N THR t 79 " --> pdb=" O VAL t 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.816A pdb=" N GLN u 63 " --> pdb=" O HIS u 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY u 64 " --> pdb=" O TRP u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.482A pdb=" N LEU w 29 " --> pdb=" O ASP w 25 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.454A 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: 3.708A pdb=" N ARG w 53 " --> pdb=" O ALA w 49 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG w 57 " --> pdb=" O ARG w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.963A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.695A 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 70 through 76' Processing helix chain 'y' and resid 4 through 42 removed outlier: 3.761A pdb=" N HIS y 20 " --> pdb=" O LYS y 16 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY y 42 " --> pdb=" O ALA y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 removed outlier: 3.762A pdb=" N ALA y 47 " --> pdb=" O ASP y 43 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.710A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 86 Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 36 removed outlier: 3.787A pdb=" N VAL z 32 " --> pdb=" O VAL z 28 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG z 34 " --> pdb=" O ALA z 30 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 65 removed outlier: 4.093A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 48 through 51 removed outlier: 5.224A pdb=" N LYS 5 48 " --> pdb=" O THR 5 71 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '5' and resid 56 through 59 removed outlier: 4.226A pdb=" N PHE 5 64 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG 5 59 " --> pdb=" O GLU 5 62 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU 5 62 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '5' and resid 88 through 92 removed outlier: 3.821A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '5' and resid 115 through 119 removed outlier: 3.774A pdb=" N SER 5 115 " --> pdb=" O LYS 5 126 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.927A pdb=" N PHE A 60 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 65 through 72 Processing sheet with id= 7, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 8, first strand: chain 'B' and resid 33 through 36 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.973A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.078A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.461A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.386A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 10 through 16 removed outlier: 4.043A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 187 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 32 through 35 removed outlier: 5.602A pdb=" N THR C 51 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.752A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.244A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.533A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.493A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 86 through 92 removed outlier: 3.924A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR E 128 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 15 through 20 removed outlier: 4.157A pdb=" N VAL F 23 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN F 22 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY F 31 " --> pdb=" O GLY F 28 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 40 through 43 removed outlier: 6.427A pdb=" N ALA F 40 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.845A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 94 through 99 Processing sheet with id= 24, first strand: chain 'G' and resid 17 through 20 removed outlier: 4.222A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 127 through 133 removed outlier: 4.026A pdb=" N PHE G 132 " --> pdb=" O ALA G 140 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 27, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.707A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 66 removed outlier: 7.185A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.993A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.970A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.550A 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: 6.353A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.596A 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: 3.737A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.996A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.338A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.173A 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: 5.482A pdb=" N LYS R 60 " --> pdb=" O GLY R 100 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.914A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.653A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.378A pdb=" N VAL S 105 " --> pdb=" O ALA S 5 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS S 102 " --> pdb=" O ASP S 77 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 79 through 88 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.586A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.998A pdb=" N LYS U 21 " --> pdb=" O VAL U 13 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 40 through 46 removed outlier: 4.872A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 44, first strand: chain 'V' and resid 1 through 6 removed outlier: 4.019A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.927A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'X' and resid 12 through 18 removed outlier: 4.238A pdb=" N THR X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.314A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'a' and resid 11 through 16 removed outlier: 3.982A pdb=" N MET a 22 " --> pdb=" O ALA a 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 8 through 13 removed outlier: 6.050A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.045A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 22 through 25 removed outlier: 6.159A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 1 through 5 removed outlier: 7.352A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER f 28 " --> pdb=" O ASN f 13 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.996A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 90 through 93 Processing sheet with id= 55, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.556A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR h 70 " --> pdb=" O ALA h 104 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 148 through 155 removed outlier: 4.012A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 141 through 144 removed outlier: 3.932A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR i 181 " --> pdb=" O GLU i 172 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 11 through 16 removed outlier: 7.106A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.654A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 32 through 40 Processing sheet with id= 61, first strand: chain 'k' and resid 38 through 43 removed outlier: 4.138A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET k 90 " --> pdb=" O GLU k 5 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 73 through 77 Processing sheet with id= 63, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.489A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS m 50 " --> pdb=" O GLU m 60 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.895A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.567A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG n 18 " --> pdb=" O THR n 66 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR n 66 " --> pdb=" O ARG n 18 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR n 64 " --> pdb=" O PHE n 20 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS n 22 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.689A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE o 6 " --> pdb=" O ILE o 76 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'o' and resid 44 through 53 removed outlier: 6.886A pdb=" N ALA o 61 " --> pdb=" O ILE o 53 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 30 through 35 removed outlier: 3.701A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 29 through 33 removed outlier: 4.955A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 35 through 41 removed outlier: 4.906A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 4 through 9 removed outlier: 5.665A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'v' and resid 39 through 48 removed outlier: 4.561A pdb=" N LYS v 19 " --> pdb=" O ASP v 48 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL v 22 " --> pdb=" O VAL v 13 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU v 26 " --> pdb=" O GLN v 9 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLN v 9 " --> pdb=" O GLU v 26 " (cutoff:3.500A) removed outlier: 12.854A pdb=" N PHE v 28 " --> pdb=" O THR v 7 " (cutoff:3.500A) removed outlier: 15.849A pdb=" N THR v 7 " --> pdb=" O PHE v 28 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 30 through 34 1851 hydrogen bonds defined for protein. 5496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3658 hydrogen bonds 5782 hydrogen bond angles 0 basepair planarities 1449 basepair parallelities 2379 stacking parallelities Total time for adding SS restraints: 278.39 Time building geometry restraints manager: 64.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 12120 1.28 - 1.41: 53770 1.41 - 1.55: 88587 1.55 - 1.68: 9984 1.68 - 1.81: 273 Bond restraints: 164734 Sorted by residual: bond pdb=" N PRO g 29 " pdb=" CD PRO g 29 " ideal model delta sigma weight residual 1.473 1.702 -0.229 1.40e-02 5.10e+03 2.67e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.150 1.435 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.150 1.435 -0.285 2.00e-02 2.50e+03 2.02e+02 bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.150 1.434 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" N PRO w 41 " pdb=" CD PRO w 41 " ideal model delta sigma weight residual 1.473 1.639 -0.166 1.40e-02 5.10e+03 1.40e+02 ... (remaining 164729 not shown) Histogram of bond angle deviations from ideal: 93.00 - 106.29: 28961 106.29 - 119.58: 141234 119.58 - 132.87: 76503 132.87 - 146.16: 71 146.16 - 159.45: 2 Bond angle restraints: 246771 Sorted by residual: angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C4 2MA 12503 " ideal model delta sigma weight residual 103.49 152.03 -48.54 3.00e+00 1.11e-01 2.62e+02 angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C8 2MA 12503 " ideal model delta sigma weight residual 144.94 97.95 46.99 3.00e+00 1.11e-01 2.45e+02 angle pdb=" C1' 2MG 2 966 " pdb=" N9 2MG 2 966 " pdb=" C4 2MG 2 966 " ideal model delta sigma weight residual 109.53 145.04 -35.51 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C1' 2MG 21207 " pdb=" N9 2MG 21207 " pdb=" C4 2MG 21207 " ideal model delta sigma weight residual 109.53 144.97 -35.44 3.00e+00 1.11e-01 1.40e+02 angle pdb=" C1' 2MG 11835 " pdb=" N9 2MG 11835 " pdb=" C4 2MG 11835 " ideal model delta sigma weight residual 109.53 144.08 -34.55 3.00e+00 1.11e-01 1.33e+02 ... (remaining 246766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 83915 35.89 - 71.77: 3403 71.77 - 107.66: 305 107.66 - 143.55: 38 143.55 - 179.43: 47 Dihedral angle restraints: 87708 sinusoidal: 71020 harmonic: 16688 Sorted by residual: dihedral pdb=" C4' G 12308 " pdb=" C3' G 12308 " pdb=" C2' G 12308 " pdb=" C1' G 12308 " ideal model delta sinusoidal sigma weight residual -35.00 34.19 -69.19 1 8.00e+00 1.56e-02 9.67e+01 dihedral pdb=" C4' U 4 221 " pdb=" C3' U 4 221 " pdb=" C2' U 4 221 " pdb=" C1' U 4 221 " ideal model delta sinusoidal sigma weight residual -35.00 32.53 -67.53 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" C4' A 1 428 " pdb=" C3' A 1 428 " pdb=" C2' A 1 428 " pdb=" C1' A 1 428 " ideal model delta sinusoidal sigma weight residual -35.00 30.33 -65.33 1 8.00e+00 1.56e-02 8.74e+01 ... (remaining 87705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 30618 0.099 - 0.199: 696 0.199 - 0.298: 126 0.298 - 0.397: 32 0.397 - 0.497: 11 Chirality restraints: 31483 Sorted by residual: chirality pdb=" CA LEU G 12 " pdb=" N LEU G 12 " pdb=" C LEU G 12 " pdb=" CB LEU G 12 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA THR e 34 " pdb=" N THR e 34 " pdb=" C THR e 34 " pdb=" CB THR e 34 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CA GLU 5 107 " pdb=" N GLU 5 107 " pdb=" C GLU 5 107 " pdb=" CB GLU 5 107 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 31480 not shown) Planarity restraints: 12983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.075 2.00e-02 2.50e+03 6.41e-01 9.25e+03 pdb=" C4' 2MG 21207 " 0.480 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.830 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.630 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.221 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.937 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.156 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -1.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12251 " 0.047 2.00e-02 2.50e+03 5.79e-01 7.54e+03 pdb=" C4' OMG 12251 " 0.428 2.00e-02 2.50e+03 pdb=" O4' OMG 12251 " 0.591 2.00e-02 2.50e+03 pdb=" C3' OMG 12251 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMG 12251 " -0.608 2.00e-02 2.50e+03 pdb=" C2' OMG 12251 " -0.183 2.00e-02 2.50e+03 pdb=" O2' OMG 12251 " 0.957 2.00e-02 2.50e+03 pdb=" C1' OMG 12251 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG 12251 " -0.871 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " -0.038 2.00e-02 2.50e+03 5.74e-01 7.43e+03 pdb=" C4' 2MG 12445 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.624 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.580 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.227 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.872 2.00e-02 2.50e+03 ... (remaining 12980 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.34: 12 1.34 - 2.23: 234 2.23 - 3.12: 107232 3.12 - 4.01: 477649 4.01 - 4.90: 780217 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1365344 Sorted by model distance: nonbonded pdb=" P U 21372 " pdb=" CB SER n 73 " model vdw 0.444 3.800 nonbonded pdb=" O LYS G 42 " pdb=" CE2 PHE G 46 " model vdw 0.891 3.340 nonbonded pdb=" OP1 U 21372 " pdb=" CA SER n 73 " model vdw 0.980 3.470 nonbonded pdb=" P U 21372 " pdb=" OG SER n 73 " model vdw 1.006 3.400 nonbonded pdb=" O5' U 21372 " pdb=" OG SER n 73 " model vdw 1.094 2.440 ... (remaining 1365339 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4916 5.49 5 Mg 212 5.21 5 S 153 5.16 5 C 75846 2.51 5 N 28215 2.21 5 O 42324 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 32.500 Check model and map are aligned: 1.660 Convert atoms to be neutral: 0.960 Process input model: 584.660 Find NCS groups from input model: 3.190 Set up NCS constraints: 0.440 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 631.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.285 164734 Z= 0.197 Angle : 0.686 48.544 246771 Z= 0.390 Chirality : 0.037 0.497 31483 Planarity : 0.018 0.641 12983 Dihedral : 15.486 179.432 76942 Min Nonbonded Distance : 0.444 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.34 % Favored : 94.26 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5750 helix: 0.98 (0.13), residues: 1826 sheet: -1.17 (0.15), residues: 1091 loop : -1.59 (0.11), residues: 2833 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1765 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1680 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 19 residues processed: 1737 average time/residue: 1.4317 time to fit residues: 4226.4280 Evaluate side-chains 994 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 975 time to evaluate : 6.467 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 1.6435 time to fit residues: 57.4804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 890 optimal weight: 20.0000 chunk 798 optimal weight: 0.0020 chunk 443 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 538 optimal weight: 0.9990 chunk 426 optimal weight: 50.0000 chunk 826 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 502 optimal weight: 5.9990 chunk 614 optimal weight: 7.9990 chunk 957 optimal weight: 30.0000 overall best weight: 4.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 48 ASN F 128 GLN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 9 ASN K 29 HIS K 93 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 107 ASN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 52 GLN Q 56 GLN Q 59 GLN S 15 GLN T 48 GLN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN b 6 ASN c 19 HIS e 28 ASN e 43 HIS ** f 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 ASN h 32 ASN h 69 HIS i 54 GLN j 73 ASN j 97 GLN k 58 HIS ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN o 56 HIS p 101 ASN q 112 GLN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 HIS u 79 ASN v 50 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.073 164734 Z= 0.273 Angle : 0.724 20.088 246771 Z= 0.377 Chirality : 0.036 0.342 31483 Planarity : 0.007 0.131 12983 Dihedral : 16.255 179.550 65410 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.63 % Favored : 93.27 % Rotamer Outliers : 4.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.27 (0.11), residues: 5750 helix: 0.33 (0.12), residues: 1904 sheet: -1.06 (0.16), residues: 1092 loop : -1.57 (0.11), residues: 2754 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1261 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 1057 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 204 outliers final: 122 residues processed: 1190 average time/residue: 1.3674 time to fit residues: 2850.4643 Evaluate side-chains 1016 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 894 time to evaluate : 6.466 Switching outliers to nearest non-outliers outliers start: 122 outliers final: 0 residues processed: 122 average time/residue: 1.1095 time to fit residues: 266.9558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 531 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 796 optimal weight: 0.0670 chunk 651 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 chunk 958 optimal weight: 6.9990 chunk 1035 optimal weight: 5.9990 chunk 853 optimal weight: 10.0000 chunk 950 optimal weight: 7.9990 chunk 326 optimal weight: 10.0000 chunk 769 optimal weight: 1.9990 overall best weight: 4.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 159 HIS B 143 ASN C 36 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 21 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN R 87 GLN S 7 HIS ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN X 6 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN o 58 ASN ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN r 52 GLN u 9 HIS u 79 ASN w 54 GLN z 9 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 164734 Z= 0.228 Angle : 0.643 17.896 246771 Z= 0.340 Chirality : 0.034 0.322 31483 Planarity : 0.006 0.131 12983 Dihedral : 16.281 179.134 65410 Min Nonbonded Distance : 1.187 Molprobity Statistics. All-atom Clashscore : 15.89 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.02 % Favored : 93.93 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.21 (0.11), residues: 5750 helix: 0.42 (0.12), residues: 1894 sheet: -1.04 (0.16), residues: 1081 loop : -1.55 (0.11), residues: 2775 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1129 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 997 time to evaluate : 6.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 132 outliers final: 56 residues processed: 1073 average time/residue: 1.3355 time to fit residues: 2522.7152 Evaluate side-chains 938 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 882 time to evaluate : 6.294 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 1.1497 time to fit residues: 127.1833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 947 optimal weight: 4.9990 chunk 720 optimal weight: 0.9980 chunk 497 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 457 optimal weight: 30.0000 chunk 643 optimal weight: 8.9990 chunk 962 optimal weight: 9.9990 chunk 1018 optimal weight: 6.9990 chunk 502 optimal weight: 5.9990 chunk 912 optimal weight: 6.9990 chunk 274 optimal weight: 10.0000 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 159 HIS ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 21 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 7 HIS T 59 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 97 GLN ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 HIS u 79 ASN z 9 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.133 164734 Z= 0.265 Angle : 0.677 15.536 246771 Z= 0.358 Chirality : 0.035 0.323 31483 Planarity : 0.006 0.130 12983 Dihedral : 16.443 179.796 65410 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 17.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.06 % Favored : 92.85 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.34 (0.11), residues: 5750 helix: 0.27 (0.12), residues: 1899 sheet: -1.12 (0.16), residues: 1091 loop : -1.59 (0.11), residues: 2760 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1070 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 936 time to evaluate : 6.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 84 residues processed: 1003 average time/residue: 1.4001 time to fit residues: 2506.5206 Evaluate side-chains 958 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 874 time to evaluate : 6.450 Switching outliers to nearest non-outliers outliers start: 84 outliers final: 0 residues processed: 84 average time/residue: 1.2095 time to fit residues: 202.6456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 848 optimal weight: 6.9990 chunk 578 optimal weight: 4.9990 chunk 14 optimal weight: 20.0000 chunk 758 optimal weight: 10.0000 chunk 420 optimal weight: 40.0000 chunk 869 optimal weight: 1.9990 chunk 704 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 914 optimal weight: 40.0000 chunk 257 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 105 ASN A 12 ASN ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN S 7 HIS ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.136 164734 Z= 0.287 Angle : 0.698 16.938 246771 Z= 0.368 Chirality : 0.037 0.315 31483 Planarity : 0.006 0.131 12983 Dihedral : 16.629 179.451 65410 Min Nonbonded Distance : 1.165 Molprobity Statistics. All-atom Clashscore : 19.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.36 % Favored : 92.56 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.53 (0.11), residues: 5750 helix: 0.13 (0.12), residues: 1901 sheet: -1.26 (0.15), residues: 1090 loop : -1.70 (0.11), residues: 2759 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1055 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 956 time to evaluate : 6.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 99 outliers final: 52 residues processed: 1015 average time/residue: 1.3076 time to fit residues: 2342.8098 Evaluate side-chains 917 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 865 time to evaluate : 6.490 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 0 residues processed: 52 average time/residue: 1.0996 time to fit residues: 115.8146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 342 optimal weight: 20.0000 chunk 917 optimal weight: 40.0000 chunk 201 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 1019 optimal weight: 0.9990 chunk 846 optimal weight: 6.9990 chunk 472 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 535 optimal weight: 6.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS B 90 ASN B 143 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 41 HIS d 16 HIS ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.170 164734 Z= 0.335 Angle : 0.744 18.827 246771 Z= 0.389 Chirality : 0.039 0.335 31483 Planarity : 0.007 0.132 12983 Dihedral : 16.855 179.597 65410 Min Nonbonded Distance : 1.150 Molprobity Statistics. All-atom Clashscore : 21.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.26 % Favored : 91.65 % Rotamer Outliers : 2.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.69 (0.11), residues: 5750 helix: -0.02 (0.12), residues: 1898 sheet: -1.33 (0.15), residues: 1079 loop : -1.80 (0.11), residues: 2773 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 908 time to evaluate : 6.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 140 outliers final: 87 residues processed: 979 average time/residue: 1.3621 time to fit residues: 2359.6970 Evaluate side-chains 932 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 845 time to evaluate : 6.467 Switching outliers to nearest non-outliers outliers start: 87 outliers final: 0 residues processed: 87 average time/residue: 1.1831 time to fit residues: 203.1517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 983 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 581 optimal weight: 7.9990 chunk 744 optimal weight: 5.9990 chunk 577 optimal weight: 7.9990 chunk 858 optimal weight: 5.9990 chunk 569 optimal weight: 1.9990 chunk 1015 optimal weight: 10.0000 chunk 635 optimal weight: 5.9990 chunk 619 optimal weight: 7.9990 chunk 469 optimal weight: 50.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS B 90 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.4743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.232 164734 Z= 0.283 Angle : 0.706 16.344 246771 Z= 0.372 Chirality : 0.037 0.309 31483 Planarity : 0.006 0.129 12983 Dihedral : 16.805 179.169 65410 Min Nonbonded Distance : 1.180 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.83 % Favored : 92.09 % Rotamer Outliers : 1.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.65 (0.11), residues: 5750 helix: 0.04 (0.12), residues: 1894 sheet: -1.29 (0.16), residues: 1085 loop : -1.81 (0.11), residues: 2771 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 909 time to evaluate : 6.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 38 residues processed: 953 average time/residue: 1.4132 time to fit residues: 2395.1555 Evaluate side-chains 893 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 855 time to evaluate : 6.361 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 1.1063 time to fit residues: 88.7011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 628 optimal weight: 10.0000 chunk 405 optimal weight: 30.0000 chunk 606 optimal weight: 1.9990 chunk 306 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 645 optimal weight: 2.9990 chunk 692 optimal weight: 8.9990 chunk 502 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 798 optimal weight: 0.0970 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 74 ASN U 99 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 ASN h 32 ASN h 123 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 70 HIS ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.098 164734 Z= 0.221 Angle : 0.671 16.168 246771 Z= 0.356 Chirality : 0.035 0.311 31483 Planarity : 0.006 0.126 12983 Dihedral : 16.677 179.567 65410 Min Nonbonded Distance : 1.195 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.81 % Favored : 92.10 % Rotamer Outliers : 1.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.57 (0.11), residues: 5750 helix: 0.10 (0.12), residues: 1902 sheet: -1.21 (0.16), residues: 1084 loop : -1.77 (0.11), residues: 2764 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 914 time to evaluate : 6.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 38 residues processed: 945 average time/residue: 1.3145 time to fit residues: 2197.2183 Evaluate side-chains 895 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 857 time to evaluate : 6.447 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 1.1494 time to fit residues: 89.2700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 924 optimal weight: 5.9990 chunk 973 optimal weight: 6.9990 chunk 887 optimal weight: 20.0000 chunk 946 optimal weight: 5.9990 chunk 972 optimal weight: 4.9990 chunk 569 optimal weight: 5.9990 chunk 412 optimal weight: 50.0000 chunk 743 optimal weight: 7.9990 chunk 290 optimal weight: 20.0000 chunk 855 optimal weight: 2.9990 chunk 895 optimal weight: 9.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS B 90 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN h 123 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.142 164734 Z= 0.267 Angle : 0.703 15.756 246771 Z= 0.370 Chirality : 0.036 0.317 31483 Planarity : 0.006 0.128 12983 Dihedral : 16.743 179.596 65410 Min Nonbonded Distance : 1.192 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.03 % Favored : 91.88 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.64 (0.11), residues: 5750 helix: 0.02 (0.12), residues: 1914 sheet: -1.27 (0.16), residues: 1089 loop : -1.81 (0.11), residues: 2747 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 928 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 880 time to evaluate : 6.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 29 residues processed: 900 average time/residue: 1.3381 time to fit residues: 2129.8685 Evaluate side-chains 884 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 855 time to evaluate : 6.421 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 1.1678 time to fit residues: 70.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 943 optimal weight: 9.9990 chunk 621 optimal weight: 8.9990 chunk 1001 optimal weight: 3.9990 chunk 610 optimal weight: 6.9990 chunk 474 optimal weight: 50.0000 chunk 695 optimal weight: 7.9990 chunk 1050 optimal weight: 6.9990 chunk 966 optimal weight: 8.9990 chunk 836 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 645 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS B 134 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN Q 81 ASN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 28 ASN h 123 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.139 164734 Z= 0.336 Angle : 0.766 15.299 246771 Z= 0.400 Chirality : 0.040 0.313 31483 Planarity : 0.007 0.132 12983 Dihedral : 17.018 179.725 65410 Min Nonbonded Distance : 1.177 Molprobity Statistics. All-atom Clashscore : 22.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.87 % Favored : 91.04 % Rotamer Outliers : 0.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.89 (0.11), residues: 5750 helix: -0.20 (0.12), residues: 1913 sheet: -1.38 (0.16), residues: 1059 loop : -1.95 (0.11), residues: 2778 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 863 time to evaluate : 6.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 24 residues processed: 874 average time/residue: 1.3225 time to fit residues: 2045.5907 Evaluate side-chains 859 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 835 time to evaluate : 6.409 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 1.1457 time to fit residues: 58.7072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 512 optimal weight: 2.9990 chunk 664 optimal weight: 9.9990 chunk 890 optimal weight: 6.9990 chunk 256 optimal weight: 10.0000 chunk 770 optimal weight: 8.9990 chunk 123 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 837 optimal weight: 10.0000 chunk 350 optimal weight: 10.0000 chunk 859 optimal weight: 20.0000 chunk 106 optimal weight: 50.0000 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS B 70 ASN B 134 ASN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.062563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.044562 restraints weight = 844631.813| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.33 r_work: 0.3264 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work: 0.3249 rms_B_bonded: 2.26 restraints_weight: 0.1250 r_work: 0.3242 rms_B_bonded: 2.30 restraints_weight: 0.0625 r_work: 0.3235 rms_B_bonded: 2.37 restraints_weight: 0.0312 r_work: 0.3227 rms_B_bonded: 2.45 restraints_weight: 0.0156 r_work: 0.3219 rms_B_bonded: 2.55 restraints_weight: 0.0078 r_work: 0.3212 rms_B_bonded: 2.66 restraints_weight: 0.0039 r_work: 0.3203 rms_B_bonded: 2.78 restraints_weight: 0.0020 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.0010 r_work: 0.3186 rms_B_bonded: 3.07 restraints_weight: 0.0005 r_work: 0.3177 rms_B_bonded: 3.24 restraints_weight: 0.0002 r_work: 0.3168 rms_B_bonded: 3.42 restraints_weight: 0.0001 r_work: 0.3158 rms_B_bonded: 3.62 restraints_weight: 0.0001 r_work: 0.3148 rms_B_bonded: 3.83 restraints_weight: 0.0000 r_work: 0.3138 rms_B_bonded: 4.06 restraints_weight: 0.0000 r_work: 0.3127 rms_B_bonded: 4.30 restraints_weight: 0.0000 r_work: 0.3116 rms_B_bonded: 4.57 restraints_weight: 0.0000 r_work: 0.3104 rms_B_bonded: 4.85 restraints_weight: 0.0000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.5429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.140 164734 Z= 0.370 Angle : 0.791 14.760 246771 Z= 0.411 Chirality : 0.041 0.321 31483 Planarity : 0.007 0.133 12983 Dihedral : 17.177 179.779 65410 Min Nonbonded Distance : 0.907 Molprobity Statistics. All-atom Clashscore : 23.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.04 % Favored : 90.87 % Rotamer Outliers : 0.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -2.06 (0.10), residues: 5750 helix: -0.33 (0.12), residues: 1897 sheet: -1.51 (0.15), residues: 1084 loop : -2.03 (0.11), residues: 2769 =============================================================================== Job complete usr+sys time: 39332.12 seconds wall clock time: 679 minutes 56.84 seconds (40796.84 seconds total)