Starting phenix.real_space_refine (version: dev) on Tue Apr 12 13:22:24 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b5k_12035/04_2022/7b5k_12035_trim_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.018 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 "5 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 148576 Number of models: 1 Model: "" Number of chains: 80 Chain: "A" Number of atoms: 62209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2897, 62209 Classifications: {'RNA': 2897} Modifications used: {'rna3p': 18, 'rna2p': 5, 'rna3p_pur': 1384, 'rna3p_pyr': 1051, 'rna2p_pur': 280, 'rna2p_pyr': 159} Link IDs: {'rna3p': 2452, 'rna2p': 444} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 50, 'rna2p_pur': 8, 'rna3p_pur': 56, 'rna2p_pyr': 6} Link IDs: {'rna3p': 105, 'rna2p': 14} Chain: "C" 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: "D" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" 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: "F" 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: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "H" 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: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "O" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 900 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 114} 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: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} 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: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 580 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 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: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "0" 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: "1" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "2" 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: "3" 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: "4" 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: "5" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 32908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1533, 32908 Classifications: {'RNA': 1533} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 750, 'rna3p_pyr': 573, 'rna2p_pur': 118, 'rna2p_pyr': 81} Link IDs: {'rna3p': 1332, 'rna2p': 200} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "c" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "d" 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: "e" Number of atoms: 1144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1144 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 5, 'TRANS': 149} Chain: "f" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 862 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "g" 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: "h" 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: "i" 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: "j" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "k" 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: "l" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'D2T:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "n" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 799 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "o" 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: "p" 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: "q" 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: "r" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "s" Number of atoms: 656 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 656 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 465 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "v" Number of atoms: 63 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 63 Classifications: {'peptide': 8} Link IDs: {'TRANS': 7} Chain: "x" Number of atoms: 1646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1646 Classifications: {'RNA': 77} Modifications used: {'rna3p_pyr': 31, 'rna2p_pur': 7, 'rna3p_pur': 34, 'rna2p_pyr': 5} Link IDs: {'rna3p': 64, 'rna2p': 12} Chain: "z" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1633 Classifications: {'RNA': 76} Modifications used: {'rna3p_pyr': 30, 'rna2p_pur': 8, 'rna3p_pur': 34, 'rna2p_pyr': 4} Link IDs: {'rna3p': 64, 'rna2p': 11} Chain: "9" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1616 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna3p_pur': 31, 'rna2p_pyr': 3, 'rna3p_pyr': 35} Link IDs: {'rna3p': 66, 'rna2p': 9} Chain breaks: 1 Chain: "6" Number of atoms: 234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 234 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 4, 'rna2p_pur': 1, 'rna3p_pur': 5, 'rna2p_pyr': 1} Link IDs: {'rna3p': 8, 'rna2p': 2} Chain: "A" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 287 Unusual residues: {' MG': 236, 'ERY': 1} Classifications: {'undetermined': 237} Link IDs: {None: 236} 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: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" 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: "0" 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: 157 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 157 Unusual residues: {' MG': 115, 'SY5': 2} Classifications: {'undetermined': 117} Link IDs: {None: 116} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 611 Classifications: {'water': 611} Link IDs: {None: 610} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 221 Classifications: {'water': 221} Link IDs: {None: 220} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "l" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "n" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "t" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "z" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 10 residue: pdb=" P A A 404 " occ=0.60 ... (20 atoms not shown) pdb=" C4 A A 404 " occ=0.60 residue: pdb=" P U A2884 " occ=0.47 ... (18 atoms not shown) pdb=" C6 U A2884 " occ=0.47 residue: pdb=" P G A2885 " occ=0.47 ... (21 atoms not shown) pdb=" C4 G A2885 " occ=0.47 residue: pdb=" P A A2886 " occ=0.47 ... (20 atoms not shown) pdb=" C4 A A2886 " occ=0.47 residue: pdb=" P A A2887 " occ=0.47 ... (20 atoms not shown) pdb=" C4 A A2887 " occ=0.47 residue: pdb=" P C A2888 " occ=0.47 ... (18 atoms not shown) pdb=" C6 C A2888 " occ=0.47 residue: pdb=" N MEQ D 150 " occ=0.49 ... (8 atoms not shown) pdb=" NE2 MEQ D 150 " occ=0.49 residue: pdb=" N ARG W 41 " occ=0.49 ... (9 atoms not shown) pdb=" NH2 ARG W 41 " occ=0.49 residue: pdb=" N ALA Z 2 " occ=0.50 ... (3 atoms not shown) pdb=" CB ALA Z 2 " occ=0.50 residue: pdb=" N LYS Z 3 " occ=0.50 ... (7 atoms not shown) pdb=" NZ LYS Z 3 " occ=0.50 Time building chain proxies: 63.10, per 1000 atoms: 0.42 Number of scatterers: 148576 At special positions: 0 Unit cell: (269.76, 280.32, 230.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 148 16.00 P 4789 15.00 Mg 359 11.99 O 42054 8.00 N 27447 7.00 C 73779 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 54.83 Conformation dependent library (CDL) restraints added in 7.6 seconds 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10442 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: 173 helices and 74 sheets defined 38.7% alpha, 19.5% beta 1632 base pairs and 2547 stacking pairs defined. Time for finding SS restraints: 60.29 Creating SS restraints... Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.201A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 4.100A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.722A pdb=" N ILE C 135 " --> pdb=" O PRO C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.784A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.830A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 3.804A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 6.067A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.765A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.420A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.431A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.555A pdb=" N ALA E 39 " --> pdb=" O TYR E 35 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 removed outlier: 3.687A pdb=" N ASP E 116 " --> pdb=" O LEU E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.677A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET E 141 " --> pdb=" O LYS E 137 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 3.543A pdb=" N ARG E 162 " --> pdb=" O PHE E 158 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 Processing helix chain 'E' and resid 189 through 201 removed outlier: 3.660A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'F' and resid 2 through 21 removed outlier: 5.336A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 46 through 62 removed outlier: 4.004A pdb=" N LEU F 50 " --> pdb=" O ASP F 46 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.674A pdb=" N ALA F 107 " --> pdb=" O LEU F 103 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'F' and resid 40 through 45 removed outlier: 5.028A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 45 " --> pdb=" O GLU F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 40 through 45' Processing helix chain 'F' and resid 134 through 139 removed outlier: 4.073A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.665A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG G 153 " --> pdb=" O ARG G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 52 removed outlier: 4.868A pdb=" N ILE H 44 " --> pdb=" O THR H 40 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N PHE H 46 " --> pdb=" O LYS H 42 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N PHE H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N GLU H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ALA H 52 " --> pdb=" O GLU H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 76 removed outlier: 3.693A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ARG H 68 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA H 69 " --> pdb=" O ALA H 65 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N GLU H 70 " --> pdb=" O ASN H 66 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ILE H 72 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N LEU H 75 " --> pdb=" O LYS H 71 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 removed outlier: 3.918A pdb=" N ILE H 99 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP H 101 " --> pdb=" O ARG H 97 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ALA H 105 " --> pdb=" O ASP H 101 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 116 removed outlier: 3.908A pdb=" N VAL H 115 " --> pdb=" O ALA H 111 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ARG H 116 " --> pdb=" O LYS H 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 111 through 116' Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.963A 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 97 through 110 removed outlier: 4.458A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.983A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.351A 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 37 through 42 removed outlier: 3.541A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.875A 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: 4.250A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.701A 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 85 removed outlier: 3.802A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 3.603A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.987A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.812A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.096A 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 Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.669A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.518A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.802A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.332A 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: 4.663A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 3.749A pdb=" N GLU O 60 " --> pdb=" O LYS O 56 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.793A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.778A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.682A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.651A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.788A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.979A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN Q 72 " --> pdb=" O ALA Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 removed outlier: 3.735A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.749A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.565A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.757A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.075A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.507A 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 Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.041A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.498A 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: 3.669A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.025A 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 10 removed outlier: 6.477A pdb=" N LEU Y 6 " --> pdb=" O LYS Y 2 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.824A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain '0' and resid 9 through 19 removed outlier: 4.816A pdb=" N HIS 0 19 " --> pdb=" O MET 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 16 Processing helix chain '2' and resid 17 through 25 removed outlier: 4.475A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) removed outlier: 5.501A pdb=" N LYS 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) Processing helix chain '2' and resid 26 through 38 Processing helix chain '3' and resid 7 through 14 removed outlier: 3.513A pdb=" N LYS 3 12 " --> pdb=" O ARG 3 8 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ARG 3 13 " --> pdb=" O GLY 3 9 " (cutoff:3.500A) Processing helix chain '3' and resid 32 through 37 removed outlier: 4.167A pdb=" N LYS 3 36 " --> pdb=" O ILE 3 32 " (cutoff:3.500A) removed outlier: 5.445A pdb=" N ALA 3 37 " --> pdb=" O LEU 3 33 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 32 through 37' Processing helix chain '3' and resid 38 through 46 removed outlier: 3.597A pdb=" N ARG 3 45 " --> pdb=" O LYS 3 41 " (cutoff:3.500A) Proline residue: 3 46 - end of helix Processing helix chain '3' and resid 51 through 63 removed outlier: 4.588A pdb=" N GLY 3 56 " --> pdb=" O LYS 3 52 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N LEU 3 57 " --> pdb=" O GLY 3 53 " (cutoff:3.500A) Proline residue: 3 63 - end of helix Processing helix chain '5' and resid 43 through 51 removed outlier: 3.743A pdb=" N LYS 5 47 " --> pdb=" O PHE 5 43 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N GLN 5 48 " --> pdb=" O PHE 5 44 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG 5 49 " --> pdb=" O THR 5 45 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N ASP 5 50 " --> pdb=" O GLY 5 46 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N VAL 5 51 " --> pdb=" O LYS 5 47 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 43 through 51' Processing helix chain '5' and resid 56 through 65 removed outlier: 3.564A pdb=" N PHE 5 60 " --> pdb=" O ARG 5 56 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG 5 63 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE 5 64 " --> pdb=" O PHE 5 60 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N ASN 5 65 " --> pdb=" O ASN 5 61 " (cutoff:3.500A) Processing helix chain 'b' and resid 5 through 13 removed outlier: 3.711A pdb=" N MET b 9 " --> pdb=" O SER b 5 " (cutoff:3.500A) Processing helix chain 'b' and resid 27 through 32 removed outlier: 3.720A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 27 through 32' Processing helix chain 'b' and resid 43 through 64 Proline residue: b 48 - end of helix removed outlier: 3.584A pdb=" N LEU b 57 " --> pdb=" O ALA b 53 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 76 through 88 removed outlier: 3.631A pdb=" N CYS b 87 " --> pdb=" O ALA b 83 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 123 removed outlier: 4.374A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LYS b 112 " --> pdb=" O ARG b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 148 removed outlier: 5.195A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG b 139 " --> pdb=" O LEU b 135 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU b 141 " --> pdb=" O ARG b 137 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER b 147 " --> pdb=" O LYS b 143 " (cutoff:3.500A) Processing helix chain 'b' and resid 165 through 170 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.031A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.731A pdb=" N ALA c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.561A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.804A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU c 87 " --> pdb=" O ASP c 83 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL c 90 " --> pdb=" O LYS c 86 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.112A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 removed outlier: 3.505A pdb=" N ILE c 120 " --> pdb=" O VAL c 116 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.670A pdb=" N LEU c 144 " --> pdb=" O ASN c 140 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.173A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU d 15 " --> pdb=" O LEU d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 Processing helix chain 'd' and resid 49 through 66 removed outlier: 4.341A pdb=" N GLN d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 68 through 83 removed outlier: 3.673A pdb=" N ASN d 74 " --> pdb=" O ARG d 70 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 3.751A pdb=" N LEU d 91 " --> pdb=" O GLY d 87 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 Processing helix chain 'd' and resid 110 through 121 removed outlier: 4.196A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.719A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 4.226A pdb=" N LYS d 156 " --> pdb=" O GLN d 152 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU d 159 " --> pdb=" O VAL d 155 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU d 160 " --> pdb=" O LYS d 156 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU d 161 " --> pdb=" O ALA d 157 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 4.256A pdb=" N LEU d 191 " --> pdb=" O GLU d 187 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 187 through 192' Processing helix chain 'd' and resid 196 through 206 removed outlier: 4.277A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N SER d 205 " --> pdb=" O VAL d 201 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'd' and resid 39 through 44 removed outlier: 3.558A pdb=" N GLY d 42 " --> pdb=" O GLY d 39 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ALA d 43 " --> pdb=" O GLN d 40 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG d 44 " --> pdb=" O HIS d 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 39 through 44' Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.508A pdb=" N GLN e 61 " --> pdb=" O PRO e 57 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 119 removed outlier: 3.627A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL e 114 " --> pdb=" O ALA e 110 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY e 119 " --> pdb=" O LEU e 115 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 148 removed outlier: 3.564A pdb=" N ASN e 146 " --> pdb=" O ASP e 142 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N MET e 147 " --> pdb=" O GLY e 143 " (cutoff:3.500A) removed outlier: 5.816A pdb=" N ASN e 148 " --> pdb=" O LEU e 144 " (cutoff:3.500A) Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'f' and resid 11 through 19 removed outlier: 4.021A pdb=" N SER f 15 " --> pdb=" O HIS f 11 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix No H-bonds generated for 'chain 'f' and resid 11 through 19' Processing helix chain 'f' and resid 20 through 33 removed outlier: 3.678A pdb=" N ALA f 27 " --> pdb=" O GLU f 23 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA f 28 " --> pdb=" O ARG f 24 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 removed outlier: 4.114A pdb=" N GLU f 73 " --> pdb=" O GLU f 69 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLU f 75 " --> pdb=" O ILE f 71 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR f 76 " --> pdb=" O ASP f 72 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ASN f 81 " --> pdb=" O THR f 77 " (cutoff:3.500A) Processing helix chain 'f' and resid 100 through 106 removed outlier: 4.316A pdb=" N LYS f 106 " --> pdb=" O MET f 102 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.541A pdb=" N THR g 49 " --> pdb=" O SER g 45 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N ARG g 53 " --> pdb=" O THR g 49 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.544A pdb=" N PHE g 62 " --> pdb=" O GLU g 58 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.700A pdb=" N ASN g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS g 110 " --> pdb=" O GLU g 106 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 132 through 149 removed outlier: 4.009A pdb=" N LYS g 136 " --> pdb=" O GLY g 132 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.590A pdb=" N VAL h 39 " --> pdb=" O ALA h 35 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 39 Processing helix chain 'i' and resid 41 through 56 removed outlier: 3.765A pdb=" N VAL i 48 " --> pdb=" O ALA i 44 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ARG i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 4.409A pdb=" N ASP i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 removed outlier: 3.553A pdb=" N THR i 84 " --> pdb=" O ARG i 80 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG i 85 " --> pdb=" O HIS i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.965A pdb=" N LYS i 100 " --> pdb=" O SER i 96 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 3.514A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LYS j 30 " --> pdb=" O VAL j 26 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N THR j 32 " --> pdb=" O THR j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 90 removed outlier: 4.341A pdb=" N ASP j 85 " --> pdb=" O GLU j 81 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA j 86 " --> pdb=" O LYS j 82 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.546A pdb=" N SER k 50 " --> pdb=" O THR k 46 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 46 through 51' Processing helix chain 'k' and resid 54 through 59 removed outlier: 3.972A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 54 through 59' Processing helix chain 'k' and resid 60 through 76 removed outlier: 3.626A pdb=" N ASP k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N VAL k 74 " --> pdb=" O CYS k 70 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU k 76 " --> pdb=" O ASP k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 4.016A pdb=" N THR k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA k 99 " --> pdb=" O SER k 95 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.215A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.294A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.516A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N SER m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.042A pdb=" N THR m 55 " --> pdb=" O GLY m 51 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU m 59 " --> pdb=" O THR m 55 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.392A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.591A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 removed outlier: 3.625A pdb=" N ARG m 93 " --> pdb=" O LEU m 89 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLY m 94 " --> pdb=" O ARG m 90 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 2 through 20 removed outlier: 3.755A pdb=" N LYS n 6 " --> pdb=" O LYS n 2 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU n 9 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASP n 17 " --> pdb=" O VAL n 13 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR n 19 " --> pdb=" O LEU n 15 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 33 removed outlier: 5.575A pdb=" N ASP n 32 " --> pdb=" O ALA n 28 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N VAL n 33 " --> pdb=" O ILE n 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 28 through 33' Processing helix chain 'n' and resid 38 through 51 removed outlier: 3.870A pdb=" N TRP n 42 " --> pdb=" O ASP n 38 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.552A pdb=" N ARG n 85 " --> pdb=" O ARG n 81 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N ARG n 90 " --> pdb=" O GLU n 86 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY n 91 " --> pdb=" O ALA n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 15 removed outlier: 3.790A pdb=" N ILE o 11 " --> pdb=" O ALA o 7 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 44 removed outlier: 3.510A pdb=" N GLN o 35 " --> pdb=" O LEU o 31 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLN o 40 " --> pdb=" O ILE o 36 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 4.104A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N MET o 59 " --> pdb=" O GLY o 55 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.517A pdb=" N GLN o 80 " --> pdb=" O ALA o 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.558A pdb=" N GLN p 63 " --> pdb=" O HIS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 82 removed outlier: 3.699A pdb=" N ALA p 82 " --> pdb=" O VAL p 78 " (cutoff:3.500A) Processing helix chain 'r' and resid 25 through 34 removed outlier: 4.009A pdb=" N ASN r 31 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.952A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 Processing helix chain 'r' and resid 48 through 66 removed outlier: 3.577A pdb=" N GLN r 54 " --> pdb=" O LYS r 50 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR r 64 " --> pdb=" O LYS r 60 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 26 removed outlier: 3.858A pdb=" N GLU s 24 " --> pdb=" O GLU s 20 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N SER s 25 " --> pdb=" O LYS s 21 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.556A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.606A pdb=" N LYS t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N VAL t 35 " --> pdb=" O PHE t 31 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLU t 40 " --> pdb=" O TYR t 36 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 Proline residue: t 56 - end of helix removed outlier: 3.610A pdb=" N GLY t 65 " --> pdb=" O GLN t 61 " (cutoff:3.500A) Processing helix chain 't' and resid 68 through 87 removed outlier: 5.231A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ALA t 87 " --> pdb=" O ILE t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 removed outlier: 3.584A pdb=" N ALA u 15 " --> pdb=" O PRO u 11 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 37 removed outlier: 5.403A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 56 removed outlier: 4.998A pdb=" N HIS u 56 " --> pdb=" O ALA u 52 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 6 removed outlier: 4.229A pdb=" N ALA C 2 " --> pdb=" O VAL C 20 " (cutoff:3.500A) removed outlier: 5.935A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.561A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.174A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN C 163 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.294A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.223A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VAL D 26 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 4.319A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 36 through 40 removed outlier: 4.036A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 179 through 182 Processing sheet with id= 8, first strand: chain 'D' and resid 24 through 28 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.755A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.483A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 44 through 47 removed outlier: 6.992A pdb=" N ARG E 44 " --> pdb=" O PRO E 89 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N ALA E 87 " --> pdb=" O GLN E 46 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 117 through 120 removed outlier: 6.154A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.616A pdb=" N LYS F 33 " --> pdb=" O THR F 157 " (cutoff:3.500A) removed outlier: 5.749A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.477A pdb=" N LYS F 72 " --> pdb=" O GLN F 81 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLN F 81 " --> pdb=" O LYS F 72 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.525A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 25 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.510A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 121 through 125 removed outlier: 6.182A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE G 131 " --> pdb=" O LEU G 87 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 18 through 21 removed outlier: 6.686A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 127 through 133 Processing sheet with id= 20, first strand: chain 'J' and resid 52 through 57 removed outlier: 5.207A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.646A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.253A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.900A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 23 Processing sheet with id= 24, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.633A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.697A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.380A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 9.114A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.541A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.710A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.721A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.746A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.220A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 57 through 60 removed outlier: 3.538A pdb=" N SER R 102 " --> pdb=" O VAL R 58 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.662A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.213A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 2 through 8 removed outlier: 6.907A pdb=" N VAL S 106 " --> pdb=" O THR S 72 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 73 through 79 removed outlier: 4.950A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 28 through 33 removed outlier: 6.398A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.195A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 40 through 45 removed outlier: 5.403A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 82 through 85 removed outlier: 7.233A pdb=" N ARG U 82 " --> pdb=" O LYS U 97 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N ARG U 94 " --> pdb=" O ILE U 103 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU U 101 " --> pdb=" O PHE U 96 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 68 through 73 removed outlier: 5.492A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 29 through 32 removed outlier: 4.707A pdb=" N GLU W 29 " --> pdb=" O VAL W 67 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ILE W 82 " --> pdb=" O GLY W 48 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.289A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.694A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 45, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.362A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain '0' and resid 29 through 32 removed outlier: 4.210A pdb=" N GLU 0 36 " --> pdb=" O ASP 0 31 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain '1' and resid 6 through 13 removed outlier: 6.261A pdb=" N HIS 1 19 " --> pdb=" O SER 1 13 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain '1' and resid 34 through 39 removed outlier: 6.807A pdb=" N LEU 1 34 " --> pdb=" O GLU 1 51 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU 1 51 " --> pdb=" O LEU 1 34 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain '3' and resid 22 through 25 removed outlier: 5.868A pdb=" N PHE 3 22 " --> pdb=" O VAL 3 50 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '4' and resid 14 through 19 Processing sheet with id= 51, first strand: chain '5' and resid 20 through 25 removed outlier: 3.771A pdb=" N LEU 5 32 " --> pdb=" O THR 5 13 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.205A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'b' and resid 67 through 71 removed outlier: 3.619A pdb=" N ALA b 185 " --> pdb=" O PHE b 198 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.670A pdb=" N ARG c 54 " --> pdb=" O HIS c 69 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL c 66 " --> pdb=" O GLN c 100 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR c 70 " --> pdb=" O ALA c 104 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'c' and resid 164 through 169 removed outlier: 5.973A pdb=" N ARG c 164 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.605A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU d 179 " --> pdb=" O ASP d 174 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N GLU d 172 " --> pdb=" O THR d 181 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'e' and resid 12 through 16 removed outlier: 6.848A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'e' and resid 84 through 88 removed outlier: 3.529A pdb=" N ALA e 99 " --> pdb=" O ASN e 122 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'e' and resid 33 through 40 Processing sheet with id= 60, first strand: chain 'f' and resid 38 through 43 removed outlier: 5.906A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N HIS f 3 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ARG f 86 " --> pdb=" O MET f 9 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'f' and resid 44 through 47 removed outlier: 5.947A pdb=" N LEU f 47 " --> pdb=" O HIS f 55 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'g' and resid 72 through 79 removed outlier: 5.943A pdb=" N THR g 72 " --> pdb=" O VAL g 91 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR g 85 " --> pdb=" O ARG g 78 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.807A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.530A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'i' and resid 5 through 11 Processing sheet with id= 66, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.433A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE j 8 " --> pdb=" O VAL j 74 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 68, first strand: chain 'k' and resid 42 through 45 removed outlier: 3.504A pdb=" N GLY k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.027A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'l' and resid 36 through 41 removed outlier: 3.680A pdb=" N ARG l 36 " --> pdb=" O ARG l 54 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'p' and resid 4 through 10 removed outlier: 6.724A pdb=" N TYR p 17 " --> pdb=" O PHE p 38 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N PHE p 38 " --> pdb=" O TYR p 17 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL p 19 " --> pdb=" O VAL p 36 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'q' and resid 19 through 30 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'q' and resid 60 through 63 removed outlier: 6.571A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 's' and resid 30 through 33 removed outlier: 4.946A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) 1763 hydrogen bonds defined for protein. 5208 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4112 hydrogen bonds 6464 hydrogen bond angles 0 basepair planarities 1632 basepair parallelities 2547 stacking parallelities Total time for adding SS restraints: 409.73 Time building geometry restraints manager: 61.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 11793 1.27 - 1.41: 50932 1.41 - 1.54: 87615 1.54 - 1.68: 9684 1.68 - 1.82: 265 Bond restraints: 160289 Sorted by residual: bond pdb=" C5 5MU A 747 " pdb=" C6 5MU A 747 " ideal model delta sigma weight residual 1.150 1.449 -0.299 2.00e-02 2.50e+03 2.23e+02 bond pdb=" C5 5MU A1939 " pdb=" C6 5MU A1939 " ideal model delta sigma weight residual 1.150 1.447 -0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.805 1.601 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.805 1.608 0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" CZ 4D4 M 81 " pdb=" NH1 4D4 M 81 " ideal model delta sigma weight residual 1.443 1.250 0.193 2.00e-02 2.50e+03 9.27e+01 ... (remaining 160284 not shown) Histogram of bond angle deviations from ideal: 80.55 - 93.06: 11 93.06 - 105.57: 24374 105.57 - 118.08: 128069 118.08 - 130.59: 85657 130.59 - 143.10: 2029 Bond angle restraints: 240140 Sorted by residual: angle pdb=" C1' 1MG A 745 " pdb=" N9 1MG A 745 " pdb=" C4 1MG A 745 " ideal model delta sigma weight residual 103.27 143.10 -39.83 3.00e+00 1.11e-01 1.76e+02 angle pdb=" C1' 1MG A 745 " pdb=" N9 1MG A 745 " pdb=" C8 1MG A 745 " ideal model delta sigma weight residual 141.41 107.29 34.12 3.00e+00 1.11e-01 1.29e+02 angle pdb=" C32 ERY A3237 " pdb=" C6 ERY A3237 " pdb=" O10 ERY A3237 " ideal model delta sigma weight residual 109.53 80.59 28.94 3.00e+00 1.11e-01 9.30e+01 angle pdb=" O3' U A2188 " pdb=" P U A2189 " pdb=" OP2 U A2189 " ideal model delta sigma weight residual 108.00 80.55 27.45 3.00e+00 1.11e-01 8.37e+01 angle pdb=" C13 ERY A3237 " pdb=" C12 ERY A3237 " pdb=" O13 ERY A3237 " ideal model delta sigma weight residual 109.42 82.97 26.45 3.00e+00 1.11e-01 7.77e+01 ... (remaining 240135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 82471 35.89 - 71.79: 2607 71.79 - 107.68: 170 107.68 - 143.57: 21 143.57 - 179.47: 19 Dihedral angle restraints: 85288 sinusoidal: 69103 harmonic: 16185 Sorted by residual: dihedral pdb=" CA ASP s 27 " pdb=" C ASP s 27 " pdb=" N LYS s 28 " pdb=" CA LYS s 28 " ideal model delta harmonic sigma weight residual -180.00 -127.39 -52.61 0 5.00e+00 4.00e-02 1.11e+02 dihedral pdb=" O4' U 9 33 " pdb=" C1' U 9 33 " pdb=" N1 U 9 33 " pdb=" C2 U 9 33 " ideal model delta sinusoidal sigma weight residual -160.00 14.51 -174.51 1 1.50e+01 4.44e-03 8.51e+01 dihedral pdb=" O4' U x 34 " pdb=" C1' U x 34 " pdb=" N1 U x 34 " pdb=" C2 U x 34 " ideal model delta sinusoidal sigma weight residual -160.00 7.56 -167.56 1 1.50e+01 4.44e-03 8.43e+01 ... (remaining 85285 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.407: 30659 0.407 - 0.815: 2 0.815 - 1.222: 0 1.222 - 1.630: 0 1.630 - 2.037: 4 Chirality restraints: 30665 Sorted by residual: chirality pdb=" C16 ERY A3237 " pdb=" C15 ERY A3237 " pdb=" C17 ERY A3237 " pdb=" C19 ERY A3237 " both_signs ideal model delta sigma weight residual False 2.69 0.65 2.04 2.00e-01 2.50e+01 1.04e+02 chirality pdb=" P U A2189 " pdb=" OP1 U A2189 " pdb=" OP2 U A2189 " pdb=" O5' U A2189 " both_signs ideal model delta sigma weight residual True 2.41 0.49 1.92 2.00e-01 2.50e+01 9.22e+01 chirality pdb=" C6 ERY A3237 " pdb=" C32 ERY A3237 " pdb=" C5 ERY A3237 " pdb=" C7 ERY A3237 " both_signs ideal model delta sigma weight residual False -2.74 -0.85 -1.90 2.00e-01 2.50e+01 8.99e+01 ... (remaining 30662 not shown) Planarity restraints: 12613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " -0.074 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' 2MG a1516 " -0.428 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.550 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.654 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.153 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -1.011 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.233 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.896 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " -0.048 2.00e-02 2.50e+03 5.91e-01 7.85e+03 pdb=" C4' 5MC a1407 " -0.443 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " -0.642 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " 0.616 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " 0.192 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " -0.947 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " -0.222 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " 0.905 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG A2251 " 0.046 2.00e-02 2.50e+03 5.78e-01 7.52e+03 pdb=" C4' OMG A2251 " 0.424 2.00e-02 2.50e+03 pdb=" O4' OMG A2251 " 0.615 2.00e-02 2.50e+03 pdb=" C3' OMG A2251 " -0.596 2.00e-02 2.50e+03 pdb=" O3' OMG A2251 " -0.586 2.00e-02 2.50e+03 pdb=" C2' OMG A2251 " -0.196 2.00e-02 2.50e+03 pdb=" O2' OMG A2251 " 0.947 2.00e-02 2.50e+03 pdb=" C1' OMG A2251 " 0.221 2.00e-02 2.50e+03 pdb=" N9 OMG A2251 " -0.875 2.00e-02 2.50e+03 ... (remaining 12610 not shown) Histogram of nonbonded interaction distances: 1.50 - 2.18: 1423 2.18 - 2.86: 46004 2.86 - 3.54: 202877 3.54 - 4.22: 477493 4.22 - 4.90: 623641 Nonbonded interactions: 1351438 Sorted by model distance: nonbonded pdb="MG MG a1661 " pdb="MG MG a1678 " model vdw 1.504 1.300 nonbonded pdb="MG MG A3045 " pdb=" O HOH A3402 " model vdw 1.878 2.170 nonbonded pdb="MG MG A3079 " pdb=" O HOH A3309 " model vdw 1.889 2.170 nonbonded pdb="MG MG A3086 " pdb=" O HOH A3349 " model vdw 1.891 2.170 nonbonded pdb="MG MG A3098 " pdb=" O HOH A3900 " model vdw 1.896 2.170 ... (remaining 1351433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4789 5.49 5 Mg 359 5.21 5 S 148 5.16 5 C 73779 2.51 5 N 27447 2.21 5 O 42054 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.40 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: 2.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 20.150 Check model and map are aligned: 1.660 Convert atoms to be neutral: 0.960 Process input model: 698.200 Find NCS groups from input model: 3.220 Set up NCS constraints: 0.450 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: 0.040 Load rotamer database and sin/cos tables:11.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 738.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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 : 0.006 0.299 160289 Z= 0.381 Angle : 0.903 39.835 240140 Z= 0.475 Chirality : 0.053 2.037 30665 Planarity : 0.018 0.594 12613 Dihedral : 14.169 179.469 74846 Min Nonbonded Distance : 1.504 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.95 % Favored : 95.95 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.09), residues: 5575 helix: -3.79 (0.07), residues: 1770 sheet: -0.92 (0.14), residues: 1097 loop : -1.69 (0.10), residues: 2708 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1146 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1125 time to evaluate : 6.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 2 residues processed: 1142 average time/residue: 2.3729 time to fit residues: 3808.6174 Evaluate side-chains 649 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 647 time to evaluate : 6.253 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 1.7103 time to fit residues: 12.0664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 861 optimal weight: 9.9990 chunk 773 optimal weight: 6.9990 chunk 428 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 521 optimal weight: 3.9990 chunk 413 optimal weight: 10.0000 chunk 799 optimal weight: 0.6980 chunk 309 optimal weight: 0.7980 chunk 486 optimal weight: 9.9990 chunk 595 optimal weight: 4.9990 chunk 926 optimal weight: 9.9990 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 163 GLN D 49 GLN D 126 ASN E 115 GLN F 21 ASN F 23 ASN F 127 ASN G 20 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 11 ASN H 20 ASN H 119 ASN K 3 GLN M 22 GLN N 13 ASN N 18 GLN P 12 GLN P 56 HIS Q 37 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 43 ASN S 31 GLN S 61 ASN T 48 GLN T 91 GLN U 40 ASN ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 42 HIS 3 43 HIS b 170 HIS b 177 ASN d 126 ASN d 152 GLN d 198 HIS e 82 GLN f 3 HIS ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 76 GLN i 37 GLN i 126 GLN j 4 GLN j 56 HIS l 77 HIS m 12 HIS n 34 ASN o 40 GLN p 40 ASN q 47 HIS r 31 ASN s 14 HIS s 53 ASN t 52 ASN t 70 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.060 160289 Z= 0.187 Angle : 0.658 29.061 240140 Z= 0.348 Chirality : 0.043 2.115 30665 Planarity : 0.006 0.128 12613 Dihedral : 13.743 179.757 63673 Min Nonbonded Distance : 1.468 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.91 % Favored : 97.06 % Rotamer Outliers : 3.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -1.55 (0.10), residues: 5575 helix: -1.15 (0.11), residues: 1829 sheet: -0.42 (0.15), residues: 1052 loop : -1.08 (0.11), residues: 2694 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 904 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 737 time to evaluate : 6.440 Fit side-chains revert: symmetry clash outliers start: 167 outliers final: 58 residues processed: 837 average time/residue: 2.1953 time to fit residues: 2657.5390 Evaluate side-chains 688 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 630 time to evaluate : 6.491 Switching outliers to nearest non-outliers outliers start: 58 outliers final: 37 residues processed: 22 average time/residue: 1.3480 time to fit residues: 58.5982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 514 optimal weight: 10.0000 chunk 287 optimal weight: 20.0000 chunk 770 optimal weight: 20.0000 chunk 630 optimal weight: 40.0000 chunk 255 optimal weight: 10.0000 chunk 927 optimal weight: 0.4980 chunk 1002 optimal weight: 20.0000 chunk 826 optimal weight: 6.9990 chunk 920 optimal weight: 10.0000 chunk 316 optimal weight: 10.0000 chunk 744 optimal weight: 20.0000 overall best weight: 7.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 126 ASN E 115 GLN E 156 ASN F 127 ASN G 38 ASN G 128 GLN G 139 GLN H 11 ASN H 20 ASN H 43 ASN K 89 ASN M 22 GLN O 98 GLN O 100 HIS P 7 GLN P 12 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 40 ASN V 24 ASN X 20 HIS Y 58 ASN Z 20 HIS 2 29 GLN d 74 ASN d 136 GLN d 198 HIS ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS h 76 GLN ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN m 14 HIS ** n 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN r 31 ASN s 83 HIS t 52 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.083 160289 Z= 0.328 Angle : 0.762 29.946 240140 Z= 0.391 Chirality : 0.048 2.112 30665 Planarity : 0.007 0.144 12613 Dihedral : 14.027 178.808 63673 Min Nonbonded Distance : 1.458 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.09 % Favored : 95.86 % Rotamer Outliers : 4.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % 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: -1.01 (0.10), residues: 5575 helix: -0.22 (0.12), residues: 1825 sheet: -0.31 (0.15), residues: 1091 loop : -1.07 (0.11), residues: 2659 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 666 time to evaluate : 6.347 Fit side-chains outliers start: 207 outliers final: 88 residues processed: 794 average time/residue: 2.1883 time to fit residues: 2543.4001 Evaluate side-chains 704 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 616 time to evaluate : 6.480 Switching outliers to nearest non-outliers outliers start: 88 outliers final: 62 residues processed: 26 average time/residue: 1.1593 time to fit residues: 63.0788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 916 optimal weight: 20.0000 chunk 697 optimal weight: 10.0000 chunk 481 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 623 optimal weight: 40.0000 chunk 931 optimal weight: 5.9990 chunk 985 optimal weight: 0.0870 chunk 486 optimal weight: 0.0970 chunk 882 optimal weight: 10.0000 chunk 265 optimal weight: 20.0000 overall best weight: 4.6364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN H 20 ASN K 89 ASN M 22 GLN P 12 GLN V 24 ASN d 54 GLN d 198 HIS e 43 ASN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 34 ASN o 40 GLN r 31 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.067 160289 Z= 0.218 Angle : 0.660 29.381 240140 Z= 0.347 Chirality : 0.043 2.111 30665 Planarity : 0.006 0.134 12613 Dihedral : 13.755 179.404 63673 Min Nonbonded Distance : 1.433 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.73 % Favored : 96.25 % Rotamer Outliers : 4.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 5575 helix: 0.37 (0.12), residues: 1828 sheet: -0.21 (0.15), residues: 1083 loop : -0.95 (0.11), residues: 2664 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 826 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 631 time to evaluate : 6.505 Fit side-chains outliers start: 195 outliers final: 109 residues processed: 763 average time/residue: 2.1717 time to fit residues: 2420.7601 Evaluate side-chains 705 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 596 time to evaluate : 6.556 Switching outliers to nearest non-outliers outliers start: 109 outliers final: 81 residues processed: 30 average time/residue: 1.3517 time to fit residues: 77.9786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 821 optimal weight: 5.9990 chunk 559 optimal weight: 2.9990 chunk 14 optimal weight: 20.0000 chunk 734 optimal weight: 20.0000 chunk 406 optimal weight: 0.0070 chunk 841 optimal weight: 10.0000 chunk 681 optimal weight: 20.0000 chunk 1 optimal weight: 10.0000 chunk 503 optimal weight: 6.9990 chunk 884 optimal weight: 9.9990 chunk 248 optimal weight: 10.0000 overall best weight: 5.2006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN G 115 HIS H 20 ASN K 89 ASN M 22 GLN P 12 GLN d 54 GLN ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 50 GLN r 31 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 160289 Z= 0.240 Angle : 0.677 29.516 240140 Z= 0.353 Chirality : 0.044 2.108 30665 Planarity : 0.006 0.136 12613 Dihedral : 13.760 178.989 63673 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.56 % Favored : 95.43 % Rotamer Outliers : 4.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 5575 helix: 0.56 (0.12), residues: 1829 sheet: -0.14 (0.15), residues: 1071 loop : -0.92 (0.11), residues: 2675 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 825 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 619 time to evaluate : 6.505 Fit side-chains revert: symmetry clash outliers start: 206 outliers final: 123 residues processed: 761 average time/residue: 2.1701 time to fit residues: 2428.6077 Evaluate side-chains 712 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 589 time to evaluate : 6.462 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 93 residues processed: 31 average time/residue: 1.2469 time to fit residues: 76.7175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 331 optimal weight: 10.0000 chunk 887 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 578 optimal weight: 7.9990 chunk 243 optimal weight: 10.0000 chunk 986 optimal weight: 6.9990 chunk 819 optimal weight: 30.0000 chunk 456 optimal weight: 0.3980 chunk 82 optimal weight: 10.0000 chunk 326 optimal weight: 10.0000 chunk 518 optimal weight: 10.0000 overall best weight: 6.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN H 20 ASN K 89 ASN M 22 GLN P 12 GLN d 198 HIS ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 160289 Z= 0.283 Angle : 0.713 29.777 240140 Z= 0.370 Chirality : 0.046 2.113 30665 Planarity : 0.007 0.140 12613 Dihedral : 13.881 179.726 63673 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.54 % Favored : 95.44 % Rotamer Outliers : 4.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.11), residues: 5575 helix: 0.51 (0.12), residues: 1834 sheet: -0.18 (0.16), residues: 1066 loop : -0.98 (0.11), residues: 2675 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 618 time to evaluate : 6.580 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 211 outliers final: 126 residues processed: 767 average time/residue: 2.1515 time to fit residues: 2430.3683 Evaluate side-chains 731 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 605 time to evaluate : 6.487 Switching outliers to nearest non-outliers outliers start: 126 outliers final: 92 residues processed: 35 average time/residue: 1.2714 time to fit residues: 87.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 951 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 562 optimal weight: 3.9990 chunk 720 optimal weight: 20.0000 chunk 558 optimal weight: 8.9990 chunk 830 optimal weight: 0.2980 chunk 551 optimal weight: 10.0000 chunk 983 optimal weight: 8.9990 chunk 615 optimal weight: 3.9990 chunk 599 optimal weight: 5.9990 chunk 453 optimal weight: 9.9990 overall best weight: 4.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 142 HIS E 115 GLN F 127 ASN H 20 ASN K 89 ASN M 22 GLN P 12 GLN ** d 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN ** t 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.179 160289 Z= 0.223 Angle : 0.669 29.449 240140 Z= 0.351 Chirality : 0.044 2.109 30665 Planarity : 0.006 0.135 12613 Dihedral : 13.776 178.967 63673 Min Nonbonded Distance : 1.421 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.14 % Favored : 95.84 % Rotamer Outliers : 4.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.11), residues: 5575 helix: 0.69 (0.12), residues: 1833 sheet: -0.15 (0.16), residues: 1073 loop : -0.92 (0.11), residues: 2669 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 613 time to evaluate : 10.451 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 199 outliers final: 123 residues processed: 760 average time/residue: 2.1301 time to fit residues: 2398.5725 Evaluate side-chains 713 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 590 time to evaluate : 6.521 Switching outliers to nearest non-outliers outliers start: 123 outliers final: 101 residues processed: 23 average time/residue: 1.3192 time to fit residues: 60.8495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 608 optimal weight: 9.9990 chunk 392 optimal weight: 20.0000 chunk 587 optimal weight: 7.9990 chunk 296 optimal weight: 20.0000 chunk 193 optimal weight: 10.0000 chunk 190 optimal weight: 20.0000 chunk 625 optimal weight: 40.0000 chunk 669 optimal weight: 20.0000 chunk 486 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 772 optimal weight: 30.0000 overall best weight: 8.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN F 127 ASN H 20 ASN K 89 ASN M 22 GLN P 12 GLN T 91 GLN V 75 GLN ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN ** t 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.367 160289 Z= 0.382 Angle : 0.799 30.335 240140 Z= 0.409 Chirality : 0.049 2.107 30665 Planarity : 0.007 0.145 12613 Dihedral : 14.136 179.271 63673 Min Nonbonded Distance : 1.425 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.91 % Favored : 95.07 % Rotamer Outliers : 4.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.11), residues: 5575 helix: 0.34 (0.12), residues: 1835 sheet: -0.30 (0.16), residues: 1070 loop : -1.08 (0.11), residues: 2670 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 622 time to evaluate : 6.481 Fit side-chains revert: symmetry clash outliers start: 193 outliers final: 128 residues processed: 766 average time/residue: 2.1280 time to fit residues: 2413.0673 Evaluate side-chains 734 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 606 time to evaluate : 6.504 Switching outliers to nearest non-outliers outliers start: 128 outliers final: 103 residues processed: 26 average time/residue: 1.3714 time to fit residues: 69.5269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 894 optimal weight: 7.9990 chunk 941 optimal weight: 3.9990 chunk 859 optimal weight: 2.9990 chunk 916 optimal weight: 5.9990 chunk 551 optimal weight: 9.9990 chunk 399 optimal weight: 10.0000 chunk 719 optimal weight: 40.0000 chunk 281 optimal weight: 10.0000 chunk 827 optimal weight: 0.4980 chunk 866 optimal weight: 9.9990 chunk 912 optimal weight: 8.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN H 20 ASN K 89 ASN M 22 GLN P 12 GLN V 75 GLN ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN s 83 HIS ** t 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.103 160289 Z= 0.204 Angle : 0.661 29.431 240140 Z= 0.348 Chirality : 0.043 2.112 30665 Planarity : 0.006 0.133 12613 Dihedral : 13.783 178.835 63673 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.98 % Favored : 96.00 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 5575 helix: 0.67 (0.12), residues: 1834 sheet: -0.22 (0.16), residues: 1074 loop : -0.97 (0.11), residues: 2667 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 766 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 610 time to evaluate : 6.467 Fit side-chains revert: symmetry clash outliers start: 156 outliers final: 113 residues processed: 739 average time/residue: 2.0763 time to fit residues: 2281.4646 Evaluate side-chains 707 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 594 time to evaluate : 6.435 Switching outliers to nearest non-outliers outliers start: 113 outliers final: 104 residues processed: 10 average time/residue: 1.2540 time to fit residues: 29.2616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 601 optimal weight: 0.1980 chunk 968 optimal weight: 8.9990 chunk 591 optimal weight: 4.9990 chunk 459 optimal weight: 10.0000 chunk 673 optimal weight: 10.0000 chunk 1016 optimal weight: 40.0000 chunk 935 optimal weight: 5.9990 chunk 809 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 625 optimal weight: 40.0000 chunk 496 optimal weight: 9.9990 overall best weight: 6.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN H 20 ASN H 43 ASN K 89 ASN M 22 GLN P 12 GLN P 15 GLN 1 46 HIS ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN s 83 HIS ** t 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.726 160289 Z= 0.337 Angle : 0.731 73.891 240140 Z= 0.377 Chirality : 0.045 2.106 30665 Planarity : 0.007 0.136 12613 Dihedral : 13.794 179.137 63673 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 5575 helix: 0.62 (0.12), residues: 1839 sheet: -0.22 (0.16), residues: 1074 loop : -1.00 (0.11), residues: 2662 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11150 Ramachandran restraints generated. 5575 Oldfield, 0 Emsley, 5575 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 731 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 590 time to evaluate : 6.431 Fit side-chains revert: symmetry clash outliers start: 141 outliers final: 120 residues processed: 707 average time/residue: 2.1199 time to fit residues: 2226.3492 Evaluate side-chains 704 residues out of total 4646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 584 time to evaluate : 6.213 Switching outliers to nearest non-outliers outliers start: 120 outliers final: 104 residues processed: 17 average time/residue: 1.3299 time to fit residues: 46.0041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1020 random chunks: chunk 642 optimal weight: 20.0000 chunk 861 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 746 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 224 optimal weight: 10.0000 chunk 810 optimal weight: 5.9990 chunk 339 optimal weight: 0.4980 chunk 832 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 149 optimal weight: 20.0000 overall best weight: 7.2992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 127 ASN H 20 ASN H 43 ASN K 89 ASN M 22 GLN P 12 GLN P 15 GLN ** i 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 31 ASN s 83 HIS ** t 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.127714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.108736 restraints weight = 226746.951| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 0.43 r_work: 0.3376 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3716 r_free = 0.3716 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.726 160289 Z= 0.344 Angle : 0.734 73.891 240140 Z= 0.379 Chirality : 0.045 2.106 30665 Planarity : 0.007 0.136 12613 Dihedral : 13.794 179.137 63673 Min Nonbonded Distance : 1.419 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.34 % Favored : 95.64 % Rotamer Outliers : 2.31 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 1.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 5575 helix: 0.62 (0.12), residues: 1839 sheet: -0.22 (0.16), residues: 1074 loop : -1.00 (0.11), residues: 2662 =============================================================================== Job complete usr+sys time: 34567.80 seconds wall clock time: 598 minutes 0.28 seconds (35880.28 seconds total)