Starting phenix.real_space_refine (version: dev) on Wed Apr 13 12:01:08 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nwt_12635/04_2022/7nwt_12635_updated.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.021 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 "L PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 149932 Number of models: 1 Model: "" Number of chains: 74 Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 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: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'TRANS': 101, 'PCIS': 1} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna3p': 16, 'rna2p': 6, 'rna3p_pur': 1378, 'rna3p_pyr': 1049, 'rna2p_pur': 289, 'rna2p_pyr': 165} Link IDs: {'rna3p': 2443, 'rna2p': 459} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna3p': 10, 'rna2p': 1, 'rna3p_pur': 751, 'rna3p_pyr': 564, 'rna2p_pur': 118, 'rna2p_pyr': 89} Link IDs: {'rna3p': 1326, 'rna2p': 207} Chain breaks: 1 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 8} Link IDs: {'rna3p': 105, 'rna2p': 14} Chain: "5" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1622 Unusual residues: {'8AN': 1} Classifications: {'undetermined': 1, 'RNA': 75} Modifications used: {'rna3p': 3, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna2p': 2, 'rna3p_pyr': 27, 'rna2p_pur': 5} Link IDs: {'p': 1, 'rna3p': 61, 'rna2p': 13} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 3 Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "XX" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 176 Classifications: {'RNA': 8} Modifications used: {'rna3p_pyr': 2, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 6, 'rna2p': 1} Chain: "AA" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1067 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "BB" Number of atoms: 1111 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 130, 1089 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 130, 1089 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 7, 'TRANS': 122} bond proxies already assigned to first conformer: 1100 Chain: "CC" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1048 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 6, 'TRANS': 118} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" 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: "1" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 290, 290 Unusual residues: {' MG': 290} Classifications: {'undetermined': 290} Link IDs: {None: 289} Chain: "2" Number of atoms: 128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 128 Unusual residues: {' MG': 128} Classifications: {'undetermined': 128} Link IDs: {None: 127} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "5" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3, 'peptide': 1} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "BB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0KPG SG CYS f 11 60.519 143.409 129.674 1.00 57.54 S ATOM A0KQ5 SG CYS f 14 61.522 142.411 133.100 1.00 54.72 S ATOM A0KT0 SG CYS f 27 59.851 139.944 130.871 1.00 55.15 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARGBB 46 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGBB 46 " occ=0.50 residue: pdb=" N AARGBB 100 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARGBB 100 " occ=0.50 residue: pdb="MG MG 13144 " occ=0.50 Time building chain proxies: 62.20, per 1000 atoms: 0.41 Number of scatterers: 149932 At special positions: 0 Unit cell: (243.96, 258.94, 273.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 169 16.00 P 4641 15.00 Mg 437 11.99 O 41094 8.00 N 27837 7.00 C 75752 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=2.04 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 55.78 Conformation dependent library (CDL) restraints added in 6.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 3 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11714 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: 194 helices and 74 sheets defined 38.6% alpha, 19.6% beta 1490 base pairs and 2552 stacking pairs defined. Time for finding SS restraints: 60.55 Creating SS restraints... Processing helix chain 'B' and resid 10 through 17 removed outlier: 3.531A pdb=" N ARG B 14 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 10 through 17' Processing helix chain 'B' and resid 30 through 35 removed outlier: 4.131A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.659A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 207 through 215 removed outlier: 4.076A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 3.750A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.008A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 6.011A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.578A pdb=" N HIS C 67 " --> pdb=" O PRO C 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.144A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'D' and resid 15 through 20 Processing helix chain 'D' and resid 24 through 40 removed outlier: 3.805A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.575A pdb=" N VAL D 113 " --> pdb=" O LEU D 109 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG D 114 " --> pdb=" O SER D 110 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN D 115 " --> pdb=" O GLU D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.513A pdb=" N MET D 141 " --> pdb=" O LYS D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.635A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.691A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.609A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.503A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.620A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA E 59 " --> pdb=" O ALA E 55 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 3.566A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.827A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.599A pdb=" N ALA E 43 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ILE E 44 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.702A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 removed outlier: 4.463A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.615A pdb=" N SER F 74 " --> pdb=" O ALA F 70 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE F 77 " --> pdb=" O ASN F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.727A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 50 removed outlier: 4.518A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU G 48 " --> pdb=" O ILE G 44 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ARG G 50 " --> pdb=" O PHE G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.712A pdb=" N LEU G 58 " --> pdb=" O LEU G 54 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LEU G 62 " --> pdb=" O LEU G 58 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 3.522A pdb=" N ALA G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA G 106 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.859A pdb=" N ALA H 10 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N VAL H 12 " --> pdb=" O LYS H 8 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLU H 14 " --> pdb=" O ALA H 10 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLU H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ALA H 19 " --> pdb=" O VAL H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.601A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N GLU H 40 " --> pdb=" O ASP H 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU H 41 " --> pdb=" O LYS H 37 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ARG H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N GLY H 45 " --> pdb=" O LEU H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 68 removed outlier: 5.649A pdb=" N GLY H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Proline residue: H 68 - end of helix No H-bonds generated for 'chain 'H' and resid 62 through 68' Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.781A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 4.502A pdb=" N GLU H 98 " --> pdb=" O ARG H 94 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ALA H 102 " --> pdb=" O GLU H 98 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N ASN H 103 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N ALA H 104 " --> pdb=" O ALA H 100 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS H 105 " --> pdb=" O LYS H 101 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 23 through 29 removed outlier: 5.026A pdb=" N LEU I 27 " --> pdb=" O VAL I 23 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 46 removed outlier: 3.778A pdb=" N PHE I 37 " --> pdb=" O ASN I 33 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N CYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA I 40 " --> pdb=" O GLU I 36 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN I 42 " --> pdb=" O CYS I 38 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N ASP I 46 " --> pdb=" O ASN I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 74 through 84 removed outlier: 4.516A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N ALA I 82 " --> pdb=" O LEU I 78 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA I 83 " --> pdb=" O LEU I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 96 Processing helix chain 'I' and resid 101 through 113 removed outlier: 5.040A pdb=" N LEU I 105 " --> pdb=" O SER I 101 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN I 106 " --> pdb=" O ARG I 102 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR I 111 " --> pdb=" O GLU I 107 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 136 removed outlier: 4.476A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR I 125 " --> pdb=" O ILE I 121 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.047A 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: 4.179A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.724A 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: 3.661A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 4.408A pdb=" N LYS J 72 " --> pdb=" O ASN J 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 67 through 72' Processing helix chain 'K' and resid 104 through 109 removed outlier: 4.533A pdb=" N ARG K 108 " --> pdb=" O THR K 104 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N SER K 109 " --> pdb=" O ARG K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.053A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.820A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 3.948A 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 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.530A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY L 139 " --> pdb=" O ILE L 135 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.519A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.647A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.765A 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 58 removed outlier: 4.325A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.619A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.807A 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: 4.656A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 4.551A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 3.578A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.836A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 4.582A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.191A 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: 3.519A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.712A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 32 through 37 removed outlier: 3.996A pdb=" N GLN Q 37 " --> pdb=" O ARG Q 33 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.963A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.616A 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: 3.501A 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: 3.827A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 40 removed outlier: 3.882A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ASN S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 3.799A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 70 removed outlier: 3.815A pdb=" N LEU S 69 " --> pdb=" O ASP S 65 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N LYS S 70 " --> pdb=" O ILE S 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 65 through 70' Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.906A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.894A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.278A 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: 3.783A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.178A 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 9 removed outlier: 4.067A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 3.535A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.784A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.539A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 44 through 51 removed outlier: 5.669A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ARG a 49 " --> pdb=" O THR a 45 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ASP a 50 " --> pdb=" O GLY a 46 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VAL a 51 " --> pdb=" O LYS a 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 44 through 51' Processing helix chain 'a' and resid 55 through 64 removed outlier: 3.615A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.747A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 24 removed outlier: 4.329A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.858A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.484A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 removed outlier: 3.711A pdb=" N ARG e 45 " --> pdb=" O LYS e 41 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.675A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.299A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'e' and resid 26 through 31 removed outlier: 4.857A pdb=" N LEU e 29 " --> pdb=" O HIS e 26 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N ARG e 30 " --> pdb=" O ALA e 27 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N HIS e 31 " --> pdb=" O ASN e 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 26 through 31' Processing helix chain 'g' and resid 5 through 13 removed outlier: 4.323A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 3.638A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 removed outlier: 3.571A pdb=" N VAL g 47 " --> pdb=" O LEU g 43 " (cutoff:3.500A) Proline residue: g 48 - end of helix removed outlier: 3.541A pdb=" N GLU g 52 " --> pdb=" O PRO g 48 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 88 removed outlier: 5.567A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ASP g 82 " --> pdb=" O GLU g 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 124 removed outlier: 4.276A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 130 removed outlier: 4.657A pdb=" N THR g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 148 removed outlier: 3.667A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 removed outlier: 3.525A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 3.574A pdb=" N SER g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.088A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 48 removed outlier: 4.389A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 82 through 96 Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.248A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.303A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.738A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.558A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.651A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.761A pdb=" N LEU i 91 " --> pdb=" O GLY i 87 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 removed outlier: 3.595A pdb=" N TYR i 103 " --> pdb=" O ASP i 99 " (cutoff:3.500A) Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.732A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.763A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.640A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.550A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.070A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.578A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.338A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU j 116 " --> pdb=" O ARG j 112 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLY j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 4.051A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 11 through 19 removed outlier: 3.711A pdb=" N SER k 15 " --> pdb=" O HIS k 11 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N GLU k 16 " --> pdb=" O PRO k 12 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N GLN k 17 " --> pdb=" O ASP k 13 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix No H-bonds generated for 'chain 'k' and resid 11 through 19' Processing helix chain 'k' and resid 20 through 33 removed outlier: 3.840A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 3.518A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLU k 73 " --> pdb=" O GLU k 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N THR k 77 " --> pdb=" O GLU k 73 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.575A pdb=" N PHE l 26 " --> pdb=" O LEU l 22 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.750A pdb=" N ARG l 53 " --> pdb=" O THR l 49 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER l 54 " --> pdb=" O LEU l 50 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.716A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 112 removed outlier: 3.957A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N GLY l 112 " --> pdb=" O ALA l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.501A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 40 removed outlier: 4.352A pdb=" N GLY n 40 " --> pdb=" O GLU n 36 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.510A pdb=" N VAL n 47 " --> pdb=" O THR n 43 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 4.031A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 92 Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.630A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.743A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLU o 27 " --> pdb=" O ALA o 23 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 91 removed outlier: 3.921A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.267A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.051A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 removed outlier: 3.510A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA p 73 " --> pdb=" O ARG p 69 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) Processing helix chain 'p' and resid 93 through 104 removed outlier: 4.071A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 10 Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.860A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.799A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.064A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.530A pdb=" N LEU r 80 " --> pdb=" O SER r 76 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.724A pdb=" N VAL s 14 " --> pdb=" O GLU s 10 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.652A pdb=" N LYS s 28 " --> pdb=" O ARG s 24 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 51 removed outlier: 3.756A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 removed outlier: 3.566A pdb=" N ARG s 85 " --> pdb=" O ARG s 81 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU s 86 " --> pdb=" O ILE s 82 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 3.568A pdb=" N GLN t 35 " --> pdb=" O LEU t 31 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 3.865A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 3.683A pdb=" N GLU t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.563A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ALA u 82 " --> pdb=" O VAL u 78 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.261A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.505A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.613A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER x 25 " --> pdb=" O LYS x 21 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.501A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 3.521A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 3.504A pdb=" N GLU y 53 " --> pdb=" O LYS y 49 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.596A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 3.542A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.549A pdb=" N ARG z 18 " --> pdb=" O VAL z 14 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 removed outlier: 3.511A pdb=" N GLU z 36 " --> pdb=" O VAL z 32 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 66 removed outlier: 3.648A pdb=" N LYS z 58 " --> pdb=" O LYS z 54 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N ALA z 65 " --> pdb=" O ALA z 61 " (cutoff:3.500A) Processing helix chain 'AA' and resid 47 through 58 Processing helix chain 'AA' and resid 114 through 127 removed outlier: 3.590A pdb=" N PHEAA 122 " --> pdb=" O LEUAA 118 " (cutoff:3.500A) Processing helix chain 'BB' and resid 47 through 58 Processing helix chain 'BB' and resid 114 through 127 Processing helix chain 'CC' and resid 47 through 58 Processing helix chain 'CC' and resid 114 through 127 Processing sheet with id= 1, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.601A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLY B 127 " --> pdb=" O GLN B 115 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN B 117 " --> pdb=" O GLY B 127 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.474A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 90 through 96 removed outlier: 5.582A pdb=" N ASN B 90 " --> pdb=" O ALA B 106 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.480A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 10 through 16 removed outlier: 3.706A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 79 through 84 removed outlier: 5.842A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 1 through 6 removed outlier: 3.869A pdb=" N VAL D 14 " --> pdb=" O MET D 1 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 42 through 46 removed outlier: 4.739A pdb=" N GLY D 42 " --> pdb=" O GLN D 90 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N ARG D 44 " --> pdb=" O ARG D 88 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG D 88 " --> pdb=" O ARG D 44 " (cutoff:3.500A) removed outlier: 5.422A pdb=" N GLN D 46 " --> pdb=" O ALA D 86 " (cutoff:3.500A) removed outlier: 5.696A pdb=" N ALA D 86 " --> pdb=" O GLN D 46 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.418A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.562A pdb=" N LYS E 33 " --> pdb=" O THR E 157 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 12, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 13, first strand: chain 'F' and resid 94 through 99 removed outlier: 6.945A pdb=" N ASN F 101 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL F 113 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 121 through 126 removed outlier: 6.677A pdb=" N GLU F 130 " --> pdb=" O PRO F 126 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'G' and resid 17 through 21 removed outlier: 4.210A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 76 through 82 removed outlier: 5.453A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 18, first strand: chain 'J' and resid 74 through 78 removed outlier: 7.599A pdb=" N GLY J 83 " --> pdb=" O THR J 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.596A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N GLY K 81 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS K 66 " --> pdb=" O GLY K 81 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 71 removed outlier: 4.005A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.700A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N LEU M 33 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS M 100 " --> pdb=" O ALA M 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 73 through 76 removed outlier: 6.781A pdb=" N ILE M 73 " --> pdb=" O GLU M 90 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ASN M 88 " --> pdb=" O GLU M 75 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'M' and resid 30 through 36 removed outlier: 7.944A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.882A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.717A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.261A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.691A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.627A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.038A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 32, first strand: chain 'R' and resid 65 through 68 Processing sheet with id= 33, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.101A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 35, first strand: chain 'T' and resid 29 through 33 removed outlier: 4.477A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'U' and resid 40 through 44 No H-bonds generated for sheet with id= 36 Processing sheet with id= 37, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 38, first strand: chain 'V' and resid 69 through 72 removed outlier: 6.614A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'W' and resid 51 through 54 removed outlier: 4.178A pdb=" N THR W 58 " --> pdb=" O GLY W 54 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 66 through 71 Processing sheet with id= 41, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.665A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 35 through 41 Processing sheet with id= 43, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.276A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.168A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 29 through 32 removed outlier: 4.162A pdb=" N GLU b 36 " --> pdb=" O ASP b 31 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'c' and resid 19 through 26 removed outlier: 6.383A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE c 48 " --> pdb=" O SER c 14 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.812A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.548A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'g' and resid 67 through 71 Processing sheet with id= 50, first strand: chain 'h' and resid 53 through 59 removed outlier: 3.581A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.707A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'i' and resid 141 through 145 removed outlier: 6.710A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 11 through 16 removed outlier: 6.622A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.870A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 32 through 41 removed outlier: 7.073A pdb=" N ARG j 45 " --> pdb=" O ASP j 41 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 38 through 42 removed outlier: 5.552A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.630A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 72 through 79 removed outlier: 6.658A pdb=" N THR l 72 " --> pdb=" O VAL l 91 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N TYR l 85 " --> pdb=" O ARG l 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.728A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.620A pdb=" N SER m 74 " --> pdb=" O ALA m 130 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'n' and resid 5 through 11 removed outlier: 4.094A pdb=" N LYS n 27 " --> pdb=" O LEU n 61 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 36 through 40 removed outlier: 7.016A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG o 7 " --> pdb=" O SER o 101 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 64, first strand: chain 'p' and resid 30 through 35 Processing sheet with id= 65, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.041A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.036A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.019A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N GLY u 49 " --> pdb=" O ASN u 40 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 7 through 11 removed outlier: 6.698A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.699A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'v' and resid 19 through 30 No H-bonds generated for sheet with id= 69 Processing sheet with id= 70, first strand: chain 'x' and resid 30 through 33 removed outlier: 4.548A pdb=" N LEU x 47 " --> pdb=" O VAL x 62 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'AA' and resid 24 through 30 removed outlier: 3.646A pdb=" N HISAA 15 " --> pdb=" O PHEAA 30 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N THRAA 88 " --> pdb=" O ARGAA 81 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VALAA 87 " --> pdb=" O TRPAA 108 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYSAA 106 " --> pdb=" O METAA 89 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VALAA 91 " --> pdb=" O VALAA 104 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VALAA 104 " --> pdb=" O VALAA 91 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'AA' and resid 36 through 39 removed outlier: 6.370A pdb=" N TRPAA 36 " --> pdb=" O HISAA 136 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'BB' and resid 36 through 42 Processing sheet with id= 74, first strand: chain 'CC' and resid 104 through 109 removed outlier: 3.831A pdb=" N VALCC 104 " --> pdb=" O VALCC 91 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VALCC 91 " --> pdb=" O VALCC 104 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYSCC 106 " --> pdb=" O METCC 89 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N METCC 89 " --> pdb=" O LYSCC 106 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N TRPCC 36 " --> pdb=" O HISCC 136 " (cutoff:3.500A) 2008 hydrogen bonds defined for protein. 5931 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3700 hydrogen bonds 5750 hydrogen bond angles 0 basepair planarities 1490 basepair parallelities 2552 stacking parallelities Total time for adding SS restraints: 322.77 Time building geometry restraints manager: 61.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.51: 125404 1.51 - 1.88: 36772 1.88 - 2.25: 0 2.25 - 2.61: 0 2.61 - 2.98: 1 Bond restraints: 162177 Sorted by residual: bond pdb=" O3' G 21276 " pdb=" P C 21277 " ideal model delta sigma weight residual 1.607 2.978 -1.371 1.50e-02 4.44e+03 8.35e+03 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.150 1.438 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C5 5MU 5 54 " pdb=" C6 5MU 5 54 " ideal model delta sigma weight residual 1.150 1.433 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.150 1.429 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.805 1.593 0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 162172 not shown) Histogram of bond angle deviations from ideal: 65.48 - 86.86: 2 86.86 - 108.25: 48155 108.25 - 129.64: 190444 129.64 - 151.03: 3363 151.03 - 172.41: 1 Bond angle restraints: 241965 Sorted by residual: angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" OP2 C 21277 " ideal model delta sigma weight residual 108.00 172.41 -64.41 3.00e+00 1.11e-01 4.61e+02 angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" O5' C 21277 " ideal model delta sigma weight residual 104.00 74.40 29.60 1.50e+00 4.44e-01 3.89e+02 angle pdb=" O3' G 21276 " pdb=" P C 21277 " pdb=" OP1 C 21277 " ideal model delta sigma weight residual 108.00 65.48 42.52 3.00e+00 1.11e-01 2.01e+02 angle pdb=" C3' G 21276 " pdb=" O3' G 21276 " pdb=" P C 21277 " ideal model delta sigma weight residual 120.20 99.20 21.00 1.50e+00 4.44e-01 1.96e+02 angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C4 2MA 12503 " ideal model delta sigma weight residual 103.49 124.16 -20.67 3.00e+00 1.11e-01 4.75e+01 ... (remaining 241960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 83793 35.89 - 71.79: 2733 71.79 - 107.68: 240 107.68 - 143.57: 8 143.57 - 179.46: 34 Dihedral angle restraints: 86808 sinusoidal: 68656 harmonic: 18152 Sorted by residual: dihedral pdb=" O4' U 2 632 " pdb=" C1' U 2 632 " pdb=" N1 U 2 632 " pdb=" C2 U 2 632 " ideal model delta sinusoidal sigma weight residual 200.00 27.26 172.74 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 30.49 169.51 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' U 2 467 " pdb=" C1' U 2 467 " pdb=" N1 U 2 467 " pdb=" C2 U 2 467 " ideal model delta sinusoidal sigma weight residual 200.00 42.56 157.44 1 1.50e+01 4.44e-03 8.21e+01 ... (remaining 86805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 26703 0.070 - 0.141: 3697 0.141 - 0.211: 262 0.211 - 0.282: 37 0.282 - 0.352: 7 Chirality restraints: 30706 Sorted by residual: chirality pdb=" C1' G 1 748 " pdb=" O4' G 1 748 " pdb=" C2' G 1 748 " pdb=" N9 G 1 748 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 3.10e+00 chirality pdb=" C1' G 1 512 " pdb=" O4' G 1 512 " pdb=" C2' G 1 512 " pdb=" N9 G 1 512 " both_signs ideal model delta sigma weight residual False 2.44 2.10 0.33 2.00e-01 2.50e+01 2.80e+00 chirality pdb=" CB 0TD q 89 " pdb=" CA 0TD q 89 " pdb=" SB 0TD q 89 " pdb=" CG 0TD q 89 " both_signs ideal model delta sigma weight residual False 3.04 2.71 0.33 2.00e-01 2.50e+01 2.80e+00 ... (remaining 30703 not shown) Planarity restraints: 13418 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " 0.088 2.00e-02 2.50e+03 6.39e-01 9.20e+03 pdb=" C4' 7MG 2 527 " 0.471 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.757 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.662 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.190 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 0.981 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.175 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -1.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.035 2.00e-02 2.50e+03 6.13e-01 8.45e+03 pdb=" C4' 2MG 12445 " 0.468 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " 0.795 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " -0.591 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " -0.594 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " -0.233 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " 0.900 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " 0.183 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " -0.963 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.060 2.00e-02 2.50e+03 6.04e-01 8.21e+03 pdb=" C4' 2MG 21207 " 0.448 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.676 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.628 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.189 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.955 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.213 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.940 2.00e-02 2.50e+03 ... (remaining 13415 not shown) Histogram of nonbonded interaction distances: 1.14 - 1.90: 21 1.90 - 2.65: 6035 2.65 - 3.40: 175517 3.40 - 4.15: 510113 4.15 - 4.90: 696545 Nonbonded interactions: 1388231 Sorted by model distance: nonbonded pdb="MG MG 21713 " pdb="MG MG 21714 " model vdw 1.145 1.300 nonbonded pdb=" OP1 G 1 962 " pdb="MG MG 13024 " model vdw 1.829 2.170 nonbonded pdb=" OP1 C 12006 " pdb="MG MG 13029 " model vdw 1.833 2.170 nonbonded pdb=" OP1 A 11272 " pdb="MG MG 13030 " model vdw 1.837 2.170 nonbonded pdb=" OP1 U 12074 " pdb="MG MG 13187 " model vdw 1.850 2.170 ... (remaining 1388226 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'AA' and (resid 12 through 45 or resid 47 through 99 or resid 101 through \ 136)) selection = (chain 'BB' and (resid 12 through 45 or resid 47 through 99 or resid 101 through \ 136)) selection = (chain 'CC' and (resid 12 through 45 or resid 47 through 99 or resid 101 through \ 136)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4641 5.49 5 Mg 437 5.21 5 S 169 5.16 5 C 75752 2.51 5 N 27837 2.21 5 O 41094 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.180 Extract box with map and model: 27.900 Check model and map are aligned: 1.630 Convert atoms to be neutral: 0.960 Process input model: 635.780 Find NCS groups from input model: 3.510 Set up NCS constraints: 0.480 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: 0.020 Load rotamer database and sin/cos tables:13.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 690.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 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 : 0.011 1.371 162177 Z= 0.670 Angle : 0.836 64.412 241965 Z= 0.394 Chirality : 0.048 0.352 30706 Planarity : 0.019 0.639 13418 Dihedral : 14.154 179.464 75091 Min Nonbonded Distance : 1.145 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.58 % Favored : 97.41 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.09), residues: 6249 helix: -2.37 (0.09), residues: 1995 sheet: -0.69 (0.14), residues: 1292 loop : -1.21 (0.10), residues: 2962 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1181 time to evaluate : 6.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 82 residues processed: 1303 average time/residue: 2.2300 time to fit residues: 4185.6773 Evaluate side-chains 1165 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1083 time to evaluate : 6.621 Switching outliers to nearest non-outliers outliers start: 82 outliers final: 70 residues processed: 14 average time/residue: 1.3529 time to fit residues: 39.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 905 optimal weight: 1.9990 chunk 812 optimal weight: 4.9990 chunk 450 optimal weight: 3.9990 chunk 277 optimal weight: 0.8980 chunk 548 optimal weight: 0.6980 chunk 434 optimal weight: 4.9990 chunk 840 optimal weight: 5.9990 chunk 325 optimal weight: 8.9990 chunk 510 optimal weight: 0.7980 chunk 625 optimal weight: 5.9990 chunk 973 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 GLN D 195 GLN E 27 GLN E 127 ASN F 104 ASN K 5 GLN O 116 GLN P 41 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN g 178 ASN h 3 GLN h 140 ASN h 185 ASN i 71 GLN i 152 GLN k 52 ASN k 63 ASN l 142 HIS o 20 GLN o 64 GLN s 4 GLN w 31 ASN w 54 GLN w 74 HIS y 55 GLN y 84 ASN AA 19 GLN AA 40 HIS AA 105 GLN ** BB 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN CC 105 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 162177 Z= 0.176 Angle : 0.625 14.575 241965 Z= 0.340 Chirality : 0.036 0.313 30706 Planarity : 0.006 0.132 13418 Dihedral : 13.792 179.213 62598 Min Nonbonded Distance : 1.142 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 3.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.97 (0.10), residues: 6249 helix: -0.37 (0.11), residues: 2040 sheet: -0.31 (0.14), residues: 1300 loop : -0.87 (0.11), residues: 2909 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 206 poor density : 1172 time to evaluate : 6.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 206 outliers final: 106 residues processed: 1284 average time/residue: 2.2227 time to fit residues: 4154.2412 Evaluate side-chains 1215 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1109 time to evaluate : 6.663 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 72 residues processed: 36 average time/residue: 1.4660 time to fit residues: 96.5405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 541 optimal weight: 10.0000 chunk 302 optimal weight: 4.9990 chunk 810 optimal weight: 7.9990 chunk 662 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 975 optimal weight: 6.9990 chunk 1053 optimal weight: 10.0000 chunk 868 optimal weight: 10.0000 chunk 967 optimal weight: 5.9990 chunk 332 optimal weight: 6.9990 chunk 782 optimal weight: 0.0030 overall best weight: 4.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 ASN ** D 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 27 GLN E 127 ASN P 41 GLN S 31 GLN T 28 ASN V 12 GLN Y 20 ASN Y 31 GLN d 26 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 140 ASN i 152 GLN l 142 HIS p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN v 9 GLN w 54 GLN w 74 HIS ** AA 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 40 HIS AA 93 HIS ** BB 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BB 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.087 162177 Z= 0.417 Angle : 0.746 14.509 241965 Z= 0.391 Chirality : 0.043 0.312 30706 Planarity : 0.007 0.148 13418 Dihedral : 13.962 179.363 62598 Min Nonbonded Distance : 1.061 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 4.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.54 (0.10), residues: 6249 helix: 0.28 (0.12), residues: 2029 sheet: -0.10 (0.14), residues: 1284 loop : -0.85 (0.11), residues: 2936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1368 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1129 time to evaluate : 6.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 239 outliers final: 152 residues processed: 1269 average time/residue: 2.2381 time to fit residues: 4117.2960 Evaluate side-chains 1260 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1108 time to evaluate : 6.316 Switching outliers to nearest non-outliers outliers start: 152 outliers final: 95 residues processed: 58 average time/residue: 1.4099 time to fit residues: 147.1626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 963 optimal weight: 8.9990 chunk 733 optimal weight: 10.0000 chunk 506 optimal weight: 5.9990 chunk 107 optimal weight: 9.9990 chunk 465 optimal weight: 30.0000 chunk 654 optimal weight: 5.9990 chunk 978 optimal weight: 4.9990 chunk 1036 optimal weight: 9.9990 chunk 511 optimal weight: 4.9990 chunk 927 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN D 195 GLN O 104 GLN S 31 GLN S 60 HIS T 28 ASN V 12 GLN Y 31 GLN c 45 GLN d 26 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN w 54 GLN w 74 HIS AA 93 HIS BB 120 HIS CC 51 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.086 162177 Z= 0.398 Angle : 0.729 14.175 241965 Z= 0.384 Chirality : 0.043 0.306 30706 Planarity : 0.007 0.147 13418 Dihedral : 13.972 179.952 62598 Min Nonbonded Distance : 1.080 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 5.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.32 (0.10), residues: 6249 helix: 0.56 (0.12), residues: 2027 sheet: 0.05 (0.14), residues: 1259 loop : -0.80 (0.11), residues: 2963 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1125 time to evaluate : 6.688 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 266 outliers final: 165 residues processed: 1281 average time/residue: 2.2510 time to fit residues: 4186.3753 Evaluate side-chains 1265 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1100 time to evaluate : 6.464 Switching outliers to nearest non-outliers outliers start: 165 outliers final: 111 residues processed: 55 average time/residue: 1.3889 time to fit residues: 136.7600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 862 optimal weight: 8.9990 chunk 588 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 771 optimal weight: 10.0000 chunk 427 optimal weight: 6.9990 chunk 884 optimal weight: 0.5980 chunk 716 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 529 optimal weight: 70.0000 chunk 930 optimal weight: 10.0000 chunk 261 optimal weight: 8.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 136 GLN D 195 GLN E 27 GLN N 18 GLN O 38 GLN O 104 GLN S 31 GLN T 28 ASN V 12 GLN Y 20 ASN Y 31 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 139 GLN h 140 ASN i 71 GLN i 152 GLN l 68 ASN l 142 HIS o 20 GLN p 28 ASN p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN v 9 GLN w 54 GLN w 74 HIS AA 34 GLN AA 93 HIS AA 120 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN CC 105 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 162177 Z= 0.346 Angle : 0.695 13.756 241965 Z= 0.370 Chirality : 0.041 0.304 30706 Planarity : 0.007 0.144 13418 Dihedral : 13.941 179.629 62598 Min Nonbonded Distance : 1.086 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer Outliers : 4.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.17 (0.10), residues: 6249 helix: 0.76 (0.12), residues: 2029 sheet: 0.07 (0.14), residues: 1276 loop : -0.75 (0.11), residues: 2944 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1113 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 256 outliers final: 163 residues processed: 1270 average time/residue: 2.2025 time to fit residues: 4064.7338 Evaluate side-chains 1261 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1098 time to evaluate : 6.641 Switching outliers to nearest non-outliers outliers start: 163 outliers final: 110 residues processed: 54 average time/residue: 1.4626 time to fit residues: 141.4749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 348 optimal weight: 20.0000 chunk 933 optimal weight: 4.9990 chunk 204 optimal weight: 10.0000 chunk 608 optimal weight: 10.0000 chunk 255 optimal weight: 3.9990 chunk 1037 optimal weight: 0.9990 chunk 861 optimal weight: 0.0670 chunk 480 optimal weight: 7.9990 chunk 86 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 544 optimal weight: 7.9990 overall best weight: 3.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN F 22 GLN G 73 ASN N 18 GLN O 104 GLN S 31 GLN T 28 ASN V 12 GLN Y 20 ASN Y 31 GLN d 26 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS o 20 GLN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 63 GLN v 9 GLN w 54 GLN w 74 HIS AA 93 HIS AA 120 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BB 120 HIS CC 51 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.1461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 162177 Z= 0.308 Angle : 0.671 13.826 241965 Z= 0.359 Chirality : 0.039 0.302 30706 Planarity : 0.007 0.142 13418 Dihedral : 13.895 179.041 62598 Min Nonbonded Distance : 1.097 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer Outliers : 4.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.03 (0.10), residues: 6249 helix: 0.90 (0.12), residues: 2027 sheet: 0.12 (0.14), residues: 1276 loop : -0.68 (0.11), residues: 2946 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1348 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 230 poor density : 1118 time to evaluate : 6.605 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 230 outliers final: 161 residues processed: 1261 average time/residue: 2.2988 time to fit residues: 4201.2871 Evaluate side-chains 1262 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1101 time to evaluate : 6.444 Switching outliers to nearest non-outliers outliers start: 161 outliers final: 120 residues processed: 42 average time/residue: 1.5971 time to fit residues: 117.5734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 999 optimal weight: 5.9990 chunk 116 optimal weight: 40.0000 chunk 590 optimal weight: 8.9990 chunk 757 optimal weight: 10.0000 chunk 586 optimal weight: 10.0000 chunk 873 optimal weight: 6.9990 chunk 579 optimal weight: 6.9990 chunk 1033 optimal weight: 6.9990 chunk 646 optimal weight: 10.0000 chunk 629 optimal weight: 10.0000 chunk 477 optimal weight: 5.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN N 18 GLN O 104 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN c 45 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 139 GLN h 140 ASN i 71 GLN i 152 GLN l 142 HIS p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 63 GLN v 9 GLN w 54 GLN w 74 HIS AA 93 HIS ** AA 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** BB 32 HIS BB 34 GLN ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.172 162177 Z= 0.538 Angle : 0.833 15.446 241965 Z= 0.428 Chirality : 0.048 0.333 30706 Planarity : 0.008 0.153 13418 Dihedral : 14.099 178.422 62598 Min Nonbonded Distance : 1.034 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer Outliers : 4.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.18 (0.10), residues: 6249 helix: 0.72 (0.12), residues: 2034 sheet: 0.09 (0.14), residues: 1241 loop : -0.75 (0.11), residues: 2974 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1113 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 233 outliers final: 170 residues processed: 1260 average time/residue: 2.2374 time to fit residues: 4094.4875 Evaluate side-chains 1278 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1108 time to evaluate : 6.633 Switching outliers to nearest non-outliers outliers start: 170 outliers final: 125 residues processed: 46 average time/residue: 1.4509 time to fit residues: 119.9243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 639 optimal weight: 6.9990 chunk 412 optimal weight: 2.9990 chunk 617 optimal weight: 10.0000 chunk 311 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 200 optimal weight: 0.8980 chunk 656 optimal weight: 5.9990 chunk 703 optimal weight: 10.0000 chunk 510 optimal weight: 2.9990 chunk 96 optimal weight: 9.9990 chunk 812 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS N 18 GLN O 104 GLN Q 20 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN d 26 ASN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 152 GLN l 142 HIS ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN v 9 GLN w 31 ASN w 74 HIS AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.102 162177 Z= 0.240 Angle : 0.646 14.056 241965 Z= 0.350 Chirality : 0.037 0.297 30706 Planarity : 0.006 0.139 13418 Dihedral : 13.894 179.260 62598 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 3.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: 0.06 (0.10), residues: 6249 helix: 0.99 (0.12), residues: 2033 sheet: 0.16 (0.14), residues: 1263 loop : -0.63 (0.11), residues: 2953 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1298 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1124 time to evaluate : 6.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 174 outliers final: 137 residues processed: 1261 average time/residue: 2.2925 time to fit residues: 4191.2502 Evaluate side-chains 1247 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1110 time to evaluate : 6.607 Switching outliers to nearest non-outliers outliers start: 137 outliers final: 119 residues processed: 18 average time/residue: 1.8611 time to fit residues: 59.3173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 939 optimal weight: 10.0000 chunk 989 optimal weight: 0.9990 chunk 903 optimal weight: 9.9990 chunk 962 optimal weight: 9.9990 chunk 579 optimal weight: 7.9990 chunk 419 optimal weight: 50.0000 chunk 756 optimal weight: 10.0000 chunk 295 optimal weight: 8.9990 chunk 870 optimal weight: 0.1980 chunk 910 optimal weight: 9.9990 chunk 959 optimal weight: 7.9990 overall best weight: 5.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN K 29 HIS N 18 GLN O 104 GLN Q 20 GLN Q 59 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN d 29 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 68 ASN l 142 HIS p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN w 54 GLN w 74 HIS AA 93 HIS AA 120 HIS BB 32 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** CC 51 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.093 162177 Z= 0.434 Angle : 0.757 14.401 241965 Z= 0.396 Chirality : 0.044 0.313 30706 Planarity : 0.007 0.148 13418 Dihedral : 13.989 179.491 62598 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.05 (0.10), residues: 6249 helix: 0.83 (0.12), residues: 2051 sheet: 0.15 (0.14), residues: 1245 loop : -0.67 (0.11), residues: 2953 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1279 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1099 time to evaluate : 6.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 180 outliers final: 146 residues processed: 1237 average time/residue: 2.2866 time to fit residues: 4108.8138 Evaluate side-chains 1241 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1095 time to evaluate : 6.237 Switching outliers to nearest non-outliers outliers start: 146 outliers final: 120 residues processed: 26 average time/residue: 1.4672 time to fit residues: 72.2851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 632 optimal weight: 6.9990 chunk 1018 optimal weight: 10.0000 chunk 621 optimal weight: 10.0000 chunk 483 optimal weight: 10.0000 chunk 707 optimal weight: 7.9990 chunk 1067 optimal weight: 30.0000 chunk 982 optimal weight: 4.9990 chunk 850 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 656 optimal weight: 6.9990 chunk 521 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN E 81 GLN K 29 HIS N 18 GLN O 104 GLN Q 20 GLN Q 59 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN c 45 GLN f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN v 9 GLN w 54 GLN w 74 HIS AA 93 HIS AA 120 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.105 162177 Z= 0.524 Angle : 0.823 15.240 241965 Z= 0.423 Chirality : 0.047 0.320 30706 Planarity : 0.008 0.152 13418 Dihedral : 14.058 178.973 62598 Min Nonbonded Distance : 1.049 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 3.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % 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: -0.15 (0.10), residues: 6249 helix: 0.73 (0.12), residues: 2044 sheet: 0.08 (0.14), residues: 1254 loop : -0.71 (0.11), residues: 2951 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12498 Ramachandran restraints generated. 6249 Oldfield, 0 Emsley, 6249 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1104 time to evaluate : 6.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 162 outliers final: 138 residues processed: 1235 average time/residue: 2.3248 time to fit residues: 4157.2704 Evaluate side-chains 1236 residues out of total 5215 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1098 time to evaluate : 6.489 Switching outliers to nearest non-outliers outliers start: 138 outliers final: 122 residues processed: 16 average time/residue: 1.5642 time to fit residues: 48.9355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1072 random chunks: chunk 675 optimal weight: 5.9990 chunk 905 optimal weight: 7.9990 chunk 260 optimal weight: 0.9990 chunk 784 optimal weight: 0.9980 chunk 125 optimal weight: 3.9990 chunk 236 optimal weight: 1.9990 chunk 851 optimal weight: 0.9990 chunk 356 optimal weight: 3.9990 chunk 874 optimal weight: 5.9990 chunk 107 optimal weight: 30.0000 chunk 156 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 GLN E 81 GLN K 29 HIS N 18 GLN O 104 GLN Q 20 GLN Q 59 GLN S 31 GLN T 28 ASN V 12 GLN Y 31 GLN a 33 ASN e 26 HIS f 13 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 109 GLN h 8 ASN h 140 ASN i 71 GLN i 152 GLN l 142 HIS p 109 ASN ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN w 31 ASN w 54 GLN w 74 HIS ** AA 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AA 93 HIS ** BB 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.129536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.107768 restraints weight = 181647.639| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 0.34 r_work: 0.3222 rms_B_bonded: 0.94 restraints_weight: 0.5000 r_work: 0.3148 rms_B_bonded: 1.85 restraints_weight: 0.2500 r_work: 0.3039 rms_B_bonded: 3.22 restraints_weight: 0.1250 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3589 r_free = 0.3589 target_work(ls_wunit_k1) = 0.130 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.078 162177 Z= 0.185 Angle : 0.642 14.762 241965 Z= 0.350 Chirality : 0.037 0.331 30706 Planarity : 0.006 0.135 13418 Dihedral : 13.979 179.234 62598 Min Nonbonded Distance : 1.109 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.37 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.10), residues: 6249 helix: 0.94 (0.12), residues: 2048 sheet: 0.14 (0.14), residues: 1273 loop : -0.62 (0.11), residues: 2928 =============================================================================== Job complete usr+sys time: 50693.93 seconds wall clock time: 867 minutes 48.48 seconds (52068.48 seconds total)