Starting phenix.real_space_refine (version: dev) on Mon May 23 02:55:35 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/05_2022/7acj_11717_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 151803 Number of models: 1 Model: "" Number of chains: 64 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': 1368, 'rna3p_pyr': 1049, 'rna2p_pur': 299, 'rna2p_pyr': 165} Link IDs: {'rna3p': 2433, 'rna2p': 469} 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': 9, 'rna2p': 2, 'rna3p_pur': 747, 'rna3p_pyr': 555, 'rna2p_pur': 122, 'rna2p_pyr': 98} Link IDs: {'rna3p': 1311, 'rna2p': 222} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 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': 9, 'rna3p_pur': 55, 'rna2p_pyr': 8} Link IDs: {'rna3p': 103, 'rna2p': 16} Chain: "4" Number of atoms: 7756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7756 Classifications: {'RNA': 363} Modifications used: {'5*END': 1, 'rna3p': 3, 'rna2p_pyr': 25, 'rna3p_pur': 160, 'rna3p_pyr': 137, 'rna2p_pur': 38} Link IDs: {'rna3p': 300, 'rna2p': 62} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Chain: "A" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 595 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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': 6, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'TRANS': 101, 'PCIS': 1} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1658 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 7, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 553 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "x" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 685 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 5, 'CIS': 1, 'TRANS': 79} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 237 Unusual residues: {' MG': 237} Classifications: {'undetermined': 237} Link IDs: {None: 236} Chain: "2" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Unusual residues: {' MG': 57} Classifications: {'undetermined': 57} Link IDs: {None: 56} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "5" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0N5S SG CYS a 16 123.685 93.179 40.799 1.00164.55 S ATOM A0N64 SG CYS a 18 123.633 94.526 37.217 1.00162.74 S ATOM A0NA2 SG CYS a 37 126.566 95.275 39.671 1.00159.12 S ATOM A0NAN SG CYS a 40 123.126 96.907 39.973 1.00163.35 S ATOM A0OVG SG CYS f 11 174.080 182.789 87.007 1.00106.21 S ATOM A0OW5 SG CYS f 14 177.535 181.833 88.319 1.00106.86 S ATOM A0OZ0 SG CYS f 27 175.607 184.744 89.904 1.00106.81 S Time building chain proxies: 61.98, per 1000 atoms: 0.41 Number of scatterers: 151803 At special positions: 0 Unit cell: (298.48, 264.16, 246.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 153 16.00 P 4919 15.00 Mg 308 11.99 O 42333 8.00 N 28222 7.00 C 75866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.00 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 9 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10774 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: 171 helices and 69 sheets defined 37.7% alpha, 18.2% beta 1421 base pairs and 2345 stacking pairs defined. Time for finding SS restraints: 61.64 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 3.727A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 46 Processing helix chain '5' and resid 93 through 103 removed outlier: 3.898A pdb=" N ASP 5 98 " --> pdb=" O GLN 5 94 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER 5 99 " --> pdb=" O ARG 5 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU 5 100 " --> pdb=" O GLU 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 160 removed outlier: 3.513A pdb=" N LYS 5 138 " --> pdb=" O LYS 5 134 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER 5 140 " --> pdb=" O HIS 5 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 5 149 " --> pdb=" O ARG 5 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 7.311A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.618A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.563A 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: 3.521A 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: 3.959A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.942A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.706A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.823A 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: 4.419A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.655A pdb=" N VAL C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 98 through 103 removed outlier: 5.969A pdb=" N PHE C 101 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 102 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP C 103 " --> pdb=" O LEU C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'D' and resid 24 through 40 Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.594A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.063A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.110A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.795A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.630A pdb=" N ARG E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.365A pdb=" N VAL E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.446A 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 60 through 81 removed outlier: 4.541A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.106A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 4.024A 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 51 removed outlier: 3.988A pdb=" N ARG G 51 " --> pdb=" O PHE G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 63 removed outlier: 5.481A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 5.066A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 74' Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 98 through 107 removed outlier: 4.070A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.314A pdb=" N ARG J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.533A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.616A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.554A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.508A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.183A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.859A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.336A 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 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.826A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.896A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.375A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.777A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.955A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.105A 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 20 removed outlier: 4.537A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.665A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.839A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.637A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.632A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 99 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.621A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.425A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.766A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.534A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.874A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.109A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.460A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.043A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.659A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.181A 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 removed outlier: 3.738A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 54 removed outlier: 3.733A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.579A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.527A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.628A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 63 removed outlier: 4.978A pdb=" N ASN a 61 " --> pdb=" O ASP a 58 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS a 62 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG a 63 " --> pdb=" O PHE a 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 58 through 63' Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.009A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.046A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.748A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.723A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 4.080A 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: 4.564A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA e 60 " --> pdb=" O GLY e 56 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 4.048A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU g 10 " --> pdb=" O MET g 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS g 11 " --> pdb=" O ARG g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 5.135A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 4.137A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 Processing helix chain 'g' and resid 103 through 121 removed outlier: 4.749A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU g 114 " --> pdb=" O SER g 110 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU g 117 " --> pdb=" O ARG g 113 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU g 118 " --> pdb=" O LEU g 114 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 149 removed outlier: 4.408A pdb=" N MET g 136 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 removed outlier: 4.380A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 removed outlier: 3.582A pdb=" N ASN g 178 " --> pdb=" O LYS g 174 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 226 removed outlier: 3.618A pdb=" N THR g 211 " --> pdb=" O ILE g 207 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.881A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 48 removed outlier: 6.089A pdb=" N PHE h 29 " --> pdb=" O ASN h 25 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.592A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.099A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS h 89 " --> pdb=" O GLU h 85 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL h 91 " --> pdb=" O LEU h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 4.715A pdb=" N SER h 119 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER h 122 " --> pdb=" O ASP h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.775A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.546A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.004A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 4.087A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.754A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.734A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.346A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.614A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.142A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.720A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 119 removed outlier: 4.356A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.885A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU j 144 " --> pdb=" O THR j 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (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 14 through 33 removed outlier: 3.901A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix Processing helix chain 'k' and resid 67 through 82 removed outlier: 5.244A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 5.638A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.539A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.711A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.674A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG l 109 " --> pdb=" O VAL l 105 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.540A pdb=" N ASN l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA l 127 " --> pdb=" O GLU l 123 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA l 128 " --> pdb=" O LEU l 124 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.954A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP l 140 " --> pdb=" O LYS l 136 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG l 143 " --> pdb=" O GLU l 139 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA l 145 " --> pdb=" O VAL l 141 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 3.858A 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 removed outlier: 3.587A pdb=" N GLY m 44 " --> pdb=" O LEU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.675A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 50 removed outlier: 3.920A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 56 removed outlier: 4.767A pdb=" N VAL n 55 " --> pdb=" O PRO n 51 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 51 through 56' Processing helix chain 'n' and resid 71 through 92 Processing helix chain 'n' and resid 93 through 102 removed outlier: 4.787A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.705A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 89 removed outlier: 4.230A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.806A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.025A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.030A 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: 3.756A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 91 through 104 removed outlier: 4.128A pdb=" N SER p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 removed outlier: 3.778A pdb=" N ARG q 9 " --> pdb=" O ASN q 5 " (cutoff:3.500A) Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.811A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 23 removed outlier: 3.886A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 4.310A pdb=" N SER r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.820A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.793A pdb=" N LEU r 80 " --> pdb=" O SER r 76 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET r 81 " --> pdb=" O ILE r 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.532A pdb=" N VAL s 11 " --> pdb=" O LYS s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.552A pdb=" N GLU s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE s 31 " --> pdb=" O LEU s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 51 removed outlier: 3.898A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 3.981A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA t 44 " --> pdb=" O GLN t 40 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.441A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 6.056A pdb=" N THR t 79 " --> pdb=" O VAL t 75 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.728A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU u 77 " --> pdb=" O ALA u 73 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 34 removed outlier: 4.896A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.412A 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 ARG w 57 " --> pdb=" O ARG w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 25 removed outlier: 3.633A pdb=" N LEU x 16 " --> pdb=" O ASP x 12 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS x 17 " --> pdb=" O LEU x 13 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.525A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.718A 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: 3.604A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER y 23 " --> pdb=" O LYS y 19 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG y 24 " --> pdb=" O HIS y 20 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 4.245A pdb=" N GLU y 53 " --> pdb=" O LYS y 49 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 4.203A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA y 62 " --> pdb=" O VAL y 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS y 64 " --> pdb=" O ARG y 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 86 Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 38 removed outlier: 3.591A pdb=" N VAL z 32 " --> pdb=" O VAL z 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG z 34 " --> pdb=" O ALA z 30 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TYR z 38 " --> pdb=" O ARG z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.724A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 48 through 51 removed outlier: 5.043A pdb=" N LYS 5 48 " --> pdb=" O THR 5 71 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '5' and resid 56 through 59 removed outlier: 4.194A pdb=" N PHE 5 64 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG 5 59 " --> pdb=" O GLU 5 62 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU 5 62 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '5' and resid 89 through 92 removed outlier: 3.968A pdb=" N LYS 5 89 " --> pdb=" O ALA 5 35 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA 5 35 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL 5 129 " --> pdb=" O GLU 5 28 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA 5 32 " --> pdb=" O VAL 5 125 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '5' and resid 115 through 119 removed outlier: 4.001A pdb=" N SER 5 115 " --> pdb=" O LYS 5 126 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.317A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 65 through 71 Processing sheet with id= 7, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 8, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.896A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.381A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.686A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.253A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 26 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 201 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 79 through 84 removed outlier: 5.620A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 32 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 179 through 182 Processing sheet with id= 14, first strand: chain 'C' and resid 105 through 108 removed outlier: 7.288A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.624A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.884A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 33 through 40 removed outlier: 3.669A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL E 40 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 127 through 133 removed outlier: 4.444A pdb=" N TYR E 128 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 16 through 19 removed outlier: 4.744A pdb=" N ASP F 16 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS F 27 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS F 18 " --> pdb=" O THR F 25 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.896A pdb=" N GLY F 53 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS F 44 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.925A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 23, first strand: chain 'G' and resid 17 through 20 removed outlier: 5.873A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 128 through 134 removed outlier: 4.659A pdb=" N HIS G 128 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE G 132 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL G 138 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.703A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 63 through 66 removed outlier: 7.270A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 71 through 74 Processing sheet with id= 28, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.504A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.164A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 38 through 45 removed outlier: 5.168A pdb=" N ARG P 39 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.867A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 33, first strand: chain 'R' and resid 18 through 22 removed outlier: 3.864A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.636A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 69 through 78 removed outlier: 5.320A pdb=" N GLU R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN R 91 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 2 through 8 removed outlier: 5.807A pdb=" N HIS S 102 " --> pdb=" O ASP S 77 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 79 through 88 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'T' and resid 28 through 33 removed outlier: 5.894A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS T 70 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 40 through 45 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 41, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.813A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.669A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.156A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'c' and resid 8 through 13 removed outlier: 5.920A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 34 through 39 removed outlier: 5.949A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.766A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'f' and resid 13 through 19 removed outlier: 8.497A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 67 through 71 removed outlier: 4.111A pdb=" N VAL g 163 " --> pdb=" O PHE g 184 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.903A pdb=" N VAL h 66 " --> pdb=" O GLN h 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'h' and resid 164 through 169 removed outlier: 6.009A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL h 200 " --> pdb=" O ASN h 185 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP h 183 " --> pdb=" O ILE h 202 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'i' and resid 140 through 145 removed outlier: 3.986A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE i 182 " --> pdb=" O ASP i 141 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TRP i 170 " --> pdb=" O LYS i 183 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 12 through 16 removed outlier: 4.852A pdb=" N GLY j 40 " --> pdb=" O GLN j 12 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.778A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 33 through 40 Processing sheet with id= 55, first strand: chain 'k' and resid 38 through 42 removed outlier: 5.718A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.748A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 73 through 77 Processing sheet with id= 58, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.521A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU m 60 " --> pdb=" O LYS m 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS m 50 " --> pdb=" O GLU m 60 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.866A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'n' and resid 7 through 11 removed outlier: 3.510A pdb=" N ARG n 18 " --> pdb=" O THR n 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE n 20 " --> pdb=" O TYR n 64 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR n 64 " --> pdb=" O PHE n 20 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU n 61 " --> pdb=" O ASN n 25 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS n 27 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE n 65 " --> pdb=" O VAL n 29 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.376A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE o 6 " --> pdb=" O ILE o 76 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 44 through 53 removed outlier: 7.837A pdb=" N ALA o 61 " --> pdb=" O ILE o 53 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 29 through 36 removed outlier: 4.319A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE p 31 " --> pdb=" O HIS p 24 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 29 through 32 removed outlier: 4.834A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.096A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 4 through 9 removed outlier: 5.981A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL u 19 " --> pdb=" O GLY u 37 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.127A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 20 through 30 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'x' and resid 30 through 34 removed outlier: 3.681A pdb=" N THR x 33 " --> pdb=" O ALA x 50 " (cutoff:3.500A) 1753 hydrogen bonds defined for protein. 5190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3582 hydrogen bonds 5624 hydrogen bond angles 0 basepair planarities 1421 basepair parallelities 2345 stacking parallelities Total time for adding SS restraints: 298.04 Time building geometry restraints manager: 65.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.22: 1000 1.22 - 1.37: 39898 1.37 - 1.52: 81336 1.52 - 1.66: 42275 1.66 - 1.81: 273 Bond restraints: 164782 Sorted by residual: bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.150 1.436 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.150 1.435 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.150 1.434 -0.284 2.00e-02 2.50e+03 2.02e+02 bond pdb=" N PRO r 96 " pdb=" CD PRO r 96 " ideal model delta sigma weight residual 1.473 1.279 0.194 1.40e-02 5.10e+03 1.92e+02 bond pdb=" C ARG C 33 " pdb=" O ARG C 33 " ideal model delta sigma weight residual 1.236 1.076 0.160 1.20e-02 6.94e+03 1.77e+02 ... (remaining 164777 not shown) Histogram of bond angle deviations from ideal: 93.26 - 106.45: 29935 106.45 - 119.63: 141893 119.63 - 132.82: 74945 132.82 - 146.01: 67 146.01 - 159.19: 2 Bond angle restraints: 246842 Sorted by residual: angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C4 2MA 12503 " ideal model delta sigma weight residual 103.49 152.74 -49.25 3.00e+00 1.11e-01 2.69e+02 angle pdb=" C1' 2MA 12503 " pdb=" N9 2MA 12503 " pdb=" C8 2MA 12503 " ideal model delta sigma weight residual 144.94 97.37 47.57 3.00e+00 1.11e-01 2.51e+02 angle pdb=" N ILE r 73 " pdb=" CA ILE r 73 " pdb=" C ILE r 73 " ideal model delta sigma weight residual 110.62 123.14 -12.52 1.02e+00 9.61e-01 1.51e+02 angle pdb=" N LYS r 103 " pdb=" CA LYS r 103 " pdb=" C LYS r 103 " ideal model delta sigma weight residual 111.71 125.15 -13.44 1.15e+00 7.56e-01 1.37e+02 angle pdb=" C1' 2MG 12445 " pdb=" N9 2MG 12445 " pdb=" C4 2MG 12445 " ideal model delta sigma weight residual 109.53 144.30 -34.77 3.00e+00 1.11e-01 1.34e+02 ... (remaining 246837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 84166 35.83 - 71.65: 3117 71.65 - 107.48: 342 107.48 - 143.30: 50 143.30 - 179.13: 58 Dihedral angle restraints: 87733 sinusoidal: 71031 harmonic: 16702 Sorted by residual: dihedral pdb=" C4' G 12677 " pdb=" C3' G 12677 " pdb=" C2' G 12677 " pdb=" C1' G 12677 " ideal model delta sinusoidal sigma weight residual -35.00 34.12 -69.12 1 8.00e+00 1.56e-02 9.65e+01 dihedral pdb=" C4' G 3 51 " pdb=" C3' G 3 51 " pdb=" C2' G 3 51 " pdb=" C1' G 3 51 " ideal model delta sinusoidal sigma weight residual -35.00 34.04 -69.04 1 8.00e+00 1.56e-02 9.63e+01 dihedral pdb=" C5' G 12677 " pdb=" C4' G 12677 " pdb=" C3' G 12677 " pdb=" O3' G 12677 " ideal model delta sinusoidal sigma weight residual 147.00 78.58 68.42 1 8.00e+00 1.56e-02 9.48e+01 ... (remaining 87730 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 30976 0.103 - 0.206: 413 0.206 - 0.309: 74 0.309 - 0.412: 25 0.412 - 0.515: 6 Chirality restraints: 31494 Sorted by residual: chirality pdb=" CA THR r 102 " pdb=" N THR r 102 " pdb=" C THR r 102 " pdb=" CB THR r 102 " both_signs ideal model delta sigma weight residual False 2.53 2.01 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CA LEU C 100 " pdb=" N LEU C 100 " pdb=" C LEU C 100 " pdb=" CB LEU C 100 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA LYS C 154 " pdb=" N LYS C 154 " pdb=" C LYS C 154 " pdb=" CB LYS C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 31491 not shown) Planarity restraints: 12988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 11939 " 0.932 2.00e-02 2.50e+03 6.09e-01 8.36e+03 pdb=" C4' 5MU 11939 " -0.192 2.00e-02 2.50e+03 pdb=" O4' 5MU 11939 " -0.808 2.00e-02 2.50e+03 pdb=" C3' 5MU 11939 " 0.236 2.00e-02 2.50e+03 pdb=" O3' 5MU 11939 " -0.885 2.00e-02 2.50e+03 pdb=" C2' 5MU 11939 " 0.608 2.00e-02 2.50e+03 pdb=" O2' 5MU 11939 " 0.599 2.00e-02 2.50e+03 pdb=" C1' 5MU 11939 " -0.466 2.00e-02 2.50e+03 pdb=" N1 5MU 11939 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.051 2.00e-02 2.50e+03 5.71e-01 7.34e+03 pdb=" C4' 2MG 21207 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.575 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.596 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.942 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.236 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.860 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.046 2.00e-02 2.50e+03 5.58e-01 7.01e+03 pdb=" C4' 2MG 21516 " -0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.550 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.575 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.196 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.930 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.237 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.827 2.00e-02 2.50e+03 ... (remaining 12985 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 30 1.66 - 2.47: 1246 2.47 - 3.28: 157553 3.28 - 4.09: 481345 4.09 - 4.90: 722270 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1362444 Sorted by model distance: nonbonded pdb=" O3' A 11367 " pdb=" NZ LYS d 25 " model vdw 0.852 2.520 nonbonded pdb=" O3' U 12746 " pdb=" NZ LYS F 138 " model vdw 0.949 2.520 nonbonded pdb=" C3' U 12746 " pdb=" NZ LYS F 138 " model vdw 0.955 3.550 nonbonded pdb=" O3' U 12746 " pdb=" CE LYS F 138 " model vdw 1.146 3.440 nonbonded pdb=" OE1 GLU 5 28 " pdb=" CG2 VAL 5 129 " model vdw 1.191 3.460 ... (remaining 1362439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4919 5.49 5 Mg 308 5.21 5 S 153 5.16 5 C 75866 2.51 5 N 28222 2.21 5 O 42333 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.180 Extract box with map and model: 33.770 Check model and map are aligned: 1.700 Convert atoms to be neutral: 0.980 Process input model: 615.880 Find NCS groups from input model: 3.350 Set up NCS constraints: 0.550 Set refine NCS operators: 0.000 Set scattering table: 0.070 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.040 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 663.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.286 164782 Z= 0.182 Angle : 0.642 49.246 246842 Z= 0.352 Chirality : 0.033 0.515 31494 Planarity : 0.017 0.609 12988 Dihedral : 15.457 179.128 76959 Min Nonbonded Distance : 0.852 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -0.99 (0.11), residues: 5756 helix: 1.11 (0.13), residues: 1837 sheet: -1.04 (0.16), residues: 1058 loop : -1.72 (0.11), residues: 2861 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1983 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1954 time to evaluate : 6.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 9 residues processed: 1972 average time/residue: 1.4468 time to fit residues: 4877.9869 Evaluate side-chains 1264 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1255 time to evaluate : 6.549 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 1.0178 time to fit residues: 24.6866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 890 optimal weight: 7.9990 chunk 798 optimal weight: 10.0000 chunk 443 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 538 optimal weight: 0.5980 chunk 426 optimal weight: 20.0000 chunk 826 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 502 optimal weight: 1.9990 chunk 614 optimal weight: 0.9990 chunk 957 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS C 32 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 148 GLN C 150 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 173 GLN D 30 GLN E 52 ASN F 115 HIS K 3 GLN K 93 GLN L 54 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN X 23 ASN Y 39 GLN b 6 ASN f 35 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS h 19 ASN h 69 HIS h 123 GLN h 176 HIS ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN ** l 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 110 GLN o 58 ASN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 66 GLN u 59 HIS ** v 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 56 HIS Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.120 164782 Z= 0.278 Angle : 0.696 16.049 246842 Z= 0.363 Chirality : 0.036 0.359 31494 Planarity : 0.007 0.132 12988 Dihedral : 16.293 179.858 65420 Min Nonbonded Distance : 0.954 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.45 % Favored : 93.50 % Rotamer Outliers : 4.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.25 (0.11), residues: 5756 helix: 0.60 (0.12), residues: 1862 sheet: -0.93 (0.16), residues: 1055 loop : -1.79 (0.11), residues: 2839 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1533 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1331 time to evaluate : 6.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 202 outliers final: 136 residues processed: 1437 average time/residue: 1.3975 time to fit residues: 3531.0914 Evaluate side-chains 1323 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1187 time to evaluate : 6.808 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 0 residues processed: 136 average time/residue: 1.1555 time to fit residues: 307.7224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 531 optimal weight: 6.9990 chunk 297 optimal weight: 20.0000 chunk 796 optimal weight: 30.0000 chunk 651 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 958 optimal weight: 6.9990 chunk 1035 optimal weight: 5.9990 chunk 853 optimal weight: 8.9990 chunk 950 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 769 optimal weight: 0.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 81 GLN F 116 GLN G 28 ASN G 33 GLN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 44 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 40 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 ASN c 45 GLN g 109 GLN ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN l 148 ASN m 67 GLN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 3 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 56 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.112 164782 Z= 0.326 Angle : 0.702 15.698 246842 Z= 0.368 Chirality : 0.038 0.425 31494 Planarity : 0.007 0.137 12988 Dihedral : 16.525 179.924 65420 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.04 % Favored : 92.89 % Rotamer Outliers : 3.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.11), residues: 5756 helix: 0.35 (0.12), residues: 1872 sheet: -1.03 (0.16), residues: 1039 loop : -1.81 (0.11), residues: 2845 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1264 time to evaluate : 6.807 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: 181 outliers final: 105 residues processed: 1371 average time/residue: 1.3665 time to fit residues: 3312.9389 Evaluate side-chains 1248 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1143 time to evaluate : 6.919 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 0 residues processed: 105 average time/residue: 1.1818 time to fit residues: 242.6150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 947 optimal weight: 1.9990 chunk 720 optimal weight: 5.9990 chunk 497 optimal weight: 7.9990 chunk 106 optimal weight: 50.0000 chunk 457 optimal weight: 20.0000 chunk 643 optimal weight: 6.9990 chunk 962 optimal weight: 20.0000 chunk 1018 optimal weight: 4.9990 chunk 502 optimal weight: 8.9990 chunk 912 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN F 64 GLN J 58 ASN K 29 HIS K 93 GLN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN Y 25 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 ASN b 42 HIS ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 GLN p 40 ASN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 105 ASN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 59 HIS ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.102 164782 Z= 0.326 Angle : 0.705 15.294 246842 Z= 0.370 Chirality : 0.038 0.375 31494 Planarity : 0.006 0.133 12988 Dihedral : 16.630 178.566 65420 Min Nonbonded Distance : 0.955 Molprobity Statistics. All-atom Clashscore : 15.90 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.44 (0.11), residues: 5756 helix: 0.32 (0.12), residues: 1872 sheet: -1.01 (0.16), residues: 1047 loop : -1.82 (0.11), residues: 2837 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1388 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1219 time to evaluate : 6.719 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: 169 outliers final: 100 residues processed: 1302 average time/residue: 1.3819 time to fit residues: 3203.9452 Evaluate side-chains 1246 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1146 time to evaluate : 6.891 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 0 residues processed: 100 average time/residue: 1.1978 time to fit residues: 234.8267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 848 optimal weight: 5.9990 chunk 578 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 758 optimal weight: 5.9990 chunk 420 optimal weight: 20.0000 chunk 869 optimal weight: 0.6980 chunk 704 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 520 optimal weight: 0.6980 chunk 914 optimal weight: 40.0000 chunk 257 optimal weight: 10.0000 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN Q 72 ASN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 ASN g 168 HIS ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS h 123 GLN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 164782 Z= 0.172 Angle : 0.622 17.588 246842 Z= 0.332 Chirality : 0.033 0.395 31494 Planarity : 0.006 0.125 12988 Dihedral : 16.474 179.999 65420 Min Nonbonded Distance : 1.040 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.74 % Favored : 93.21 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 5756 helix: 0.50 (0.12), residues: 1883 sheet: -0.95 (0.16), residues: 1066 loop : -1.71 (0.11), residues: 2807 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1244 time to evaluate : 6.922 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: 114 outliers final: 62 residues processed: 1300 average time/residue: 1.3411 time to fit residues: 3085.7249 Evaluate side-chains 1210 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 1148 time to evaluate : 6.735 Switching outliers to nearest non-outliers outliers start: 62 outliers final: 0 residues processed: 62 average time/residue: 1.1405 time to fit residues: 141.0479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 342 optimal weight: 10.0000 chunk 917 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 598 optimal weight: 8.9990 chunk 251 optimal weight: 10.0000 chunk 1019 optimal weight: 7.9990 chunk 846 optimal weight: 6.9990 chunk 472 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 535 optimal weight: 1.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 33 ASN e 31 HIS ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS i 89 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 52 GLN ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN y 13 GLN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.122 164782 Z= 0.408 Angle : 0.760 15.762 246842 Z= 0.395 Chirality : 0.041 0.392 31494 Planarity : 0.007 0.138 12988 Dihedral : 16.787 179.815 65420 Min Nonbonded Distance : 0.951 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.39 % Favored : 91.56 % Rotamer Outliers : 3.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.50 (0.11), residues: 5756 helix: 0.23 (0.12), residues: 1880 sheet: -1.13 (0.16), residues: 1064 loop : -1.80 (0.11), residues: 2812 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1156 time to evaluate : 6.645 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 outliers start: 153 outliers final: 99 residues processed: 1227 average time/residue: 1.3977 time to fit residues: 3043.9470 Evaluate side-chains 1215 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1116 time to evaluate : 6.804 Switching outliers to nearest non-outliers outliers start: 99 outliers final: 0 residues processed: 99 average time/residue: 1.1614 time to fit residues: 228.2697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 983 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 581 optimal weight: 6.9990 chunk 744 optimal weight: 0.4980 chunk 577 optimal weight: 4.9990 chunk 858 optimal weight: 9.9990 chunk 569 optimal weight: 5.9990 chunk 1015 optimal weight: 5.9990 chunk 635 optimal weight: 8.9990 chunk 619 optimal weight: 20.0000 chunk 469 optimal weight: 40.0000 overall best weight: 4.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** Y 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 ASN ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 5 ASN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 105 ASN ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.158 164782 Z= 0.273 Angle : 0.680 15.389 246842 Z= 0.360 Chirality : 0.037 0.451 31494 Planarity : 0.006 0.131 12988 Dihedral : 16.691 179.976 65420 Min Nonbonded Distance : 0.988 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.80 % Favored : 92.15 % Rotamer Outliers : 1.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.43 (0.11), residues: 5756 helix: 0.32 (0.12), residues: 1872 sheet: -1.11 (0.16), residues: 1039 loop : -1.76 (0.11), residues: 2845 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1184 time to evaluate : 8.973 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: 69 outliers final: 39 residues processed: 1219 average time/residue: 1.3564 time to fit residues: 2933.4464 Evaluate side-chains 1163 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1124 time to evaluate : 6.910 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 1.1259 time to fit residues: 90.3681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 628 optimal weight: 0.8980 chunk 405 optimal weight: 20.0000 chunk 606 optimal weight: 9.9990 chunk 306 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 645 optimal weight: 4.9990 chunk 692 optimal weight: 0.9990 chunk 502 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 798 optimal weight: 8.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 163 GLN ** B 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 90 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN g 15 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.108 164782 Z= 0.270 Angle : 0.678 15.432 246842 Z= 0.359 Chirality : 0.037 0.525 31494 Planarity : 0.006 0.130 12988 Dihedral : 16.673 179.749 65420 Min Nonbonded Distance : 0.987 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.30 % Favored : 91.64 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.41 (0.11), residues: 5756 helix: 0.29 (0.12), residues: 1885 sheet: -1.10 (0.16), residues: 1054 loop : -1.73 (0.11), residues: 2817 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1224 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1153 time to evaluate : 6.768 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: 71 outliers final: 48 residues processed: 1181 average time/residue: 1.3296 time to fit residues: 2780.8907 Evaluate side-chains 1169 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1121 time to evaluate : 6.772 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 1.1133 time to fit residues: 109.4180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 924 optimal weight: 8.9990 chunk 973 optimal weight: 4.9990 chunk 887 optimal weight: 9.9990 chunk 946 optimal weight: 0.3980 chunk 972 optimal weight: 10.0000 chunk 569 optimal weight: 3.9990 chunk 412 optimal weight: 20.0000 chunk 743 optimal weight: 2.9990 chunk 290 optimal weight: 10.0000 chunk 855 optimal weight: 6.9990 chunk 895 optimal weight: 2.9990 overall best weight: 3.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 90 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN g 15 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 118 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN v 51 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.4483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.108 164782 Z= 0.210 Angle : 0.650 15.232 246842 Z= 0.345 Chirality : 0.035 0.448 31494 Planarity : 0.006 0.127 12988 Dihedral : 16.583 179.427 65420 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.51 % Favored : 92.44 % Rotamer Outliers : 0.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.35 (0.11), residues: 5756 helix: 0.33 (0.12), residues: 1893 sheet: -1.04 (0.16), residues: 1063 loop : -1.69 (0.11), residues: 2800 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1177 time to evaluate : 6.706 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: 46 outliers final: 31 residues processed: 1191 average time/residue: 1.3454 time to fit residues: 2839.3704 Evaluate side-chains 1153 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1122 time to evaluate : 6.863 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 1.1436 time to fit residues: 74.8195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 943 optimal weight: 9.9990 chunk 621 optimal weight: 30.0000 chunk 1001 optimal weight: 3.9990 chunk 610 optimal weight: 0.8980 chunk 474 optimal weight: 50.0000 chunk 695 optimal weight: 0.9990 chunk 1050 optimal weight: 10.0000 chunk 966 optimal weight: 1.9990 chunk 836 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 645 optimal weight: 0.5980 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 90 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN g 15 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** g 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 8 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 GLN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN y 61 GLN ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.124 164782 Z= 0.157 Angle : 0.629 19.428 246842 Z= 0.334 Chirality : 0.033 0.375 31494 Planarity : 0.006 0.121 12988 Dihedral : 16.434 179.599 65420 Min Nonbonded Distance : 1.088 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.09 % Favored : 92.84 % Rotamer Outliers : 0.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % 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: -1.23 (0.11), residues: 5756 helix: 0.43 (0.12), residues: 1889 sheet: -0.96 (0.16), residues: 1056 loop : -1.63 (0.11), residues: 2811 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1203 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1179 time to evaluate : 6.836 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: 24 outliers final: 14 residues processed: 1188 average time/residue: 1.4310 time to fit residues: 3019.2125 Evaluate side-chains 1148 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1134 time to evaluate : 6.905 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 1.1456 time to fit residues: 37.8698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 512 optimal weight: 0.9980 chunk 664 optimal weight: 6.9990 chunk 890 optimal weight: 5.9990 chunk 256 optimal weight: 10.0000 chunk 770 optimal weight: 9.9990 chunk 123 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 837 optimal weight: 8.9990 chunk 350 optimal weight: 10.0000 chunk 859 optimal weight: 10.0000 chunk 106 optimal weight: 50.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 239 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 90 ASN ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 79 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.072501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.051490 restraints weight = 556405.646| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 1.59 r_work: 0.3088 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 1.51 restraints_weight: 0.2500 r_work: 0.3072 rms_B_bonded: 1.55 restraints_weight: 0.1250 r_work: 0.3064 rms_B_bonded: 1.61 restraints_weight: 0.0625 r_work: 0.3056 rms_B_bonded: 1.71 restraints_weight: 0.0312 r_work: 0.3047 rms_B_bonded: 1.82 restraints_weight: 0.0156 r_work: 0.3038 rms_B_bonded: 1.95 restraints_weight: 0.0078 r_work: 0.3029 rms_B_bonded: 2.10 restraints_weight: 0.0039 r_work: 0.3019 rms_B_bonded: 2.26 restraints_weight: 0.0020 r_work: 0.3009 rms_B_bonded: 2.45 restraints_weight: 0.0010 r_work: 0.2998 rms_B_bonded: 2.65 restraints_weight: 0.0005 r_work: 0.2987 rms_B_bonded: 2.87 restraints_weight: 0.0002 r_work: 0.2975 rms_B_bonded: 3.12 restraints_weight: 0.0001 r_work: 0.2962 rms_B_bonded: 3.39 restraints_weight: 0.0001 r_work: 0.2949 rms_B_bonded: 3.68 restraints_weight: 0.0000 r_work: 0.2934 rms_B_bonded: 4.00 restraints_weight: 0.0000 r_work: 0.2919 rms_B_bonded: 4.34 restraints_weight: 0.0000 r_work: 0.2903 rms_B_bonded: 4.72 restraints_weight: 0.0000 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.4750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.117 164782 Z= 0.385 Angle : 0.752 15.924 246842 Z= 0.391 Chirality : 0.041 0.465 31494 Planarity : 0.007 0.136 12988 Dihedral : 16.685 178.416 65420 Min Nonbonded Distance : 0.954 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.36 % Favored : 91.59 % Rotamer Outliers : 0.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.11), residues: 5756 helix: 0.15 (0.12), residues: 1881 sheet: -1.02 (0.16), residues: 1062 loop : -1.72 (0.11), residues: 2813 =============================================================================== Job complete usr+sys time: 46949.45 seconds wall clock time: 806 minutes 52.36 seconds (48412.36 seconds total)