Starting phenix.real_space_refine (version: dev) on Sat Apr 16 06:01:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/04_2022/7ac7_11713_updated.pdb" } resolution = 3.08 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 "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 154883 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna3p': 17, 'rna2p': 5, 'rna3p_pur': 1383, 'rna3p_pyr': 1049, 'rna2p_pur': 284, 'rna2p_pyr': 165} Link IDs: {'rna3p': 2449, 'rna2p': 453} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 33049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33049 Classifications: {'RNA': 1540} Modifications used: {'rna3p': 9, 'rna2p': 2, 'rna3p_pur': 751, 'rna3p_pyr': 567, 'rna2p_pur': 118, 'rna2p_pyr': 92} Link IDs: {'rna3p': 1327, 'rna2p': 212} 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': 50, 'rna2p_pur': 8, 'rna3p_pur': 56, 'rna2p_pyr': 6} Link IDs: {'rna3p': 106, 'rna2p': 13} Chain: "4" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7759 Classifications: {'RNA': 363} Modifications used: {'rna3p_pyr': 140, 'rna2p_pur': 36, 'rna3p_pur': 162, 'rna2p_pyr': 22, 'rna3p': 3} Link IDs: {'rna3p': 304, 'rna2p': 58} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1191 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "7" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1635 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna3p': 9, 'rna2p': 1, 'rna3p_pur': 30, 'rna3p_pyr': 27, 'rna2p_pur': 7, 'rna2p_pyr': 2} Link IDs: {'rna3p': 66, 'rna2p': 9} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 3 Chain: "8" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 324 Classifications: {'RNA': 15} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna3p': 12, 'rna2p': 2} Chain: "A" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 202, 'PCIS': 1} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "J" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1121 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'TRANS': 101, 'PCIS': 1} Chain: "S" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} 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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 115, 'PCIS': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "u" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "x" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 303 Unusual residues: {' MG': 303} Classifications: {'undetermined': 303} Link IDs: {None: 302} Chain: "2" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Unusual residues: {' MG': 118} Classifications: {'undetermined': 118} Link IDs: {None: 117} Chain: "3" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0PHS SG CYS a 16 127.816 62.831 51.629 1.00118.01 S ATOM A0PI4 SG CYS a 18 126.172 63.218 48.263 1.00118.69 S ATOM A0PM2 SG CYS a 37 129.541 64.841 48.909 1.00115.85 S ATOM A0PMN SG CYS a 40 126.468 66.294 50.503 1.00116.70 S ATOM A0R79 SG CYS f 11 175.751 163.840 62.710 1.00 89.32 S ATOM A0RAT SG CYS f 27 176.766 165.974 63.682 1.00 88.06 S Time building chain proxies: 63.78, per 1000 atoms: 0.41 Number of scatterers: 154883 At special positions: 0 Unit cell: (315.12, 270.4, 231.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 156 16.00 P 5015 15.00 Mg 441 11.99 O 43172 8.00 N 28740 7.00 C 77357 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: 59.59 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " Number of angles added : 6 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10986 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: 180 helices and 72 sheets defined 38.7% alpha, 19.3% beta 1407 base pairs and 2186 stacking pairs defined. Time for finding SS restraints: 63.26 Creating SS restraints... Processing helix chain '5' and resid 18 through 24 Processing helix chain '5' and resid 38 through 45 removed outlier: 4.404A pdb=" N LYS 5 42 " --> pdb=" O GLY 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 107 removed outlier: 4.629A pdb=" N GLU 5 107 " --> pdb=" O ARG 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 157 removed outlier: 3.907A pdb=" N ARG 5 145 " --> pdb=" O ASP 5 141 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN 5 157 " --> pdb=" O ARG 5 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 removed outlier: 5.187A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 17' Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.877A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.726A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 4.860A 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: 4.868A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.401A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.952A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.756A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.639A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 24 through 41 removed outlier: 5.418A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.820A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.299A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.879A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.320A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.960A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix No H-bonds generated for 'chain 'E' and resid 24 through 29' Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.105A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 47' Processing helix chain 'E' and resid 48 through 62 removed outlier: 3.640A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.977A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.593A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.112A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.054A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 3.853A 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 48 removed outlier: 3.922A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 76 removed outlier: 4.311A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 4.194A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.720A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.879A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.591A pdb=" N THR H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Proline residue: H 68 - end of helix removed outlier: 3.895A pdb=" N CYS H 71 " --> pdb=" O THR H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 79 removed outlier: 4.924A pdb=" N PHE H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 72 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.922A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 114 removed outlier: 6.588A pdb=" N ALA H 112 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU H 114 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.360A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.716A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.951A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.776A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.141A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 4.469A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.881A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.803A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.114A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.864A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.940A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.041A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.761A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.784A pdb=" N LYS N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.655A 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 3 through 20 removed outlier: 3.931A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.424A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.002A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.186A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 5.081A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.778A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.982A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.672A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (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: 4.001A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.554A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.269A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.698A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.839A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.863A 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: 3.649A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.697A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.500A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 5 through 10 removed outlier: 5.186A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 5 through 10' Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.606A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 60 removed outlier: 4.128A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 3.646A pdb=" N LEU Z 24 " --> pdb=" O HIS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 41 through 46 Processing helix chain 'a' and resid 55 through 64 removed outlier: 4.438A pdb=" N ARG a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 21 removed outlier: 4.489A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.535A pdb=" N SER d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.788A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.427A 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 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.651A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.588A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 24 through 29 removed outlier: 4.256A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix No H-bonds generated for 'chain 'g' and resid 24 through 29' Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 3.907A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.271A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 4.620A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.771A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.501A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 4.317A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 81 through 96 removed outlier: 3.533A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.224A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 removed outlier: 4.067A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.205A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.633A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.507A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.761A pdb=" N ASN i 74 " --> pdb=" O ARG i 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR i 75 " --> pdb=" O GLN i 71 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.539A 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 Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.846A pdb=" N LEU i 159 " --> pdb=" O VAL i 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.843A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.496A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU i 203 " --> pdb=" O LEU i 199 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.714A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.741A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU j 116 " --> pdb=" O ARG j 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.601A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 17 through 33 Processing helix chain 'k' and resid 67 through 82 removed outlier: 3.656A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 4.463A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 Processing helix chain 'l' and resid 57 through 70 Processing helix chain 'l' and resid 92 through 111 Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 Processing helix chain 'm' and resid 112 through 120 removed outlier: 3.818A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.739A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 4.120A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.575A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 Processing helix chain 'o' and resid 80 through 91 removed outlier: 5.659A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.316A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.712A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.585A 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 Processing helix chain 'p' and resid 91 through 104 removed outlier: 4.307A pdb=" N SER p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.945A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.686A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.532A pdb=" N ILE r 33 " --> pdb=" O ARG r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.073A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.616A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 51 removed outlier: 3.663A pdb=" N TRP s 42 " --> pdb=" O ASP s 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 removed outlier: 3.553A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 43 removed outlier: 4.290A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.498A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.806A pdb=" N GLN u 63 " --> pdb=" O HIS u 59 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 81 removed outlier: 4.459A pdb=" N ALA u 81 " --> pdb=" O GLU u 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.821A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.407A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.887A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.749A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.963A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.598A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 70 through 76' Processing helix chain 'y' and resid 4 through 42 removed outlier: 3.807A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE y 31 " --> pdb=" O MET y 27 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU y 40 " --> pdb=" O TYR y 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY y 42 " --> pdb=" O ALA y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 4.055A pdb=" N GLN y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 86 removed outlier: 3.552A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.701A pdb=" N ALA z 15 " --> pdb=" O PRO z 11 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 38 removed outlier: 4.198A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR z 38 " --> pdb=" O ARG z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 66 removed outlier: 4.066A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 49 through 52 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain '5' and resid 89 through 92 removed outlier: 4.899A pdb=" N LYS 5 89 " --> pdb=" O ALA 5 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY 5 33 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.564A pdb=" N GLY A 54 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 65 through 71 Processing sheet with id= 5, first strand: chain 'B' and resid 33 through 36 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.927A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.180A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.416A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.176A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 13.409A pdb=" N GLY C 198 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 11.714A pdb=" N LYS C 114 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.761A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.751A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.706A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.519A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.686A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.698A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP D 168 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.768A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 18, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 19, first strand: chain 'F' and resid 94 through 98 removed outlier: 4.184A pdb=" N ARG F 95 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER F 106 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.364A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG F 163 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 18 through 21 removed outlier: 4.441A pdb=" N MET G 1 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 77 through 82 removed outlier: 6.448A pdb=" N VAL G 138 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY G 126 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.562A pdb=" N ALA H 25 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.887A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.648A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 120 through 123 removed outlier: 4.195A pdb=" N LYS L 141 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.703A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.810A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 53 removed outlier: 4.136A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS O 34 " --> pdb=" O THR O 31 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.570A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 52 removed outlier: 4.343A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.595A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 19 through 22 Processing sheet with id= 35, first strand: chain 'R' and resid 31 through 36 removed outlier: 4.405A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.415A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.806A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY S 79 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.343A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.354A 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 46 removed outlier: 4.964A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN U 46 " --> pdb=" O GLY U 57 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 83 through 86 removed outlier: 3.701A pdb=" N PHE U 95 " --> pdb=" O GLY U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 75 through 78 removed outlier: 3.758A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 71 through 74 removed outlier: 5.220A pdb=" N LYS V 71 " --> pdb=" O ALA V 94 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.638A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 34 through 41 removed outlier: 3.599A pdb=" N VAL X 51 " --> pdb=" O HIS X 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG X 45 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.340A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN Z 9 " --> pdb=" O HIS Z 34 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.503A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 19 through 24 removed outlier: 5.926A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'e' and resid 22 through 25 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'f' and resid 1 through 4 removed outlier: 6.905A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.717A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 89 through 93 removed outlier: 3.620A pdb=" N ILE g 186 " --> pdb=" O VAL g 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 53, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.844A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.593A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 11 through 16 removed outlier: 3.876A pdb=" N GLY j 40 " --> pdb=" O GLN j 12 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.636A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 33 through 40 Processing sheet with id= 58, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.753A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.972A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR k 59 " --> pdb=" O GLY k 43 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 73 through 79 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.370A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.539A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 64, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.557A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 66, first strand: chain 'p' and resid 29 through 36 removed outlier: 4.077A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.145A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 36 through 41 removed outlier: 4.786A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.140A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 7 through 11 removed outlier: 3.591A pdb=" N LEU v 8 " --> pdb=" O ILE v 61 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 19 through 31 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'x' and resid 30 through 34 1932 hydrogen bonds defined for protein. 5718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3598 hydrogen bonds 5988 hydrogen bond angles 0 basepair planarities 1407 basepair parallelities 2186 stacking parallelities Total time for adding SS restraints: 313.80 Time building geometry restraints manager: 66.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12376 1.29 - 1.42: 71640 1.42 - 1.55: 73637 1.55 - 1.68: 10057 1.68 - 1.82: 275 Bond restraints: 167985 Sorted by residual: bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.150 1.441 -0.291 2.00e-02 2.50e+03 2.11e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.150 1.440 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.150 1.440 -0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" C5 5MU 7 54 " pdb=" C6 5MU 7 54 " ideal model delta sigma weight residual 1.150 1.438 -0.288 2.00e-02 2.50e+03 2.08e+02 bond pdb=" C4 5MU 7 54 " pdb=" C5 5MU 7 54 " ideal model delta sigma weight residual 1.805 1.611 0.194 2.00e-02 2.50e+03 9.42e+01 ... (remaining 167980 not shown) Histogram of bond angle deviations from ideal: 98.64 - 109.18: 66321 109.18 - 119.72: 112032 119.72 - 130.25: 70841 130.25 - 140.79: 2452 140.79 - 151.33: 3 Bond angle restraints: 251649 Sorted by residual: angle pdb=" N1 MIA 7 37 " pdb=" C2 MIA 7 37 " pdb=" S10 MIA 7 37 " ideal model delta sigma weight residual 75.64 128.57 -52.93 3.00e+00 1.11e-01 3.11e+02 angle pdb=" N3 MIA 7 37 " pdb=" C2 MIA 7 37 " pdb=" S10 MIA 7 37 " ideal model delta sigma weight residual 164.14 111.21 52.93 3.00e+00 1.11e-01 3.11e+02 angle pdb=" C1' MIA 7 37 " pdb=" N9 MIA 7 37 " pdb=" C8 MIA 7 37 " ideal model delta sigma weight residual 81.43 123.59 -42.16 3.00e+00 1.11e-01 1.98e+02 angle pdb=" C1' MA6 21518 " pdb=" N9 MA6 21518 " pdb=" C4 MA6 21518 " ideal model delta sigma weight residual 112.44 151.33 -38.89 3.00e+00 1.11e-01 1.68e+02 angle pdb=" C1' MA6 21519 " pdb=" N9 MA6 21519 " pdb=" C4 MA6 21519 " ideal model delta sigma weight residual 112.44 150.82 -38.38 3.00e+00 1.11e-01 1.64e+02 ... (remaining 251644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 86218 35.79 - 71.58: 2833 71.58 - 107.37: 265 107.37 - 143.15: 34 143.15 - 178.94: 48 Dihedral angle restraints: 89398 sinusoidal: 72372 harmonic: 17026 Sorted by residual: dihedral pdb=" C5* PSU 2 516 " pdb=" C4* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" O3* PSU 2 516 " ideal model delta sinusoidal sigma weight residual 147.00 76.76 70.24 1 8.00e+00 1.56e-02 9.93e+01 dihedral pdb=" C4' A 8 9 " pdb=" C3' A 8 9 " pdb=" C2' A 8 9 " pdb=" C1' A 8 9 " ideal model delta sinusoidal sigma weight residual -35.00 34.85 -69.85 1 8.00e+00 1.56e-02 9.83e+01 dihedral pdb=" C4' U 12506 " pdb=" C3' U 12506 " pdb=" C2' U 12506 " pdb=" C1' U 12506 " ideal model delta sinusoidal sigma weight residual -35.00 34.78 -69.78 1 8.00e+00 1.56e-02 9.82e+01 ... (remaining 89395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 31636 0.113 - 0.226: 415 0.226 - 0.339: 38 0.339 - 0.453: 7 0.453 - 0.566: 4 Chirality restraints: 32100 Sorted by residual: chirality pdb=" C3' C 4 78 " pdb=" C4' C 4 78 " pdb=" O3' C 4 78 " pdb=" C2' C 4 78 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.00e+00 chirality pdb=" CA THR e 34 " pdb=" N THR e 34 " pdb=" C THR e 34 " pdb=" CB THR e 34 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C3' C 4 314 " pdb=" C4' C 4 314 " pdb=" O3' C 4 314 " pdb=" C2' C 4 314 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 32097 not shown) Planarity restraints: 13244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.053 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 2MG 21516 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.669 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.622 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.191 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.953 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.008 2.00e-02 2.50e+03 5.92e-01 7.88e+03 pdb=" C4' 2MG 12445 " -0.472 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.879 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.570 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.487 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.298 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.771 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.178 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.035 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 2MG 21207 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.687 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.584 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.916 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.214 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.908 2.00e-02 2.50e+03 ... (remaining 13241 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 17 1.93 - 2.67: 8285 2.67 - 3.41: 197224 3.41 - 4.16: 493365 4.16 - 4.90: 690005 Nonbonded interactions: 1388896 Sorted by model distance: nonbonded pdb=" N6 A 11046 " pdb=" OD1 ASN H 4 " model vdw 1.183 2.520 nonbonded pdb=" O ASN G 66 " pdb=" OE1 GLU G 70 " model vdw 1.247 3.040 nonbonded pdb=" OP1 U 11083 " pdb=" CB LEU H 41 " model vdw 1.254 3.440 nonbonded pdb=" OE2 GLU n 42 " pdb=" NH1 ARG n 45 " model vdw 1.254 2.520 nonbonded pdb=" O3' A 4 363 " pdb=" C ALA W 2 " model vdw 1.285 3.270 ... (remaining 1388891 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 5015 5.49 5 Mg 441 5.21 5 S 156 5.16 5 C 77357 2.51 5 N 28740 2.21 5 O 43172 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: 6.070 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: 0.160 Extract box with map and model: 33.690 Check model and map are aligned: 1.710 Convert atoms to be neutral: 0.980 Process input model: 630.940 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.420 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 679.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 0.291 167985 Z= 0.183 Angle : 0.582 52.932 251649 Z= 0.315 Chirality : 0.032 0.566 32100 Planarity : 0.019 0.600 13244 Dihedral : 14.376 178.942 78412 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.05 % Favored : 96.74 % Rotamer Outliers : 0.66 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 5865 helix: 1.34 (0.13), residues: 1928 sheet: -0.56 (0.15), residues: 1174 loop : -1.33 (0.11), residues: 2763 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1887 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1855 time to evaluate : 6.568 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 outliers start: 32 outliers final: 6 residues processed: 1874 average time/residue: 1.6768 time to fit residues: 5387.6332 Evaluate side-chains 1183 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1177 time to evaluate : 6.753 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 1.4464 time to fit residues: 23.5683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 906 optimal weight: 10.0000 chunk 813 optimal weight: 9.9990 chunk 451 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 548 optimal weight: 3.9990 chunk 434 optimal weight: 10.0000 chunk 841 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 511 optimal weight: 1.9990 chunk 625 optimal weight: 4.9990 chunk 974 optimal weight: 0.0980 overall best weight: 3.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 130 GLN C 173 GLN D 163 ASN E 127 ASN F 104 ASN L 38 GLN ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN Q 37 GLN X 34 HIS Y 20 ASN Y 31 GLN f 37 GLN g 39 HIS i 116 GLN i 131 ASN l 68 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 56 HIS q 46 ASN ** s 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN x 14 HIS y 3 ASN y 13 GLN y 61 GLN y 82 GLN y 84 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 167985 Z= 0.257 Angle : 0.648 15.564 251649 Z= 0.346 Chirality : 0.034 0.409 32100 Planarity : 0.006 0.128 13244 Dihedral : 14.915 179.799 66665 Min Nonbonded Distance : 1.065 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.58 % Favored : 96.28 % Rotamer Outliers : 3.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.11), residues: 5865 helix: 1.12 (0.12), residues: 1975 sheet: -0.50 (0.15), residues: 1113 loop : -1.21 (0.11), residues: 2777 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1488 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1302 time to evaluate : 6.642 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: 186 outliers final: 98 residues processed: 1392 average time/residue: 1.4414 time to fit residues: 3511.1904 Evaluate side-chains 1286 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1188 time to evaluate : 6.779 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 1.1788 time to fit residues: 229.1883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 541 optimal weight: 5.9990 chunk 302 optimal weight: 10.0000 chunk 810 optimal weight: 0.5980 chunk 663 optimal weight: 7.9990 chunk 268 optimal weight: 7.9990 chunk 976 optimal weight: 20.0000 chunk 1054 optimal weight: 6.9990 chunk 869 optimal weight: 10.0000 chunk 968 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 783 optimal weight: 8.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 136 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN F 104 ASN J 58 ASN J 138 GLN N 11 ASN N 62 ASN T 48 GLN V 12 GLN Y 45 GLN b 42 HIS c 19 HIS i 116 GLN ** j 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 52 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN r 105 ASN s 35 ASN s 43 ASN t 38 HIS t 46 HIS t 80 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN y 75 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.3699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.101 167985 Z= 0.439 Angle : 0.727 14.219 251649 Z= 0.382 Chirality : 0.040 0.301 32100 Planarity : 0.007 0.150 13244 Dihedral : 15.335 179.574 66665 Min Nonbonded Distance : 0.971 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.36 % Favored : 95.55 % Rotamer Outliers : 2.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.11), residues: 5865 helix: 0.83 (0.12), residues: 1985 sheet: -0.43 (0.15), residues: 1114 loop : -1.23 (0.11), residues: 2766 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1407 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1285 time to evaluate : 6.754 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 outliers start: 122 outliers final: 66 residues processed: 1345 average time/residue: 1.4681 time to fit residues: 3460.2347 Evaluate side-chains 1255 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1189 time to evaluate : 6.853 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 1.2454 time to fit residues: 164.1775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 964 optimal weight: 5.9990 chunk 733 optimal weight: 7.9990 chunk 506 optimal weight: 20.0000 chunk 108 optimal weight: 40.0000 chunk 465 optimal weight: 50.0000 chunk 655 optimal weight: 0.9980 chunk 979 optimal weight: 10.0000 chunk 1037 optimal weight: 8.9990 chunk 511 optimal weight: 9.9990 chunk 928 optimal weight: 7.9990 chunk 279 optimal weight: 20.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS A 76 ASN ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN F 104 ASN K 5 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 59 GLN S 9 HIS V 12 GLN ** a 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 ASN k 68 GLN l 130 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 81 HIS p 22 HIS t 80 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.4009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.106 167985 Z= 0.464 Angle : 0.719 14.690 251649 Z= 0.381 Chirality : 0.041 0.308 32100 Planarity : 0.007 0.141 13244 Dihedral : 15.380 179.680 66665 Min Nonbonded Distance : 0.956 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.33 % Favored : 95.58 % Rotamer Outliers : 3.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.11), residues: 5865 helix: 0.78 (0.12), residues: 1992 sheet: -0.42 (0.16), residues: 1107 loop : -1.27 (0.11), residues: 2766 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1239 time to evaluate : 6.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 102 residues processed: 1320 average time/residue: 1.4431 time to fit residues: 3339.7401 Evaluate side-chains 1293 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1191 time to evaluate : 6.749 Switching outliers to nearest non-outliers outliers start: 102 outliers final: 0 residues processed: 102 average time/residue: 1.1408 time to fit residues: 232.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 863 optimal weight: 0.9980 chunk 588 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 772 optimal weight: 0.9980 chunk 427 optimal weight: 10.0000 chunk 885 optimal weight: 10.0000 chunk 716 optimal weight: 5.9990 chunk 1 optimal weight: 7.9990 chunk 529 optimal weight: 5.9990 chunk 930 optimal weight: 0.6980 chunk 261 optimal weight: 5.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 163 ASN F 104 ASN H 88 HIS ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN a 20 ASN g 146 ASN i 131 ASN k 63 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN ** s 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 80 GLN u 26 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.065 167985 Z= 0.239 Angle : 0.608 13.833 251649 Z= 0.331 Chirality : 0.034 0.292 32100 Planarity : 0.006 0.129 13244 Dihedral : 15.175 179.329 66665 Min Nonbonded Distance : 1.015 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.80 % Favored : 96.10 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.11), residues: 5865 helix: 1.15 (0.12), residues: 1987 sheet: -0.34 (0.16), residues: 1096 loop : -1.13 (0.11), residues: 2782 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1280 time to evaluate : 6.693 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 40 residues processed: 1313 average time/residue: 1.4443 time to fit residues: 3350.2301 Evaluate side-chains 1232 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1192 time to evaluate : 6.746 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 1.2815 time to fit residues: 103.7415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 348 optimal weight: 10.0000 chunk 934 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 608 optimal weight: 7.9990 chunk 256 optimal weight: 8.9990 chunk 1038 optimal weight: 10.0000 chunk 861 optimal weight: 20.0000 chunk 480 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 545 optimal weight: 6.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN i 131 ASN j 73 ASN ** j 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN r 105 ASN s 35 ASN s 43 ASN t 80 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.4357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.122 167985 Z= 0.566 Angle : 0.784 14.841 251649 Z= 0.409 Chirality : 0.045 0.322 32100 Planarity : 0.007 0.148 13244 Dihedral : 15.503 179.966 66665 Min Nonbonded Distance : 0.932 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.84 % Favored : 95.06 % Rotamer Outliers : 2.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.11), residues: 5865 helix: 0.78 (0.12), residues: 1988 sheet: -0.52 (0.15), residues: 1127 loop : -1.28 (0.11), residues: 2750 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1318 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1184 time to evaluate : 6.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 134 outliers final: 86 residues processed: 1247 average time/residue: 1.3912 time to fit residues: 3042.7862 Evaluate side-chains 1245 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1159 time to evaluate : 6.733 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 1.1386 time to fit residues: 194.5312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 1000 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 591 optimal weight: 4.9990 chunk 758 optimal weight: 2.9990 chunk 587 optimal weight: 0.9990 chunk 873 optimal weight: 0.8980 chunk 579 optimal weight: 0.9990 chunk 1034 optimal weight: 1.9990 chunk 647 optimal weight: 0.9980 chunk 630 optimal weight: 9.9990 chunk 477 optimal weight: 50.0000 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN F 104 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN S 31 GLN V 12 GLN g 42 ASN i 116 GLN i 131 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 50 GLN p 109 ASN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN w 74 HIS y 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 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 : 0.002 0.070 167985 Z= 0.138 Angle : 0.590 14.308 251649 Z= 0.323 Chirality : 0.033 0.265 32100 Planarity : 0.006 0.122 13244 Dihedral : 15.145 179.765 66665 Min Nonbonded Distance : 1.108 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.36 % Favored : 96.54 % Rotamer Outliers : 1.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5865 helix: 1.26 (0.12), residues: 2002 sheet: -0.37 (0.16), residues: 1113 loop : -1.09 (0.11), residues: 2750 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 1272 time to evaluate : 6.577 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 56 outliers final: 24 residues processed: 1291 average time/residue: 1.4137 time to fit residues: 3204.6538 Evaluate side-chains 1224 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1200 time to evaluate : 6.522 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 1.2155 time to fit residues: 62.7996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 639 optimal weight: 30.0000 chunk 412 optimal weight: 10.0000 chunk 617 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 200 optimal weight: 8.9990 chunk 657 optimal weight: 7.9990 chunk 704 optimal weight: 5.9990 chunk 511 optimal weight: 9.9990 chunk 96 optimal weight: 8.9990 chunk 812 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN E 127 ASN F 104 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN V 12 GLN Y 45 GLN Z 20 HIS a 20 ASN c 45 GLN i 74 ASN i 131 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 126 GLN p 38 GLN r 8 ASN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.116 167985 Z= 0.536 Angle : 0.763 13.658 251649 Z= 0.399 Chirality : 0.043 0.311 32100 Planarity : 0.007 0.148 13244 Dihedral : 15.420 179.958 66665 Min Nonbonded Distance : 0.941 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.76 % Favored : 95.12 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.11), residues: 5865 helix: 0.91 (0.12), residues: 1992 sheet: -0.49 (0.16), residues: 1117 loop : -1.23 (0.11), residues: 2756 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1190 time to evaluate : 6.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 94 outliers final: 70 residues processed: 1226 average time/residue: 1.3917 time to fit residues: 3024.7669 Evaluate side-chains 1234 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1164 time to evaluate : 6.613 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 0 residues processed: 70 average time/residue: 1.1387 time to fit residues: 161.7147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 940 optimal weight: 4.9990 chunk 990 optimal weight: 6.9990 chunk 903 optimal weight: 3.9990 chunk 963 optimal weight: 1.9990 chunk 580 optimal weight: 0.9990 chunk 419 optimal weight: 10.0000 chunk 756 optimal weight: 2.9990 chunk 295 optimal weight: 8.9990 chunk 870 optimal weight: 2.9990 chunk 911 optimal weight: 0.9990 chunk 960 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN E 127 ASN F 104 ASN G 20 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN V 12 GLN Y 45 GLN c 45 GLN i 131 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 35 ASN t 80 GLN u 26 ASN v 9 GLN y 13 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.116 167985 Z= 0.188 Angle : 0.602 14.856 251649 Z= 0.329 Chirality : 0.034 0.283 32100 Planarity : 0.006 0.152 13244 Dihedral : 15.160 179.911 66665 Min Nonbonded Distance : 1.043 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.53 % Favored : 96.37 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5865 helix: 1.22 (0.12), residues: 1995 sheet: -0.37 (0.16), residues: 1113 loop : -1.09 (0.11), residues: 2757 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1253 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1228 time to evaluate : 6.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 9 residues processed: 1232 average time/residue: 1.4069 time to fit residues: 3029.9368 Evaluate side-chains 1204 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1195 time to evaluate : 6.632 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 1.1946 time to fit residues: 27.3053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 632 optimal weight: 0.1980 chunk 1019 optimal weight: 2.9990 chunk 622 optimal weight: 7.9990 chunk 483 optimal weight: 50.0000 chunk 708 optimal weight: 0.9980 chunk 1068 optimal weight: 20.0000 chunk 983 optimal weight: 0.9990 chunk 851 optimal weight: 7.9990 chunk 88 optimal weight: 30.0000 chunk 657 optimal weight: 6.9990 chunk 521 optimal weight: 0.0370 overall best weight: 1.0462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 136 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 54 GLN V 12 GLN Y 45 GLN c 45 GLN i 131 ASN k 52 ASN k 68 GLN n 5 GLN n 126 GLN t 20 ASN t 80 GLN u 26 ASN x 14 HIS ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.4032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.256 167985 Z= 0.147 Angle : 0.570 22.006 251649 Z= 0.314 Chirality : 0.031 0.317 32100 Planarity : 0.006 0.134 13244 Dihedral : 14.961 179.850 66665 Min Nonbonded Distance : 1.107 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.65 % Favored : 96.25 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.11), residues: 5865 helix: 1.42 (0.12), residues: 1983 sheet: -0.23 (0.16), residues: 1116 loop : -0.93 (0.11), residues: 2766 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 1255 time to evaluate : 9.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 1261 average time/residue: 1.3905 time to fit residues: 3072.6252 Evaluate side-chains 1207 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1200 time to evaluate : 6.882 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 1.1279 time to fit residues: 22.6918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 676 optimal weight: 1.9990 chunk 906 optimal weight: 0.9990 chunk 260 optimal weight: 9.9990 chunk 784 optimal weight: 0.0060 chunk 125 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 852 optimal weight: 8.9990 chunk 356 optimal weight: 10.0000 chunk 875 optimal weight: 2.9990 chunk 107 optimal weight: 50.0000 chunk 157 optimal weight: 10.0000 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 52 ASN J 131 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN U 54 GLN V 12 GLN c 45 GLN i 131 ASN k 52 ASN k 68 GLN l 130 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN n 126 GLN s 35 ASN s 49 GLN t 20 ASN u 26 ASN v 9 GLN ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.103543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.068144 restraints weight = 302795.261| |-----------------------------------------------------------------------------| r_work (start): 0.2885 rms_B_bonded: 1.07 r_work: 0.2874 rms_B_bonded: 1.01 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 1.03 restraints_weight: 0.2500 r_work: 0.2854 rms_B_bonded: 1.09 restraints_weight: 0.1250 r_work: 0.2844 rms_B_bonded: 1.19 restraints_weight: 0.0625 r_work: 0.2834 rms_B_bonded: 1.32 restraints_weight: 0.0312 r_work: 0.2823 rms_B_bonded: 1.47 restraints_weight: 0.0156 r_work: 0.2811 rms_B_bonded: 1.65 restraints_weight: 0.0078 r_work: 0.2798 rms_B_bonded: 1.85 restraints_weight: 0.0039 r_work: 0.2784 rms_B_bonded: 2.08 restraints_weight: 0.0020 r_work: 0.2769 rms_B_bonded: 2.35 restraints_weight: 0.0010 r_work: 0.2753 rms_B_bonded: 2.64 restraints_weight: 0.0005 r_work: 0.2735 rms_B_bonded: 2.98 restraints_weight: 0.0002 r_work: 0.2715 rms_B_bonded: 3.35 restraints_weight: 0.0001 r_work: 0.2694 rms_B_bonded: 3.78 restraints_weight: 0.0001 r_work: 0.2671 rms_B_bonded: 4.26 restraints_weight: 0.0000 r_work: 0.2645 rms_B_bonded: 4.80 restraints_weight: 0.0000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8941 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.161 167985 Z= 0.246 Angle : 0.604 18.487 251649 Z= 0.328 Chirality : 0.033 0.283 32100 Planarity : 0.006 0.148 13244 Dihedral : 14.975 179.653 66665 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.79 % Favored : 96.11 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.11), residues: 5865 helix: 1.38 (0.12), residues: 1987 sheet: -0.32 (0.15), residues: 1126 loop : -0.94 (0.11), residues: 2752 =============================================================================== Job complete usr+sys time: 47259.89 seconds wall clock time: 811 minutes 10.22 seconds (48670.22 seconds total)