Starting phenix.real_space_refine on Fri Dec 8 09:25:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odt_12847/12_2023/7odt_12847_updated.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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= 0.006 sd= 0.105 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 Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 10 8.98 5 Fe 2 7.16 5 Zn 2 6.06 5 P 1528 5.49 5 Mg 95 5.21 5 S 338 5.16 5 C 64170 2.51 5 N 20005 2.21 5 O 24323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 PHE 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 164": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 110473 Number of models: 1 Model: "" Number of chains: 71 Chain: "t" Number of atoms: 2398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2398 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 14, 'TRANS': 301} Chain breaks: 2 Chain: "u" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 919 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "x" Number of atoms: 2750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2750 Classifications: {'peptide': 346} Link IDs: {'PCIS': 2, 'PTRANS': 15, 'TRANS': 328} Chain breaks: 1 Chain: "y" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1980 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 10, 'TRANS': 233} Chain: "0" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 102} Chain: "1" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "3" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 832 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 342 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3210 Classifications: {'peptide': 394} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 361} Chain: "6" Number of atoms: 2948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 354, 2948 Classifications: {'peptide': 354} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 319} Chain: "7" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2390 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 276} Chain: "8" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 91} Chain: "9" Number of atoms: 997 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 997 Classifications: {'peptide': 124} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 113} Chain: "A" Number of atoms: 30850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1453, 30850 Classifications: {'RNA': 1453} Modifications used: {'rna2p_pur': 159, 'rna2p_pyr': 109, 'rna3p': 2, 'rna3p_pur': 607, 'rna3p_pyr': 576} Link IDs: {'rna2p': 267, 'rna3p': 1185} Chain breaks: 7 Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1522 Classifications: {'RNA': 72} Modifications used: {'p5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 6, 'rna3p_pur': 32, 'rna3p_pyr': 31} Link IDs: {'rna2p': 8, 'rna3p': 63} Chain: "D" Number of atoms: 1872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1872 Classifications: {'peptide': 240} Link IDs: {'PTRANS': 13, 'TRANS': 226} Chain: "E" Number of atoms: 2406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2406 Classifications: {'peptide': 305} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 23, 'TRANS': 280} Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2031 Classifications: {'peptide': 252} Link IDs: {'PCIS': 2, 'PTRANS': 19, 'TRANS': 230} Chain: "H" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "I" Number of atoms: 1358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 1358 Classifications: {'peptide': 168} Link IDs: {'PTRANS': 15, 'TRANS': 152} Chain: "J" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1330 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 165} Chain: "K" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1455 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 161} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'SAC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 890 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 106} Chain: "M" Number of atoms: 2327 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2327 Classifications: {'peptide': 291} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 26, 'TRANS': 264} Chain: "N" Number of atoms: 1786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1786 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 204} Chain: "O" Number of atoms: 1259 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1259 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 9, 'TRANS': 144} Chain: "P" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1173 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 136} Chain: "Q" Number of atoms: 1843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1843 Classifications: {'peptide': 221} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 206} Chain: "R" Number of atoms: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1154 Classifications: {'peptide': 140} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 136} Chain: "S" Number of atoms: 1293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 161, 1293 Classifications: {'peptide': 161} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 149} Chain: "T" Number of atoms: 1369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1369 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1251 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 139} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1676 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 186} Chain: "W" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 835 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 99} Chain: "X" Number of atoms: 2044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2044 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 18, 'TRANS': 225} Chain: "Y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1556 Classifications: {'peptide': 181} Link IDs: {'PTRANS': 8, 'TRANS': 172} Chain: "Z" Number of atoms: 996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 996 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 11, 'TRANS': 110} Chain: "a" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 840 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 88} Chain breaks: 1 Chain: "b" Number of atoms: 1189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1189 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 9, 'TRANS': 139} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'THC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "c" Number of atoms: 2299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2299 Classifications: {'peptide': 286} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 268} Chain breaks: 1 Chain: "d" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2124 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 20, 'TRANS': 238} Chain: "e" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1848 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 217} Chain breaks: 1 Chain: "f" Number of atoms: 1196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1196 Classifications: {'peptide': 150} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain breaks: 1 Chain: "g" Number of atoms: 1113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1113 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 117} Chain: "h" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 895 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 100} Chain: "i" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 828 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 91} Chain: "j" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 745 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 7, 'TRANS': 86} Chain: "k" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 774 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'AYA:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "l" Number of atoms: 688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 688 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 8, 'TRANS': 73} Chain: "m" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 419 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "o" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 798 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "p" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1205 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain breaks: 2 Chain: "q" Number of atoms: 1177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1177 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 14, 'TRANS': 126} Chain: "r" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1322 Classifications: {'peptide': 162} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 142} Chain: "s" Number of atoms: 3155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3155 Classifications: {'peptide': 386} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 358} Chain breaks: 1 Chain: "t" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 29 Unusual residues: {' MG': 1, 'GDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "w" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'PM8': 1} Classifications: {'undetermined': 1} Chain: "x" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 98 Unusual residues: {' K': 10, ' MG': 88} Classifications: {'undetermined': 98} Link IDs: {None: 97} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9537 SG CYS 0 110 133.694 106.144 212.861 1.00 84.36 S ATOM 9559 SG CYS 0 113 137.371 107.342 212.782 1.00 77.68 S ATOM 9639 SG CYS 0 123 135.979 105.483 209.831 1.00 69.32 S ATOM 9662 SG CYS 0 126 136.387 103.684 213.207 1.00 76.49 S ATOM 11929 SG CYS 4 76 64.104 104.979 122.887 1.00 88.18 S ATOM 11952 SG CYS 4 79 66.819 106.733 124.887 1.00 87.17 S ATOM 12076 SG CYS 4 92 64.741 103.965 126.491 1.00 81.99 S ATOM 62352 SG CYS I 64 65.148 145.705 127.582 1.00 98.75 S ATOM A04P8 SG CYS r 73 62.033 146.383 129.694 1.00 87.11 S ATOM A04ON SG CYS r 70 61.028 142.502 131.025 1.00 78.99 S ATOM A04XE SG CYS r 108 63.484 140.238 129.406 1.00 73.16 S Time building chain proxies: 40.42, per 1000 atoms: 0.37 Number of scatterers: 110473 At special positions: 0 Unit cell: (257.58, 223.66, 254.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 Fe 2 26.01 K 10 19.00 S 338 16.00 P 1528 15.00 Mg 95 11.99 O 24323 8.00 N 20005 7.00 C 64170 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 35.72 Conformation dependent library (CDL) restraints added in 10.2 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES r 201 " pdb="FE2 FES r 201 " - pdb=" SG CYS r 70 " pdb="FE1 FES r 201 " - pdb=" SG CYS I 64 " pdb="FE1 FES r 201 " - pdb=" SG CYS r 73 " pdb="FE2 FES r 201 " - pdb=" SG CYS r 108 " Number of angles added : 6 Zn2+ tetrahedral coordination pdb=" ZN 0 201 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 123 " pdb=" ZN 4 201 " pdb="ZN ZN 4 201 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 92 " Number of angles added : 9 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 18034 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 329 helices and 81 sheets defined 43.0% alpha, 13.5% beta 333 base pairs and 839 stacking pairs defined. Time for finding SS restraints: 63.92 Creating SS restraints... Processing helix chain 't' and resid 191 through 197 removed outlier: 4.138A pdb=" N PHE t 195 " --> pdb=" O GLY t 191 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU t 196 " --> pdb=" O ASN t 192 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ALA t 197 " --> pdb=" O ARG t 193 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 191 through 197' Processing helix chain 't' and resid 236 through 246 Processing helix chain 't' and resid 293 through 302 removed outlier: 3.971A pdb=" N ARG t 302 " --> pdb=" O ARG t 298 " (cutoff:3.500A) Processing helix chain 't' and resid 316 through 332 Processing helix chain 't' and resid 333 through 339 removed outlier: 3.586A pdb=" N ALA t 337 " --> pdb=" O LYS t 333 " (cutoff:3.500A) Proline residue: t 339 - end of helix Processing helix chain 't' and resid 346 through 351 Proline residue: t 350 - end of helix No H-bonds generated for 'chain 't' and resid 346 through 351' Processing helix chain 't' and resid 352 through 363 Processing helix chain 't' and resid 377 through 400 removed outlier: 3.728A pdb=" N LEU t 381 " --> pdb=" O ASN t 377 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS t 384 " --> pdb=" O GLN t 380 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA t 391 " --> pdb=" O VAL t 387 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N TYR t 392 " --> pdb=" O LEU t 388 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 149 removed outlier: 3.651A pdb=" N VAL u 143 " --> pdb=" O ALA u 139 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 removed outlier: 3.697A pdb=" N ILE u 187 " --> pdb=" O GLU u 183 " (cutoff:3.500A) Processing helix chain 'u' and resid 190 through 197 Processing helix chain 'v' and resid 5 through 24 removed outlier: 3.604A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 45 removed outlier: 3.586A pdb=" N PHE v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN v 43 " --> pdb=" O PHE v 39 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N LYS v 44 " --> pdb=" O ARG v 40 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU v 45 " --> pdb=" O LYS v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 removed outlier: 3.691A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N VAL v 60 " --> pdb=" O GLU v 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.679A pdb=" N ILE w 79 " --> pdb=" O THR w 75 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN w 80 " --> pdb=" O LEU w 76 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 5.139A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 4.389A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.523A pdb=" N ASP w 150 " --> pdb=" O ASP w 146 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 109 removed outlier: 3.524A pdb=" N LEU w 108 " --> pdb=" O HIS w 103 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 57 removed outlier: 4.052A pdb=" N VAL x 54 " --> pdb=" O MET x 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 58 through 70 removed outlier: 4.515A pdb=" N SER x 62 " --> pdb=" O ASP x 58 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER x 66 " --> pdb=" O SER x 62 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLU x 70 " --> pdb=" O SER x 66 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 94 removed outlier: 3.646A pdb=" N LEU x 93 " --> pdb=" O LYS x 89 " (cutoff:3.500A) Processing helix chain 'x' and resid 97 through 109 removed outlier: 3.521A pdb=" N TRP x 106 " --> pdb=" O ALA x 102 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLU x 107 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU x 108 " --> pdb=" O SER x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 159 through 170 removed outlier: 3.752A pdb=" N LEU x 163 " --> pdb=" O ASP x 159 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N LEU x 164 " --> pdb=" O ALA x 160 " (cutoff:3.500A) Proline residue: x 165 - end of helix removed outlier: 3.959A pdb=" N GLY x 170 " --> pdb=" O VAL x 166 " (cutoff:3.500A) Processing helix chain 'x' and resid 185 through 195 removed outlier: 4.259A pdb=" N ALA x 190 " --> pdb=" O GLY x 186 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU x 192 " --> pdb=" O THR x 188 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY x 195 " --> pdb=" O LEU x 191 " (cutoff:3.500A) Processing helix chain 'x' and resid 206 through 221 Processing helix chain 'x' and resid 222 through 228 removed outlier: 3.810A pdb=" N ARG x 226 " --> pdb=" O PRO x 222 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N GLY x 228 " --> pdb=" O GLU x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 237 through 244 removed outlier: 4.148A pdb=" N TRP x 241 " --> pdb=" O ASP x 237 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLY x 242 " --> pdb=" O GLY x 238 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N GLU x 243 " --> pdb=" O ARG x 239 " (cutoff:3.500A) Processing helix chain 'x' and resid 260 through 267 removed outlier: 3.852A pdb=" N HIS x 266 " --> pdb=" O ARG x 262 " (cutoff:3.500A) Processing helix chain 'x' and resid 274 through 300 removed outlier: 4.808A pdb=" N LYS x 279 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N GLU x 280 " --> pdb=" O SER x 276 " (cutoff:3.500A) Proline residue: x 285 - end of helix removed outlier: 5.727A pdb=" N LYS x 300 " --> pdb=" O LEU x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 313 through 331 removed outlier: 4.715A pdb=" N TYR x 319 " --> pdb=" O LEU x 315 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N VAL x 320 " --> pdb=" O GLN x 316 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N VAL x 321 " --> pdb=" O ASN x 317 " (cutoff:3.500A) Processing helix chain 'x' and resid 341 through 350 removed outlier: 3.732A pdb=" N VAL x 347 " --> pdb=" O HIS x 343 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE x 348 " --> pdb=" O PHE x 344 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N ASP x 350 " --> pdb=" O ARG x 346 " (cutoff:3.500A) Processing helix chain 'y' and resid 88 through 103 removed outlier: 3.577A pdb=" N VAL y 95 " --> pdb=" O GLU y 91 " (cutoff:3.500A) Processing helix chain 'y' and resid 105 through 116 Processing helix chain 'y' and resid 120 through 135 Processing helix chain 'y' and resid 137 through 149 Proline residue: y 149 - end of helix Processing helix chain 'y' and resid 155 through 170 removed outlier: 3.502A pdb=" N MET y 159 " --> pdb=" O PRO y 155 " (cutoff:3.500A) Processing helix chain 'y' and resid 173 through 183 removed outlier: 6.212A pdb=" N LYS y 177 " --> pdb=" O GLU y 173 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG y 178 " --> pdb=" O GLY y 174 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VAL y 179 " --> pdb=" O LYS y 175 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N TYR y 181 " --> pdb=" O LYS y 177 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 203 removed outlier: 3.615A pdb=" N ILE y 194 " --> pdb=" O ARG y 190 " (cutoff:3.500A) Processing helix chain 'y' and resid 208 through 219 Processing helix chain 'y' and resid 220 through 226 removed outlier: 4.502A pdb=" N ARG y 224 " --> pdb=" O PRO y 220 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N ASP y 226 " --> pdb=" O VAL y 222 " (cutoff:3.500A) Processing helix chain 'y' and resid 227 through 239 removed outlier: 3.638A pdb=" N ALA y 237 " --> pdb=" O LYS y 233 " (cutoff:3.500A) Processing helix chain 'y' and resid 244 through 252 Processing helix chain 'y' and resid 257 through 272 Processing helix chain 'y' and resid 289 through 295 Processing helix chain 'y' and resid 297 through 305 Processing helix chain 'y' and resid 309 through 331 removed outlier: 3.700A pdb=" N PHE y 313 " --> pdb=" O SER y 309 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 removed outlier: 3.504A pdb=" N CYS 0 92 " --> pdb=" O GLU 0 88 " (cutoff:3.500A) Processing helix chain '0' and resid 96 through 101 removed outlier: 5.336A pdb=" N ILE 0 101 " --> pdb=" O PRO 0 97 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 72 removed outlier: 4.120A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 removed outlier: 3.576A pdb=" N VAL 2 78 " --> pdb=" O ALA 2 74 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 3.662A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.040A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N THR 3 137 " --> pdb=" O LEU 3 133 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 132 through 137' Processing helix chain '3' and resid 138 through 147 removed outlier: 3.524A pdb=" N ARG 3 143 " --> pdb=" O ALA 3 139 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N PHE 3 147 " --> pdb=" O ARG 3 143 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 3.601A pdb=" N LYS 3 160 " --> pdb=" O LYS 3 156 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET 3 161 " --> pdb=" O LEU 3 157 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR 3 162 " --> pdb=" O LEU 3 158 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.362A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 53 removed outlier: 4.512A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) Proline residue: 5 53 - end of helix No H-bonds generated for 'chain '5' and resid 47 through 53' Processing helix chain '5' and resid 116 through 125 removed outlier: 3.570A pdb=" N TRP 5 122 " --> pdb=" O LYS 5 118 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 142 removed outlier: 3.663A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASP 5 142 " --> pdb=" O SER 5 138 " (cutoff:3.500A) Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 196 removed outlier: 3.508A pdb=" N TYR 5 176 " --> pdb=" O LYS 5 172 " (cutoff:3.500A) Proline residue: 5 178 - end of helix removed outlier: 3.649A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LEU 5 184 " --> pdb=" O ILE 5 180 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS 5 194 " --> pdb=" O SER 5 190 " (cutoff:3.500A) Proline residue: 5 196 - end of helix Processing helix chain '5' and resid 241 through 252 removed outlier: 3.820A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.261A pdb=" N LEU 5 304 " --> pdb=" O ARG 5 300 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.315A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 53 through 68 removed outlier: 3.773A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA 6 67 " --> pdb=" O GLN 6 63 " (cutoff:3.500A) Proline residue: 6 68 - end of helix Processing helix chain '6' and resid 73 through 78 removed outlier: 3.824A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 116 removed outlier: 3.557A pdb=" N ASN 6 116 " --> pdb=" O GLU 6 112 " (cutoff:3.500A) Processing helix chain '6' and resid 117 through 126 Processing helix chain '6' and resid 131 through 143 removed outlier: 3.608A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 removed outlier: 3.521A pdb=" N TYR 6 155 " --> pdb=" O LEU 6 151 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 244 through 249 removed outlier: 3.889A pdb=" N GLY 6 248 " --> pdb=" O ARG 6 244 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N GLN 6 249 " --> pdb=" O VAL 6 245 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 244 through 249' Processing helix chain '6' and resid 292 through 297 Processing helix chain '6' and resid 299 through 308 removed outlier: 3.581A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.138A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE 6 330 " --> pdb=" O SER 6 326 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 371 removed outlier: 3.581A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 3.946A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 4.013A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N MET 7 43 " --> pdb=" O GLU 7 39 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG 7 44 " --> pdb=" O LEU 7 40 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) Proline residue: 7 60 - end of helix Processing helix chain '7' and resid 87 through 96 removed outlier: 3.526A pdb=" N HIS 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU 7 95 " --> pdb=" O CYS 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 3.608A pdb=" N VAL 7 153 " --> pdb=" O MET 7 149 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ILE 7 154 " --> pdb=" O MET 7 150 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU 7 155 " --> pdb=" O GLY 7 151 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 191 removed outlier: 4.053A pdb=" N ASP 7 190 " --> pdb=" O ASP 7 186 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N GLU 7 191 " --> pdb=" O SER 7 187 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 186 through 191' Processing helix chain '7' and resid 195 through 213 removed outlier: 3.526A pdb=" N PHE 7 202 " --> pdb=" O ASN 7 198 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 removed outlier: 3.616A pdb=" N ILE 7 229 " --> pdb=" O VAL 7 225 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 248 removed outlier: 3.662A pdb=" N VAL 7 237 " --> pdb=" O SER 7 233 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ASP 7 238 " --> pdb=" O LYS 7 234 " (cutoff:3.500A) Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 323 removed outlier: 3.577A pdb=" N LYS 7 315 " --> pdb=" O THR 7 311 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG 7 319 " --> pdb=" O LYS 7 315 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) removed outlier: 5.420A pdb=" N MET 7 323 " --> pdb=" O ARG 7 319 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.688A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.548A pdb=" N LYS 8 119 " --> pdb=" O ALA 8 115 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS 8 120 " --> pdb=" O LEU 8 116 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU 8 123 " --> pdb=" O LYS 8 119 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLU 8 128 " --> pdb=" O TYR 8 124 " (cutoff:3.500A) Processing helix chain '8' and resid 155 through 163 removed outlier: 3.728A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 35 removed outlier: 5.713A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.522A pdb=" N VAL 9 57 " --> pdb=" O ILE 9 53 " (cutoff:3.500A) Proline residue: 9 58 - end of helix No H-bonds generated for 'chain '9' and resid 53 through 58' Processing helix chain '9' and resid 87 through 96 Processing helix chain '9' and resid 97 through 107 Processing helix chain '9' and resid 113 through 118 Processing helix chain 'D' and resid 259 through 267 removed outlier: 4.078A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 276 through 285 Processing helix chain 'D' and resid 289 through 296 removed outlier: 4.480A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.645A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 3.705A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 Processing helix chain 'E' and resid 158 through 169 removed outlier: 3.556A pdb=" N GLU E 167 " --> pdb=" O GLU E 163 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU E 168 " --> pdb=" O PHE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.896A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ARG E 199 " --> pdb=" O ALA E 195 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 194 through 199' Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 108 removed outlier: 4.567A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.545A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 removed outlier: 3.753A pdb=" N LEU F 174 " --> pdb=" O ARG F 170 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS F 175 " --> pdb=" O ALA F 171 " (cutoff:3.500A) Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.716A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.399A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 4.926A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 4.044A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.732A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VAL H 79 " --> pdb=" O ARG H 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 74 through 79' Processing helix chain 'H' and resid 85 through 90 removed outlier: 4.190A pdb=" N ARG H 89 " --> pdb=" O ASP H 85 " (cutoff:3.500A) Proline residue: H 90 - end of helix No H-bonds generated for 'chain 'H' and resid 85 through 90' Processing helix chain 'H' and resid 115 through 122 removed outlier: 3.658A pdb=" N ARG H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 149 removed outlier: 3.554A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.745A pdb=" N GLU I 52 " --> pdb=" O MET I 48 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 66 Proline residue: I 66 - end of helix Processing helix chain 'I' and resid 76 through 92 removed outlier: 3.599A pdb=" N ARG I 84 " --> pdb=" O ARG I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.639A pdb=" N HIS I 119 " --> pdb=" O GLN I 115 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 Proline residue: I 133 - end of helix removed outlier: 3.866A pdb=" N ASP I 137 " --> pdb=" O PRO I 133 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N SER I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.950A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N VAL I 148 " --> pdb=" O LEU I 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 143 through 148' Processing helix chain 'I' and resid 160 through 172 removed outlier: 3.685A pdb=" N ARG I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ILE I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N VAL I 171 " --> pdb=" O ILE I 167 " (cutoff:3.500A) Proline residue: I 172 - end of helix Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 33 through 43 Proline residue: J 37 - end of helix removed outlier: 3.670A pdb=" N ARG J 42 " --> pdb=" O VAL J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 58 Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.535A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 4.109A pdb=" N ILE J 123 " --> pdb=" O GLU J 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 134 Processing helix chain 'J' and resid 136 through 152 removed outlier: 3.533A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLY J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 192 removed outlier: 4.291A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 40 removed outlier: 3.599A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG K 38 " --> pdb=" O MET K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 112 removed outlier: 3.634A pdb=" N MET K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.587A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.491A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.693A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU K 141 " --> pdb=" O ILE K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 159 through 167 Proline residue: K 167 - end of helix Processing helix chain 'K' and resid 70 through 75 removed outlier: 4.262A pdb=" N LYS K 75 " --> pdb=" O ASN K 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 70 through 75' Processing helix chain 'L' and resid 44 through 49 Processing helix chain 'L' and resid 126 through 131 removed outlier: 3.508A pdb=" N ARG L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 126 through 131' Processing helix chain 'L' and resid 133 through 142 removed outlier: 4.871A pdb=" N VAL L 137 " --> pdb=" O GLU L 133 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE L 140 " --> pdb=" O LYS L 136 " (cutoff:3.500A) removed outlier: 5.730A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 20 removed outlier: 3.585A pdb=" N ALA M 10 " --> pdb=" O GLN M 6 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG M 17 " --> pdb=" O LEU M 13 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU M 19 " --> pdb=" O LEU M 15 " (cutoff:3.500A) Proline residue: M 20 - end of helix Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.600A pdb=" N ARG M 59 " --> pdb=" O GLY M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 79 removed outlier: 3.533A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Proline residue: M 79 - end of helix Processing helix chain 'M' and resid 86 through 91 removed outlier: 6.056A pdb=" N ARG M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.663A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.526A pdb=" N ASP M 185 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) Proline residue: M 190 - end of helix Processing helix chain 'M' and resid 191 through 197 removed outlier: 3.853A pdb=" N ARG M 196 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 216 Proline residue: M 212 - end of helix removed outlier: 3.556A pdb=" N ASP M 216 " --> pdb=" O PRO M 212 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.785A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix removed outlier: 3.510A pdb=" N LEU M 236 " --> pdb=" O ALA M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.057A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N GLU M 251 " --> pdb=" O ILE M 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 246 through 251' Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.525A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 69 through 74 removed outlier: 4.126A pdb=" N ARG N 73 " --> pdb=" O LEU N 69 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N GLY N 74 " --> pdb=" O SER N 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 69 through 74' Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.744A pdb=" N VAL N 172 " --> pdb=" O GLU N 168 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLY N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU N 183 " --> pdb=" O VAL N 179 " (cutoff:3.500A) Proline residue: N 184 - end of helix Processing helix chain 'N' and resid 191 through 209 Processing helix chain 'N' and resid 214 through 222 Processing helix chain 'N' and resid 225 through 231 removed outlier: 4.776A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.434A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 66 removed outlier: 4.037A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ASP O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY O 66 " --> pdb=" O TYR O 62 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 82 through 98 removed outlier: 4.313A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.735A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ALA O 94 " --> pdb=" O PHE O 90 " (cutoff:3.500A) Proline residue: O 95 - end of helix Processing helix chain 'O' and resid 143 through 162 Processing helix chain 'P' and resid 52 through 60 removed outlier: 4.576A pdb=" N LEU P 56 " --> pdb=" O ASN P 52 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N GLU P 57 " --> pdb=" O PRO P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 117 removed outlier: 4.809A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 Processing helix chain 'P' and resid 149 through 156 removed outlier: 5.575A pdb=" N ASP P 156 " --> pdb=" O GLU P 152 " (cutoff:3.500A) Processing helix chain 'P' and resid 157 through 169 Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.255A pdb=" N ILE Q 81 " --> pdb=" O SER Q 77 " (cutoff:3.500A) Proline residue: Q 82 - end of helix No H-bonds generated for 'chain 'Q' and resid 77 through 82' Processing helix chain 'Q' and resid 88 through 106 removed outlier: 3.867A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 193 removed outlier: 4.676A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ASP Q 192 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 4.294A pdb=" N SER Q 198 " --> pdb=" O LEU Q 194 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.045A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.720A pdb=" N GLN Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.036A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 removed outlier: 3.559A pdb=" N ALA Q 280 " --> pdb=" O SER Q 276 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N SER Q 289 " --> pdb=" O GLU Q 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.599A pdb=" N GLU R 23 " --> pdb=" O PHE R 19 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 44 removed outlier: 4.134A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 64 removed outlier: 3.773A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 80 removed outlier: 3.517A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.712A pdb=" N ASN R 89 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N CYS R 93 " --> pdb=" O ASN R 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 108 Processing helix chain 'R' and resid 109 through 134 removed outlier: 4.869A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 90 removed outlier: 3.817A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE S 87 " --> pdb=" O VAL S 83 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL S 88 " --> pdb=" O ASN S 84 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N THR S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY S 90 " --> pdb=" O MET S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.591A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.342A pdb=" N ARG S 155 " --> pdb=" O LYS S 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 150 through 155' Processing helix chain 'T' and resid 43 through 51 removed outlier: 3.907A pdb=" N LYS T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ASN T 49 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LYS T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE T 51 " --> pdb=" O LYS T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 89 removed outlier: 4.080A pdb=" N TYR T 83 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N LEU T 84 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE T 88 " --> pdb=" O LEU T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 3.813A pdb=" N PHE T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 125 removed outlier: 4.121A pdb=" N LYS T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 200 removed outlier: 3.663A pdb=" N ARG T 200 " --> pdb=" O GLN T 196 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 60 Processing helix chain 'U' and resid 112 through 118 Proline residue: U 118 - end of helix Processing helix chain 'U' and resid 124 through 138 removed outlier: 5.063A pdb=" N GLN U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 Proline residue: V 36 - end of helix Processing helix chain 'V' and resid 50 through 55 removed outlier: 5.757A pdb=" N TYR V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 121 removed outlier: 5.043A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) Processing helix chain 'V' and resid 178 through 184 removed outlier: 3.730A pdb=" N GLU V 184 " --> pdb=" O GLU V 180 " (cutoff:3.500A) Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 121 removed outlier: 3.501A pdb=" N LEU W 116 " --> pdb=" O GLU W 112 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (cutoff:3.500A) Proline residue: W 121 - end of helix Processing helix chain 'X' and resid 7 through 19 removed outlier: 3.663A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 35 removed outlier: 5.893A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.117A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LEU X 79 " --> pdb=" O SER X 75 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 79' Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 192 removed outlier: 3.569A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.768A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VAL X 204 " --> pdb=" O GLU X 200 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 245 removed outlier: 3.541A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 69 removed outlier: 4.888A pdb=" N PHE Y 67 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 63 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 5.833A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 4.021A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.948A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.378A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.869A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 3.828A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ARG Y 198 " --> pdb=" O TYR Y 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 193 through 198' Processing helix chain 'Y' and resid 202 through 239 removed outlier: 4.302A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS Y 236 " --> pdb=" O LYS Y 232 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS Y 237 " --> pdb=" O ILE Y 233 " (cutoff:3.500A) Proline residue: Y 239 - end of helix Processing helix chain 'Z' and resid 42 through 48 removed outlier: 4.217A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ALA Z 48 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 48' Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.640A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS Z 55 " --> pdb=" O GLU Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 114 removed outlier: 3.677A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 removed outlier: 3.520A pdb=" N MET Z 134 " --> pdb=" O ALA Z 130 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N SER Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 130 through 135' Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.486A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N TYR a 124 " --> pdb=" O LYS a 120 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 119 through 124' Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 2 through 7 Proline residue: b 7 - end of helix Processing helix chain 'b' and resid 16 through 21 removed outlier: 4.735A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ARG b 21 " --> pdb=" O ASN b 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 16 through 21' Processing helix chain 'b' and resid 37 through 50 removed outlier: 3.988A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 5.660A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 137 removed outlier: 4.668A pdb=" N ASN b 135 " --> pdb=" O HIS b 131 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS b 136 " --> pdb=" O PRO b 132 " (cutoff:3.500A) Proline residue: b 137 - end of helix No H-bonds generated for 'chain 'b' and resid 131 through 137' Processing helix chain 'c' and resid 34 through 54 removed outlier: 5.302A pdb=" N ALA c 38 " --> pdb=" O GLY c 34 " (cutoff:3.500A) Proline residue: c 54 - end of helix Processing helix chain 'c' and resid 59 through 64 removed outlier: 3.528A pdb=" N LYS c 63 " --> pdb=" O ARG c 59 " (cutoff:3.500A) Proline residue: c 64 - end of helix No H-bonds generated for 'chain 'c' and resid 59 through 64' Processing helix chain 'c' and resid 67 through 80 removed outlier: 3.515A pdb=" N PHE c 75 " --> pdb=" O GLU c 71 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS c 77 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.626A pdb=" N THR c 90 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 109 removed outlier: 3.665A pdb=" N ARG c 105 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU c 108 " --> pdb=" O LYS c 104 " (cutoff:3.500A) Processing helix chain 'c' and resid 122 through 146 Proline residue: c 146 - end of helix Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 163 through 174 removed outlier: 3.724A pdb=" N CYS c 167 " --> pdb=" O GLU c 163 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU c 173 " --> pdb=" O VAL c 169 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N ALA c 174 " --> pdb=" O ALA c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.734A pdb=" N LEU c 213 " --> pdb=" O GLU c 209 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N PHE c 214 " --> pdb=" O ARG c 210 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.552A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.667A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG c 248 " --> pdb=" O GLU c 244 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 49 through 54 removed outlier: 3.805A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.790A pdb=" N SER d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 115 Processing helix chain 'd' and resid 116 through 130 removed outlier: 3.726A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ARG d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG d 124 " --> pdb=" O VAL d 120 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 155 Proline residue: d 138 - end of helix removed outlier: 3.540A pdb=" N LYS d 142 " --> pdb=" O PRO d 138 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ASP d 143 " --> pdb=" O GLU d 139 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.661A pdb=" N HIS d 161 " --> pdb=" O HIS d 157 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU d 163 " --> pdb=" O ARG d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 165 through 177 Proline residue: d 170 - end of helix removed outlier: 4.575A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE d 176 " --> pdb=" O MET d 172 " (cutoff:3.500A) Processing helix chain 'e' and resid 64 through 82 Processing helix chain 'e' and resid 85 through 101 Processing helix chain 'e' and resid 116 through 132 removed outlier: 3.514A pdb=" N MET e 123 " --> pdb=" O ASP e 119 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP e 124 " --> pdb=" O LEU e 120 " (cutoff:3.500A) removed outlier: 4.990A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 Processing helix chain 'e' and resid 183 through 195 removed outlier: 3.555A pdb=" N ALA e 188 " --> pdb=" O LEU e 184 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 218 through 223 removed outlier: 6.323A pdb=" N ARG e 222 " --> pdb=" O PRO e 218 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N THR e 223 " --> pdb=" O GLN e 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 218 through 223' Processing helix chain 'e' and resid 256 through 264 removed outlier: 4.634A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N TYR e 263 " --> pdb=" O GLU e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 265 through 277 removed outlier: 3.824A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.815A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N LYS f 64 " --> pdb=" O LYS f 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 59 through 64' Processing helix chain 'f' and resid 99 through 118 Processing helix chain 'f' and resid 164 through 178 removed outlier: 4.167A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 200 through 212 removed outlier: 3.510A pdb=" N GLU f 206 " --> pdb=" O PRO f 202 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU f 207 " --> pdb=" O GLU f 203 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU f 211 " --> pdb=" O LEU f 207 " (cutoff:3.500A) Processing helix chain 'g' and resid 41 through 53 removed outlier: 5.488A pdb=" N TYR g 45 " --> pdb=" O SER g 41 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLN g 46 " --> pdb=" O VAL g 42 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N PHE g 47 " --> pdb=" O ASP g 43 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Proline residue: g 53 - end of helix Processing helix chain 'g' and resid 116 through 132 removed outlier: 3.892A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 removed outlier: 3.613A pdb=" N LYS g 164 " --> pdb=" O TRP g 160 " (cutoff:3.500A) Processing helix chain 'h' and resid 65 through 79 Processing helix chain 'h' and resid 93 through 108 Processing helix chain 'h' and resid 113 through 121 removed outlier: 4.760A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.611A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.437A pdb=" N ASN h 147 " --> pdb=" O LEU h 143 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 54 Processing helix chain 'i' and resid 59 through 64 Processing helix chain 'i' and resid 69 through 74 removed outlier: 3.858A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 74' Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 103 through 123 Processing helix chain 'j' and resid 24 through 32 Processing helix chain 'j' and resid 36 through 41 removed outlier: 4.600A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLY j 41 " --> pdb=" O PRO j 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 36 through 41' Processing helix chain 'j' and resid 60 through 108 removed outlier: 3.724A pdb=" N GLN j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG j 103 " --> pdb=" O GLN j 99 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU j 106 " --> pdb=" O GLN j 102 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.933A pdb=" N LEU k 8 " --> pdb=" O ALA k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.642A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.600A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU k 47 " --> pdb=" O ARG k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 102 Processing helix chain 'l' and resid 64 through 71 Processing helix chain 'l' and resid 72 through 77 removed outlier: 4.237A pdb=" N ASN l 76 " --> pdb=" O ALA l 72 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ILE l 77 " --> pdb=" O MET l 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 72 through 77' Processing helix chain 'l' and resid 88 through 93 removed outlier: 3.801A pdb=" N TYR l 92 " --> pdb=" O PRO l 88 " (cutoff:3.500A) Proline residue: l 93 - end of helix No H-bonds generated for 'chain 'l' and resid 88 through 93' Processing helix chain 'l' and resid 94 through 99 removed outlier: 4.275A pdb=" N GLU l 98 " --> pdb=" O GLU l 94 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N MET l 99 " --> pdb=" O TRP l 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 94 through 99' Processing helix chain 'l' and resid 106 through 111 removed outlier: 3.598A pdb=" N LEU l 110 " --> pdb=" O THR l 106 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N ASP l 111 " --> pdb=" O LEU l 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 106 through 111' Processing helix chain 'l' and resid 114 through 136 removed outlier: 3.679A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS l 136 " --> pdb=" O LEU l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 39 removed outlier: 5.156A pdb=" N ALA m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER m 39 " --> pdb=" O SER m 35 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 34 through 39' Processing helix chain 'o' and resid 28 through 52 removed outlier: 3.680A pdb=" N TYR o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N MET o 51 " --> pdb=" O TYR o 47 " (cutoff:3.500A) Proline residue: o 52 - end of helix Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 63 through 81 removed outlier: 3.998A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.907A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LYS o 100 " --> pdb=" O ASN o 96 " (cutoff:3.500A) Processing helix chain 'p' and resid 44 through 50 Proline residue: p 50 - end of helix Processing helix chain 'p' and resid 73 through 78 removed outlier: 4.075A pdb=" N LEU p 77 " --> pdb=" O PRO p 73 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N THR p 78 " --> pdb=" O LEU p 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 73 through 78' Processing helix chain 'p' and resid 112 through 123 removed outlier: 3.540A pdb=" N ILE p 121 " --> pdb=" O GLN p 117 " (cutoff:3.500A) Processing helix chain 'p' and resid 142 through 164 Processing helix chain 'p' and resid 173 through 190 removed outlier: 4.234A pdb=" N ARG p 177 " --> pdb=" O VAL p 173 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE p 180 " --> pdb=" O HIS p 176 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG p 187 " --> pdb=" O MET p 183 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.610A pdb=" N THR p 57 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA p 58 " --> pdb=" O SER p 55 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N TRP p 59 " --> pdb=" O ASP p 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'q' and resid 48 through 53 removed outlier: 4.132A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 54 through 65 Processing helix chain 'q' and resid 71 through 76 removed outlier: 4.588A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N TRP q 76 " --> pdb=" O PRO q 72 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 71 through 76' Processing helix chain 'q' and resid 78 through 93 removed outlier: 3.632A pdb=" N ARG q 83 " --> pdb=" O PRO q 79 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 165 removed outlier: 3.553A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.730A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.009A pdb=" N GLN r 91 " --> pdb=" O LEU r 87 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE r 92 " --> pdb=" O LEU r 88 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ARG r 94 " --> pdb=" O SER r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 removed outlier: 3.503A pdb=" N ARG r 113 " --> pdb=" O GLN r 109 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.288A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP r 183 " --> pdb=" O PRO r 179 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 178 through 183' Processing helix chain 's' and resid 55 through 74 removed outlier: 3.592A pdb=" N HIS s 71 " --> pdb=" O GLN s 67 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N GLU s 74 " --> pdb=" O VAL s 70 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.554A pdb=" N TYR s 108 " --> pdb=" O ARG s 104 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 155 removed outlier: 3.549A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N HIS s 154 " --> pdb=" O LEU s 150 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 193 removed outlier: 4.851A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N GLU s 170 " --> pdb=" O TYR s 166 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER s 173 " --> pdb=" O SER s 169 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N LEU s 174 " --> pdb=" O GLU s 170 " (cutoff:3.500A) Proline residue: s 175 - end of helix Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 194 through 199 removed outlier: 3.909A pdb=" N ALA s 198 " --> pdb=" O ALA s 194 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALA s 199 " --> pdb=" O LEU s 195 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 194 through 199' Processing helix chain 's' and resid 267 through 272 removed outlier: 4.781A pdb=" N LEU s 271 " --> pdb=" O LYS s 267 " (cutoff:3.500A) Proline residue: s 272 - end of helix No H-bonds generated for 'chain 's' and resid 267 through 272' Processing helix chain 's' and resid 307 through 315 removed outlier: 3.564A pdb=" N LEU s 312 " --> pdb=" O ARG s 308 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG s 313 " --> pdb=" O GLU s 309 " (cutoff:3.500A) Processing helix chain 's' and resid 317 through 344 removed outlier: 5.000A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N GLY s 344 " --> pdb=" O ALA s 340 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 388 removed outlier: 3.667A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Proline residue: s 388 - end of helix Processing helix chain 's' and resid 414 through 427 removed outlier: 3.907A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 't' and resid 170 through 173 removed outlier: 4.697A pdb=" N THR t 161 " --> pdb=" O LEU t 173 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS t 164 " --> pdb=" O HIS t 218 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLY t 209 " --> pdb=" O GLY t 86 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLY t 86 " --> pdb=" O GLY t 209 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ASN t 84 " --> pdb=" O PRO t 211 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLN t 213 " --> pdb=" O GLY t 82 " (cutoff:3.500A) removed outlier: 9.852A pdb=" N GLN t 133 " --> pdb=" O VAL t 114 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N VAL t 114 " --> pdb=" O GLN t 133 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N PHE t 135 " --> pdb=" O GLY t 112 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY t 137 " --> pdb=" O ASN t 110 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ASN t 110 " --> pdb=" O GLY t 137 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASP t 139 " --> pdb=" O GLY t 108 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N GLY t 108 " --> pdb=" O ASP t 139 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N GLY t 141 " --> pdb=" O GLY t 106 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL t 114 " --> pdb=" O ALA t 182 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N ASP t 178 " --> pdb=" O VAL t 118 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 't' and resid 227 through 231 removed outlier: 3.567A pdb=" N ALA t 341 " --> pdb=" O LEU t 306 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 't' and resid 261 through 268 Processing sheet with id= 4, first strand: chain 't' and resid 82 through 86 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 't' and resid 107 through 114 removed outlier: 4.350A pdb=" N GLY t 189 " --> pdb=" O GLY t 108 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N ASN t 110 " --> pdb=" O ALA t 187 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N ALA t 187 " --> pdb=" O ASN t 110 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N GLY t 112 " --> pdb=" O GLY t 185 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY t 185 " --> pdb=" O GLY t 112 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA t 183 " --> pdb=" O VAL t 114 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.645A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY u 129 " --> pdb=" O MET u 180 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'x' and resid 130 through 133 removed outlier: 4.974A pdb=" N ARG x 130 " --> pdb=" O VAL x 77 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'x' and resid 230 through 236 removed outlier: 3.922A pdb=" N TRP x 236 " --> pdb=" O ASP x 204 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG x 251 " --> pdb=" O ILE x 176 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP x 255 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N ASP x 250 " --> pdb=" O GLY x 302 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLY x 303 " --> pdb=" O ARG x 382 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER x 311 " --> pdb=" O PRO x 374 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS x 379 " --> pdb=" O GLU x 339 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'x' and resid 361 through 365 Processing sheet with id= 10, first strand: chain '0' and resid 155 through 161 Processing sheet with id= 11, first strand: chain '1' and resid 16 through 22 removed outlier: 6.073A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '1' and resid 41 through 46 removed outlier: 6.310A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '4' and resid 66 through 70 removed outlier: 5.473A pdb=" N HIS 4 98 " --> pdb=" O CYS 4 92 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N CYS 4 92 " --> pdb=" O HIS 4 98 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '5' and resid 126 through 130 removed outlier: 5.348A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '5' and resid 208 through 214 removed outlier: 4.375A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '6' and resid 183 through 187 removed outlier: 3.592A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '6' and resid 231 through 234 removed outlier: 3.510A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain '6' and resid 311 through 314 removed outlier: 6.715A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '6' and resid 213 through 220 removed outlier: 3.980A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain '7' and resid 77 through 82 removed outlier: 4.446A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYS 7 123 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LYS 7 68 " --> pdb=" O CYS 7 123 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N PHE 7 127 " --> pdb=" O VAL 7 70 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '7' and resid 164 through 167 removed outlier: 3.740A pdb=" N PHE 7 297 " --> pdb=" O TYR 7 181 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain '7' and resid 217 through 221 Processing sheet with id= 23, first strand: chain '9' and resid 42 through 45 removed outlier: 3.604A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.580A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ASP D 180 " --> pdb=" O VAL D 244 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'D' and resid 190 through 193 removed outlier: 3.645A pdb=" N VAL D 215 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'D' and resid 138 through 144 removed outlier: 5.112A pdb=" N ASP D 138 " --> pdb=" O ALA D 153 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG D 147 " --> pdb=" O GLY D 144 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 98 through 101 removed outlier: 3.517A pdb=" N VAL E 206 " --> pdb=" O GLU E 268 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA E 208 " --> pdb=" O ARG E 266 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.854A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'E' and resid 176 through 182 removed outlier: 6.715A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS E 127 " --> pdb=" O LEU E 193 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR E 191 " --> pdb=" O VAL E 129 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'E' and resid 275 through 278 removed outlier: 8.072A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 32, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 33, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.142A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 35, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.615A pdb=" N HIS I 150 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET I 95 " --> pdb=" O SER I 156 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'J' and resid 18 through 24 removed outlier: 3.901A pdb=" N GLY J 18 " --> pdb=" O VAL J 72 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.522A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'L' and resid 58 through 61 removed outlier: 3.770A pdb=" N HIS L 59 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N GLN L 72 " --> pdb=" O TYR L 61 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 40, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 41, first strand: chain 'N' and resid 94 through 97 Processing sheet with id= 42, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.663A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.357A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.483A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 130 through 135 removed outlier: 6.363A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'Q' and resid 139 through 143 removed outlier: 3.988A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ARG Q 143 " --> pdb=" O GLY Q 146 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 105 through 109 removed outlier: 7.019A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 111 through 117 removed outlier: 3.922A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.811A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'S' and resid 168 through 175 removed outlier: 4.039A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 65 through 72 removed outlier: 4.743A pdb=" N ALA T 65 " --> pdb=" O GLU T 174 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N LYS T 171 " --> pdb=" O ALA T 137 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN T 133 " --> pdb=" O GLY T 175 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 138 through 144 removed outlier: 3.749A pdb=" N GLU T 138 " --> pdb=" O LYS T 171 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N TYR T 165 " --> pdb=" O GLY T 144 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 146 through 153 removed outlier: 3.719A pdb=" N LEU T 147 " --> pdb=" O LYS T 163 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG T 157 " --> pdb=" O HIS T 153 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'U' and resid 38 through 44 removed outlier: 6.934A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ALA U 67 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 60 through 65 removed outlier: 4.308A pdb=" N ASP V 60 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS V 72 " --> pdb=" O ILE V 64 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 78 through 81 removed outlier: 3.771A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.074A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 75 through 78 removed outlier: 6.339A pdb=" N VAL W 133 " --> pdb=" O GLY W 78 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 80 through 84 removed outlier: 7.547A pdb=" N HIS W 80 " --> pdb=" O LEU W 92 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.230A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'X' and resid 85 through 91 Processing sheet with id= 62, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 63, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.144A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'a' and resid 45 through 52 removed outlier: 6.199A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'b' and resid 61 through 68 removed outlier: 3.852A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N GLU b 86 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N VAL b 84 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 67, first strand: chain 'c' and resid 269 through 275 removed outlier: 3.842A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'd' and resid 212 through 219 removed outlier: 6.732A pdb=" N TYR d 245 " --> pdb=" O LYS d 264 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LYS d 264 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 174 through 178 removed outlier: 5.997A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.650A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'e' and resid 197 through 201 removed outlier: 7.691A pdb=" N GLU e 197 " --> pdb=" O SER e 244 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ASN e 199 " --> pdb=" O ASP e 242 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N THR e 240 " --> pdb=" O GLU e 201 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'e' and resid 211 through 216 removed outlier: 3.753A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE e 215 " --> pdb=" O ALA e 229 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ALA e 229 " --> pdb=" O PHE e 215 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'e' and resid 44 through 53 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'f' and resid 90 through 98 removed outlier: 5.485A pdb=" N GLU f 154 " --> pdb=" O PRO f 128 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL f 156 " --> pdb=" O ALA f 126 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA f 126 " --> pdb=" O VAL f 156 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N VAL f 134 " --> pdb=" O ASP f 147 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.578A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'k' and resid 49 through 56 removed outlier: 3.834A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG k 56 " --> pdb=" O PHE k 20 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N HIS k 72 " --> pdb=" O PHE k 68 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'm' and resid 62 through 66 removed outlier: 4.770A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'p' and resid 79 through 83 Processing sheet with id= 78, first strand: chain 'r' and resid 35 through 42 removed outlier: 3.729A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 's' and resid 90 through 93 removed outlier: 4.062A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 's' and resid 112 through 116 Processing sheet with id= 81, first strand: chain 's' and resid 297 through 302 removed outlier: 5.566A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) 2864 hydrogen bonds defined for protein. 8508 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 790 hydrogen bonds 1362 hydrogen bond angles 0 basepair planarities 333 basepair parallelities 839 stacking parallelities Total time for adding SS restraints: 70.61 Time building geometry restraints manager: 39.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.41: 46266 1.41 - 1.61: 68133 1.61 - 1.80: 1555 1.80 - 2.00: 103 2.00 - 2.20: 4 Bond restraints: 116061 Sorted by residual: bond pdb=" C1' SAM x 401 " pdb=" C2' SAM x 401 " ideal model delta sigma weight residual 1.307 1.518 -0.211 2.00e-02 2.50e+03 1.12e+02 bond pdb=" C1' SAM x 401 " pdb=" O4' SAM x 401 " ideal model delta sigma weight residual 1.616 1.412 0.204 2.00e-02 2.50e+03 1.04e+02 bond pdb=" C2 OMU A3039 " pdb=" N3 OMU A3039 " ideal model delta sigma weight residual 1.499 1.323 0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N3 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 1.492 1.344 0.148 2.00e-02 2.50e+03 5.46e+01 bond pdb=" N3 OMU A3039 " pdb=" C4 OMU A3039 " ideal model delta sigma weight residual 1.457 1.325 0.132 2.00e-02 2.50e+03 4.37e+01 ... (remaining 116056 not shown) Histogram of bond angle deviations from ideal: 75.00 - 87.21: 2 87.21 - 99.43: 1 99.43 - 111.65: 64674 111.65 - 123.87: 91136 123.87 - 136.08: 8439 Bond angle restraints: 164252 Sorted by residual: angle pdb=" C4' OMU A3039 " pdb=" C3' OMU A3039 " pdb=" C2' OMU A3039 " ideal model delta sigma weight residual 102.60 96.07 6.53 1.00e+00 1.00e+00 4.26e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C4 OMG A3040 " ideal model delta sigma weight residual 108.29 125.63 -17.34 3.00e+00 1.11e-01 3.34e+01 angle pdb=" C1' OMG A3040 " pdb=" N9 OMG A3040 " pdb=" C8 OMG A3040 " ideal model delta sigma weight residual 142.82 125.54 17.28 3.00e+00 1.11e-01 3.32e+01 angle pdb=" P OMG A3040 " pdb=" O5' OMG A3040 " pdb=" C5' OMG A3040 " ideal model delta sigma weight residual 120.90 112.31 8.59 1.50e+00 4.44e-01 3.28e+01 angle pdb=" C ASP s 407 " pdb=" CA ASP s 407 " pdb=" CB ASP s 407 " ideal model delta sigma weight residual 116.54 110.42 6.12 1.15e+00 7.56e-01 2.84e+01 ... (remaining 164247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 67501 35.85 - 71.71: 2323 71.71 - 107.56: 462 107.56 - 143.42: 7 143.42 - 179.27: 23 Dihedral angle restraints: 70316 sinusoidal: 42431 harmonic: 27885 Sorted by residual: dihedral pdb=" O4' U A2898 " pdb=" C1' U A2898 " pdb=" N1 U A2898 " pdb=" C2 U A2898 " ideal model delta sinusoidal sigma weight residual -160.00 18.73 -178.73 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A2493 " pdb=" C1' C A2493 " pdb=" N1 C A2493 " pdb=" C2 C A2493 " ideal model delta sinusoidal sigma weight residual 200.00 30.27 169.73 1 1.50e+01 4.44e-03 8.46e+01 dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual 200.00 38.18 161.82 1 1.50e+01 4.44e-03 8.32e+01 ... (remaining 70313 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 16282 0.039 - 0.078: 1979 0.078 - 0.117: 831 0.117 - 0.156: 54 0.156 - 0.195: 7 Chirality restraints: 19153 Sorted by residual: chirality pdb=" C2' U A3038 " pdb=" C3' U A3038 " pdb=" O2' U A3038 " pdb=" C1' U A3038 " both_signs ideal model delta sigma weight residual False -2.75 -2.56 -0.20 2.00e-01 2.50e+01 9.55e-01 chirality pdb=" C3' C A2186 " pdb=" C4' C A2186 " pdb=" O3' C A2186 " pdb=" C2' C A2186 " both_signs ideal model delta sigma weight residual False -2.48 -2.30 -0.18 2.00e-01 2.50e+01 8.28e-01 chirality pdb=" C2' U A3037 " pdb=" C3' U A3037 " pdb=" O2' U A3037 " pdb=" C1' U A3037 " both_signs ideal model delta sigma weight residual False -2.75 -2.58 -0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 19150 not shown) Planarity restraints: 15513 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMG A3040 " 0.091 2.00e-02 2.50e+03 5.77e-01 7.49e+03 pdb=" C4' OMG A3040 " 0.449 2.00e-02 2.50e+03 pdb=" O4' OMG A3040 " 0.512 2.00e-02 2.50e+03 pdb=" C3' OMG A3040 " -0.624 2.00e-02 2.50e+03 pdb=" O3' OMG A3040 " -0.650 2.00e-02 2.50e+03 pdb=" C2' OMG A3040 " -0.176 2.00e-02 2.50e+03 pdb=" O2' OMG A3040 " 0.977 2.00e-02 2.50e+03 pdb=" C1' OMG A3040 " 0.237 2.00e-02 2.50e+03 pdb=" N9 OMG A3040 " -0.817 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' SAM x 401 " -0.349 2.00e-02 2.50e+03 3.45e-01 2.68e+03 pdb=" C2' SAM x 401 " 0.444 2.00e-02 2.50e+03 pdb=" C3' SAM x 401 " 0.448 2.00e-02 2.50e+03 pdb=" C4' SAM x 401 " -0.340 2.00e-02 2.50e+03 pdb=" C5' SAM x 401 " 0.300 2.00e-02 2.50e+03 pdb=" N9 SAM x 401 " 0.313 2.00e-02 2.50e+03 pdb=" O2' SAM x 401 " -0.205 2.00e-02 2.50e+03 pdb=" O3' SAM x 401 " -0.204 2.00e-02 2.50e+03 pdb=" O4' SAM x 401 " -0.407 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C32 PM8 w 200 " -0.022 2.00e-02 2.50e+03 7.73e-02 7.47e+01 pdb=" C34 PM8 w 200 " -0.022 2.00e-02 2.50e+03 pdb=" C37 PM8 w 200 " 0.091 2.00e-02 2.50e+03 pdb=" N36 PM8 w 200 " -0.122 2.00e-02 2.50e+03 pdb=" O35 PM8 w 200 " 0.076 2.00e-02 2.50e+03 ... (remaining 15510 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.62: 1434 2.62 - 3.25: 104071 3.25 - 3.88: 232841 3.88 - 4.51: 323946 4.51 - 5.14: 465912 Nonbonded interactions: 1128204 Sorted by model distance: nonbonded pdb=" OP1 C A2915 " pdb="MG MG A3344 " model vdw 1.988 2.170 nonbonded pdb=" OP1 A A1961 " pdb="MG MG A3314 " model vdw 1.992 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3344 " model vdw 1.994 2.170 nonbonded pdb=" OP1 A A2509 " pdb="MG MG A3332 " model vdw 2.012 2.170 nonbonded pdb=" O4 U A2475 " pdb="MG MG A3331 " model vdw 2.016 2.170 ... (remaining 1128199 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 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: 3.870 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: 0.060 Extract box with map and model: 21.870 Check model and map are aligned: 1.170 Set scattering table: 0.760 Process input model: 324.090 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 357.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 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 0.211 116061 Z= 0.159 Angle : 0.415 17.336 164252 Z= 0.230 Chirality : 0.031 0.195 19153 Planarity : 0.006 0.577 15513 Dihedral : 15.514 179.273 52282 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.53 % Allowed : 1.55 % Favored : 97.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.09), residues: 9449 helix: 1.10 (0.09), residues: 3161 sheet: 0.32 (0.14), residues: 1336 loop : 0.73 (0.09), residues: 4952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP s 346 HIS 0.002 0.000 HIS D 100 PHE 0.009 0.001 PHE x 38 TYR 0.012 0.001 TYR 5 176 ARG 0.003 0.000 ARG D 85 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1838 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1793 time to evaluate : 7.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 11 residues processed: 1829 average time/residue: 1.0609 time to fit residues: 3214.7934 Evaluate side-chains 871 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 860 time to evaluate : 7.626 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.9568 time to fit residues: 28.0161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 918 optimal weight: 10.0000 chunk 824 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 chunk 556 optimal weight: 5.9990 chunk 440 optimal weight: 8.9990 chunk 852 optimal weight: 10.0000 chunk 330 optimal weight: 10.0000 chunk 518 optimal weight: 9.9990 chunk 634 optimal weight: 0.9990 chunk 988 optimal weight: 20.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 120 GLN t 121 GLN t 198 ASN t 199 ASN t 234 ASN t 271 HIS t 273 GLN t 362 HIS u 136 HIS v 19 GLN v 63 ASN x 85 HIS x 109 GLN x 172 GLN x 230 GLN x 316 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 122 GLN y 123 GLN y 235 GLN y 255 GLN y 284 GLN 1 31 ASN 1 52 GLN 5 165 GLN 5 266 HIS ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 7 84 ASN 7 207 HIS 7 290 GLN ** 8 177 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 271 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 223 HIS I 43 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 133 GLN K 40 GLN K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN N 68 ASN N 237 HIS O 27 HIS ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 HIS P 162 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 149 HIS S 118 ASN T 73 GLN T 126 HIS T 127 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 101 HIS V 78 GLN Y 179 HIS Z 64 HIS a 46 ASN b 107 GLN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN d 58 GLN d 167 HIS d 220 GLN d 262 HIS e 67 GLN e 75 GLN f 158 GLN g 65 HIS g 92 HIS h 131 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN k 35 GLN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 82 GLN m 65 HIS o 94 HIS p 117 GLN p 182 ASN q 161 GLN r 79 HIS r 96 HIS r 112 HIS s 239 ASN s 343 GLN s 358 GLN Total number of N/Q/H flips: 78 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 116061 Z= 0.412 Angle : 0.700 20.888 164252 Z= 0.350 Chirality : 0.043 0.294 19153 Planarity : 0.006 0.133 15513 Dihedral : 18.562 179.705 32137 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.49 % Allowed : 7.84 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.70 (0.08), residues: 9449 helix: 0.89 (0.09), residues: 3260 sheet: 0.06 (0.14), residues: 1346 loop : 0.46 (0.09), residues: 4843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP x 83 HIS 0.018 0.002 HIS I 114 PHE 0.023 0.002 PHE N 175 TYR 0.029 0.002 TYR h 73 ARG 0.009 0.001 ARG d 198 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1089 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 879 time to evaluate : 7.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 210 outliers final: 119 residues processed: 1022 average time/residue: 0.9761 time to fit residues: 1731.8576 Evaluate side-chains 865 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 746 time to evaluate : 7.579 Switching outliers to nearest non-outliers outliers start: 119 outliers final: 0 residues processed: 119 average time/residue: 0.8044 time to fit residues: 190.6143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 549 optimal weight: 2.9990 chunk 306 optimal weight: 7.9990 chunk 822 optimal weight: 0.3980 chunk 672 optimal weight: 10.0000 chunk 272 optimal weight: 10.0000 chunk 989 optimal weight: 1.9990 chunk 1069 optimal weight: 0.8980 chunk 881 optimal weight: 8.9990 chunk 981 optimal weight: 3.9990 chunk 337 optimal weight: 20.0000 chunk 794 optimal weight: 9.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 314 GLN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 185 ASN 5 165 GLN 5 384 GLN ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 7 207 HIS 7 255 HIS ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 126 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 129 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 67 HIS b 27 GLN ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 67 GLN g 93 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 117 GLN p 194 HIS r 76 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 116061 Z= 0.181 Angle : 0.541 17.902 164252 Z= 0.271 Chirality : 0.037 0.246 19153 Planarity : 0.004 0.123 15513 Dihedral : 18.561 179.888 32137 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 1.08 % Allowed : 9.13 % Favored : 89.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.92 (0.09), residues: 9449 helix: 1.18 (0.09), residues: 3272 sheet: 0.16 (0.14), residues: 1314 loop : 0.50 (0.09), residues: 4863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP x 83 HIS 0.015 0.001 HIS d 193 PHE 0.028 0.001 PHE y 316 TYR 0.024 0.001 TYR 8 124 ARG 0.006 0.000 ARG t 76 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 853 time to evaluate : 7.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 38 residues processed: 905 average time/residue: 0.9970 time to fit residues: 1568.1443 Evaluate side-chains 779 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 741 time to evaluate : 6.752 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.7506 time to fit residues: 63.2231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 977 optimal weight: 8.9990 chunk 744 optimal weight: 6.9990 chunk 513 optimal weight: 30.0000 chunk 109 optimal weight: 10.0000 chunk 472 optimal weight: 10.0000 chunk 664 optimal weight: 0.5980 chunk 993 optimal weight: 0.0980 chunk 1051 optimal weight: 4.9990 chunk 518 optimal weight: 20.0000 chunk 941 optimal weight: 10.0000 chunk 283 optimal weight: 20.0000 overall best weight: 4.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 188 HIS ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 151 ASN K 40 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 30 ASN ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 195 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 27 GLN V 78 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 155 ASN d 59 HIS ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 26 ASN ** k 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 93 HIS m 59 GLN ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 116061 Z= 0.313 Angle : 0.603 17.947 164252 Z= 0.302 Chirality : 0.040 0.250 19153 Planarity : 0.005 0.125 15513 Dihedral : 18.587 178.987 32137 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.51 % Allowed : 10.09 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.73 (0.09), residues: 9449 helix: 1.07 (0.09), residues: 3288 sheet: 0.01 (0.14), residues: 1295 loop : 0.35 (0.09), residues: 4866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP t 318 HIS 0.013 0.001 HIS d 193 PHE 0.040 0.002 PHE y 316 TYR 0.040 0.002 TYR 8 124 ARG 0.007 0.001 ARG D 218 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 782 time to evaluate : 7.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 76 residues processed: 867 average time/residue: 0.9774 time to fit residues: 1473.3860 Evaluate side-chains 793 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 717 time to evaluate : 7.587 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.7845 time to fit residues: 123.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 875 optimal weight: 20.0000 chunk 596 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 783 optimal weight: 8.9990 chunk 433 optimal weight: 6.9990 chunk 897 optimal weight: 0.0170 chunk 726 optimal weight: 0.0870 chunk 1 optimal weight: 0.2980 chunk 537 optimal weight: 8.9990 chunk 943 optimal weight: 4.9990 chunk 265 optimal weight: 6.9990 overall best weight: 2.4800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 314 GLN ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 47 ASN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 157 GLN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 222 GLN d 235 GLN ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 46 ASN ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 116061 Z= 0.198 Angle : 0.537 17.887 164252 Z= 0.269 Chirality : 0.037 0.245 19153 Planarity : 0.004 0.120 15513 Dihedral : 18.586 179.711 32137 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.84 % Allowed : 11.06 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.83 (0.09), residues: 9449 helix: 1.25 (0.09), residues: 3288 sheet: -0.04 (0.14), residues: 1341 loop : 0.38 (0.09), residues: 4820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP x 83 HIS 0.014 0.001 HIS d 193 PHE 0.024 0.001 PHE H 140 TYR 0.046 0.001 TYR 8 124 ARG 0.006 0.000 ARG 6 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 794 time to evaluate : 7.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 39 residues processed: 839 average time/residue: 0.9900 time to fit residues: 1446.8320 Evaluate side-chains 767 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 728 time to evaluate : 9.334 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 0.7902 time to fit residues: 68.6765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 353 optimal weight: 10.0000 chunk 947 optimal weight: 2.9990 chunk 207 optimal weight: 0.6980 chunk 617 optimal weight: 10.0000 chunk 259 optimal weight: 10.0000 chunk 1052 optimal weight: 0.9990 chunk 873 optimal weight: 4.9990 chunk 487 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 chunk 552 optimal weight: 0.9980 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 358 GLN ** 6 249 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 103 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN T 195 GLN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 121 GLN ** h 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 116061 Z= 0.181 Angle : 0.526 17.896 164252 Z= 0.263 Chirality : 0.036 0.237 19153 Planarity : 0.004 0.118 15513 Dihedral : 18.547 179.574 32137 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.69 % Allowed : 11.53 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.89 (0.09), residues: 9449 helix: 1.36 (0.09), residues: 3291 sheet: -0.06 (0.14), residues: 1350 loop : 0.39 (0.09), residues: 4808 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 8 121 HIS 0.013 0.001 HIS d 193 PHE 0.024 0.001 PHE y 316 TYR 0.045 0.001 TYR 8 124 ARG 0.007 0.000 ARG 6 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 776 time to evaluate : 7.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 34 residues processed: 808 average time/residue: 0.9971 time to fit residues: 1397.0511 Evaluate side-chains 767 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 733 time to evaluate : 7.935 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.8541 time to fit residues: 63.5197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 1014 optimal weight: 1.9990 chunk 118 optimal weight: 9.9990 chunk 599 optimal weight: 2.9990 chunk 768 optimal weight: 9.9990 chunk 595 optimal weight: 0.2980 chunk 886 optimal weight: 8.9990 chunk 587 optimal weight: 0.9980 chunk 1048 optimal weight: 6.9990 chunk 656 optimal weight: 9.9990 chunk 639 optimal weight: 10.0000 chunk 484 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 52 GLN 6 249 GLN 7 207 HIS 7 298 GLN ** 9 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 98 GLN F 184 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 115 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 127 ASN ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 93 ASN g 121 GLN h 131 ASN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 116061 Z= 0.146 Angle : 0.508 17.953 164252 Z= 0.254 Chirality : 0.035 0.230 19153 Planarity : 0.004 0.116 15513 Dihedral : 18.510 179.574 32137 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.55 % Allowed : 11.81 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.09), residues: 9449 helix: 1.48 (0.09), residues: 3304 sheet: 0.06 (0.14), residues: 1331 loop : 0.43 (0.09), residues: 4814 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 7 143 HIS 0.012 0.001 HIS d 193 PHE 0.028 0.001 PHE h 129 TYR 0.044 0.001 TYR 8 124 ARG 0.011 0.000 ARG t 302 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 831 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 785 time to evaluate : 7.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 21 residues processed: 813 average time/residue: 0.9960 time to fit residues: 1413.6625 Evaluate side-chains 742 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 721 time to evaluate : 7.652 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.8078 time to fit residues: 41.8931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 648 optimal weight: 0.0370 chunk 418 optimal weight: 20.0000 chunk 626 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 206 optimal weight: 10.0000 chunk 203 optimal weight: 20.0000 chunk 666 optimal weight: 3.9990 chunk 714 optimal weight: 10.0000 chunk 518 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 824 optimal weight: 0.7980 overall best weight: 4.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 314 HIS ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 52 GLN 7 207 HIS 7 298 GLN ** 7 309 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 116061 Z= 0.317 Angle : 0.601 17.615 164252 Z= 0.300 Chirality : 0.039 0.233 19153 Planarity : 0.005 0.123 15513 Dihedral : 18.588 178.706 32137 Min Nonbonded Distance : 1.806 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.51 % Allowed : 12.23 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.74 (0.09), residues: 9449 helix: 1.24 (0.09), residues: 3301 sheet: -0.09 (0.14), residues: 1318 loop : 0.27 (0.09), residues: 4830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP 7 143 HIS 0.011 0.001 HIS d 193 PHE 0.033 0.002 PHE y 316 TYR 0.039 0.002 TYR 8 124 ARG 0.008 0.001 ARG t 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 730 time to evaluate : 8.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 29 residues processed: 760 average time/residue: 0.9712 time to fit residues: 1285.3360 Evaluate side-chains 722 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 693 time to evaluate : 7.626 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.8031 time to fit residues: 53.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 953 optimal weight: 4.9990 chunk 1004 optimal weight: 0.8980 chunk 916 optimal weight: 1.9990 chunk 977 optimal weight: 20.0000 chunk 588 optimal weight: 7.9990 chunk 425 optimal weight: 10.0000 chunk 767 optimal weight: 5.9990 chunk 299 optimal weight: 10.0000 chunk 883 optimal weight: 20.0000 chunk 924 optimal weight: 7.9990 chunk 973 optimal weight: 0.6980 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 109 GLN ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS 7 298 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 100 GLN ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 HIS ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 116061 Z= 0.221 Angle : 0.551 17.786 164252 Z= 0.276 Chirality : 0.037 0.229 19153 Planarity : 0.004 0.118 15513 Dihedral : 18.585 179.198 32137 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.31 % Allowed : 12.54 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.78 (0.09), residues: 9449 helix: 1.31 (0.09), residues: 3309 sheet: -0.12 (0.14), residues: 1349 loop : 0.27 (0.09), residues: 4791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 8 121 HIS 0.011 0.001 HIS d 193 PHE 0.037 0.001 PHE y 316 TYR 0.045 0.001 TYR 8 124 ARG 0.007 0.000 ARG M 238 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 737 time to evaluate : 7.637 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 outliers start: 26 outliers final: 14 residues processed: 751 average time/residue: 1.0096 time to fit residues: 1323.2717 Evaluate side-chains 715 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 701 time to evaluate : 7.142 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.8007 time to fit residues: 30.9107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 641 optimal weight: 10.0000 chunk 1033 optimal weight: 3.9990 chunk 630 optimal weight: 4.9990 chunk 490 optimal weight: 9.9990 chunk 718 optimal weight: 4.9990 chunk 1083 optimal weight: 0.0570 chunk 997 optimal weight: 6.9990 chunk 863 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 666 optimal weight: 4.9990 chunk 529 optimal weight: 7.9990 overall best weight: 2.3704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 299 HIS ** v 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 98 GLN 7 207 HIS ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN V 92 ASN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 116061 Z= 0.194 Angle : 0.541 17.824 164252 Z= 0.270 Chirality : 0.037 0.227 19153 Planarity : 0.004 0.117 15513 Dihedral : 18.555 179.385 32137 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.24 % Allowed : 12.76 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.83 (0.09), residues: 9449 helix: 1.36 (0.09), residues: 3304 sheet: -0.06 (0.14), residues: 1352 loop : 0.29 (0.09), residues: 4793 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP 7 143 HIS 0.026 0.001 HIS t 299 PHE 0.041 0.001 PHE y 316 TYR 0.054 0.001 TYR 7 142 ARG 0.008 0.000 ARG M 238 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18898 Ramachandran restraints generated. 9449 Oldfield, 0 Emsley, 9449 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 744 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 724 time to evaluate : 8.047 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 outliers start: 20 outliers final: 10 residues processed: 734 average time/residue: 1.0150 time to fit residues: 1296.9828 Evaluate side-chains 716 residues out of total 8430 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 706 time to evaluate : 6.860 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.7452 time to fit residues: 22.8940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1088 random chunks: chunk 685 optimal weight: 1.9990 chunk 919 optimal weight: 20.0000 chunk 264 optimal weight: 8.9990 chunk 795 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 239 optimal weight: 0.0870 chunk 864 optimal weight: 9.9990 chunk 361 optimal weight: 10.0000 chunk 887 optimal weight: 9.9990 chunk 109 optimal weight: 6.9990 chunk 159 optimal weight: 0.9980 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: t 345 ASN ** x 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 207 HIS 7 298 GLN ** I 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 97 GLN ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 92 ASN Z 67 HIS ** c 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 76 GLN ** i 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.099119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.078241 restraints weight = 360292.945| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 2.06 r_work: 0.3369 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 116061 Z= 0.185 Angle : 0.534 17.820 164252 Z= 0.266 Chirality : 0.036 0.224 19153 Planarity : 0.004 0.116 15513 Dihedral : 18.531 179.373 32137 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.20 % Allowed : 12.80 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.82 % 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: 0.88 (0.09), residues: 9449 helix: 1.42 (0.09), residues: 3303 sheet: -0.05 (0.14), residues: 1365 loop : 0.32 (0.09), residues: 4781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP 7 143 HIS 0.010 0.001 HIS I 114 PHE 0.042 0.001 PHE y 316 TYR 0.050 0.001 TYR 7 142 ARG 0.011 0.000 ARG Q 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27907.74 seconds wall clock time: 487 minutes 49.30 seconds (29269.30 seconds total)