Starting phenix.real_space_refine (version: dev) on Mon Apr 4 11:32:31 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7odr_12845/04_2022/7odr_12845_neut_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.118 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "7 TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 107464 Number of models: 1 Model: "" Number of chains: 68 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: 2660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2660 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 14, 'TRANS': 319, 'PCIS': 2} 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: {'PTRANS': 31, 'TRANS': 361, 'PCIS': 1} 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: {'PTRANS': 33, 'TRANS': 319, 'PCIS': 1} Chain: "7" Number of atoms: 2390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2390 Classifications: {'peptide': 294} Link IDs: {'PTRANS': 16, 'TRANS': 276, 'PCIS': 1} Chain: "8" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 860 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 9, 'TRANS': 91, 'PCIS': 1} 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: {'PTRANS': 9, 'TRANS': 113, 'PCIS': 1} Chain: "A" Number of atoms: 30460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1448, 30460 Classifications: {'RNA': 1448} Modifications used: {'rna3p_pyr': 554, 'rna2p_pur': 143, 'rna3p_pur': 607, 'rna2p_pyr': 113, 'rna3p': 31} Link IDs: {'rna3p': 1191, 'rna2p': 256} Chain breaks: 10 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 31 Chain: "B" Number of atoms: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 1522 Classifications: {'RNA': 72} Modifications used: {'rna2p_pyr': 6, 'rna3p_pyr': 31, 'p5*END': 1, 'rna3p_pur': 32, 'rna2p_pur': 3} Link IDs: {'rna3p': 63, 'rna2p': 8} 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: {'PTRANS': 23, 'TRANS': 280, 'PCIS': 1} Chain: "F" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 252, 2031 Classifications: {'peptide': 252} Link IDs: {'PTRANS': 19, 'TRANS': 230, 'PCIS': 2} 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: 1324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1324 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 15, 'TRANS': 147} 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: {'PTRANS': 8, 'TRANS': 165, 'PCIS': 1} 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: 1723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1723 Classifications: {'peptide': 212} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 194} Chain breaks: 1 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: {'PTRANS': 6, 'TRANS': 136, 'PCIS': 1} 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: {'PTRANS': 13, 'TRANS': 206, 'PCIS': 1} 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: {'PTRANS': 10, 'TRANS': 149, 'PCIS': 1} 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: {'PTRANS': 16, 'TRANS': 268, 'PCIS': 1} 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: {'PTRANS': 14, 'TRANS': 117, 'PCIS': 2} 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: {'PTRANS': 26, 'TRANS': 358, 'PCIS': 1} Chain breaks: 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} Modifications used: {'COO': 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: "9" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Unusual residues: {' K': 2, ' MG': 92} Classifications: {'undetermined': 94} Link IDs: {None: 93} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "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: "g" 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 7049 SG CYS 0 110 133.750 107.056 212.760 1.00 51.97 S ATOM 7071 SG CYS 0 113 137.398 108.249 212.678 1.00 51.62 S ATOM 7151 SG CYS 0 123 136.034 106.390 209.729 1.00 38.60 S ATOM 7174 SG CYS 0 126 136.498 104.558 213.056 1.00 47.85 S ATOM 9441 SG CYS 4 76 63.737 105.846 123.291 1.00 59.30 S ATOM 9464 SG CYS 4 79 66.426 107.662 125.252 1.00 53.98 S ATOM 9588 SG CYS 4 92 64.418 104.885 126.903 1.00 51.36 S ATOM 59440 SG CYS I 64 65.346 146.668 127.341 1.00 64.01 S ATOM A02EL SG CYS r 73 62.141 147.221 129.443 1.00 54.90 S ATOM A02E0 SG CYS r 70 61.253 143.593 130.774 1.00 53.21 S ATOM A02MR SG CYS r 108 63.679 141.172 129.165 1.00 53.66 S Time building chain proxies: 45.23, per 1000 atoms: 0.42 Number of scatterers: 107464 At special positions: 0 Unit cell: (257.58, 224.72, 253.34, 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 2 19.00 S 329 16.00 P 1521 15.00 Mg 97 11.99 O 23772 8.00 N 19392 7.00 C 62347 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: 34.75 Conformation dependent library (CDL) restraints added in 9.4 seconds Dynamic metal coordination Iron sulfur cluster 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="FE2 FES r 201 " - pdb=" SG CYS r 108 " pdb="FE1 FES r 201 " - pdb=" SG CYS r 73 " Number of angles added : 6 Zn2+ tetrahedral coordination 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 0 113 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 201 " - pdb=" SG CYS 0 110 " pdb=" ZN 4 201 " pdb="ZN ZN 4 201 " - pdb=" ND1 HIS 4 98 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 201 " - pdb=" SG CYS 4 92 " Number of angles added : 9 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17448 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 322 helices and 78 sheets defined 43.5% alpha, 13.3% beta 332 base pairs and 834 stacking pairs defined. Time for finding SS restraints: 47.77 Creating SS restraints... Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 149 removed outlier: 3.843A pdb=" N VAL u 143 " --> pdb=" O ALA u 139 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 removed outlier: 3.541A 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: 3.812A pdb=" N VAL v 9 " --> pdb=" O SER v 5 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N LEU v 10 " --> pdb=" O ARG v 6 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU v 12 " --> pdb=" O ALA v 8 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N TYR v 13 " --> pdb=" O VAL v 9 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU v 17 " --> pdb=" O TYR v 13 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LEU v 23 " --> pdb=" O GLN v 19 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ARG v 24 " --> pdb=" O GLY v 20 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 45 removed outlier: 3.611A pdb=" N PHE v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN v 42 " --> pdb=" O GLU v 38 " (cutoff:3.500A) removed outlier: 4.949A pdb=" N LYS v 44 " --> pdb=" O ARG v 40 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N LEU v 45 " --> pdb=" O LYS v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 47 through 64 removed outlier: 4.098A pdb=" N GLN v 54 " --> pdb=" O ALA v 50 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL v 60 " --> pdb=" O GLU v 56 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 91 removed outlier: 5.854A pdb=" N ASP w 91 " --> pdb=" O LEU w 87 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 126 removed outlier: 3.586A pdb=" N ASP w 124 " --> pdb=" O MET w 120 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU w 125 " --> pdb=" O ALA w 121 " (cutoff:3.500A) Processing helix chain 'w' and resid 131 through 139 removed outlier: 3.720A pdb=" N GLU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LYS w 137 " --> pdb=" O ILE w 133 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU w 138 " --> pdb=" O ASP w 134 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N MET w 139 " --> pdb=" O ALA w 135 " (cutoff:3.500A) Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.516A pdb=" N ASP w 150 " --> pdb=" O ASP w 146 " (cutoff:3.500A) Processing helix chain 'w' and resid 103 through 109 removed outlier: 3.682A pdb=" N GLY w 109 " --> pdb=" O PHE w 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 39 through 57 removed outlier: 4.241A pdb=" N VAL x 54 " --> pdb=" O MET x 50 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN x 55 " --> pdb=" O THR x 51 " (cutoff:3.500A) Processing helix chain 'x' and resid 58 through 70 removed outlier: 4.449A pdb=" N SER x 62 " --> pdb=" O ASP x 58 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER x 66 " --> pdb=" O SER x 62 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU x 70 " --> pdb=" O SER x 66 " (cutoff:3.500A) Processing helix chain 'x' and resid 82 through 94 removed outlier: 3.501A pdb=" N LEU x 93 " --> pdb=" O LYS x 89 " (cutoff:3.500A) Processing helix chain 'x' and resid 97 through 109 removed outlier: 3.515A pdb=" N HIS x 105 " --> pdb=" O GLU x 101 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N TRP x 106 " --> pdb=" O ALA x 102 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU x 107 " --> pdb=" O ILE x 103 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU x 108 " --> pdb=" O SER x 104 " (cutoff:3.500A) Processing helix chain 'x' and resid 159 through 170 removed outlier: 3.953A pdb=" N LEU x 163 " --> pdb=" O ASP x 159 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU x 164 " --> pdb=" O ALA x 160 " (cutoff:3.500A) Proline residue: x 165 - end of helix removed outlier: 3.948A pdb=" N GLY x 170 " --> pdb=" O VAL x 166 " (cutoff:3.500A) Processing helix chain 'x' and resid 185 through 195 removed outlier: 4.156A pdb=" N ALA x 190 " --> pdb=" O GLY x 186 " (cutoff:3.500A) removed outlier: 3.622A 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: 3.561A pdb=" N ARG x 226 " --> pdb=" O PRO x 222 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY x 228 " --> pdb=" O GLU x 224 " (cutoff:3.500A) Processing helix chain 'x' and resid 237 through 244 removed outlier: 4.119A pdb=" N TRP x 241 " --> pdb=" O ASP x 237 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLY x 242 " --> pdb=" O GLY x 238 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N GLU x 243 " --> pdb=" O ARG x 239 " (cutoff:3.500A) Processing helix chain 'x' and resid 260 through 267 removed outlier: 3.796A pdb=" N HIS x 266 " --> pdb=" O ARG x 262 " (cutoff:3.500A) Processing helix chain 'x' and resid 274 through 300 removed outlier: 4.854A pdb=" N LYS x 279 " --> pdb=" O ARG x 275 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N GLU x 280 " --> pdb=" O SER x 276 " (cutoff:3.500A) Proline residue: x 285 - end of helix removed outlier: 5.741A pdb=" N LYS x 300 " --> pdb=" O LEU x 296 " (cutoff:3.500A) Processing helix chain 'x' and resid 313 through 331 removed outlier: 4.687A pdb=" N TYR x 319 " --> pdb=" O LEU x 315 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N VAL x 320 " --> pdb=" O GLN x 316 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL x 321 " --> pdb=" O ASN x 317 " (cutoff:3.500A) Processing helix chain 'x' and resid 341 through 349 removed outlier: 3.710A pdb=" N VAL x 347 " --> pdb=" O HIS x 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE x 348 " --> pdb=" O PHE x 344 " (cutoff:3.500A) Processing helix chain 'y' and resid 88 through 103 removed outlier: 3.517A pdb=" N GLY y 103 " --> pdb=" O LEU y 99 " (cutoff:3.500A) Processing helix chain 'y' and resid 105 through 116 removed outlier: 3.543A pdb=" N ARG y 116 " --> pdb=" O LEU y 112 " (cutoff:3.500A) Processing helix chain 'y' and resid 120 through 135 removed outlier: 3.684A pdb=" N GLY y 135 " --> pdb=" O PHE y 131 " (cutoff:3.500A) 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: 3.507A pdb=" N GLY y 170 " --> pdb=" O LEU y 166 " (cutoff:3.500A) Processing helix chain 'y' and resid 173 through 183 removed outlier: 6.298A pdb=" N LYS y 177 " --> pdb=" O GLU y 173 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ARG y 178 " --> pdb=" O GLY y 174 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N VAL y 179 " --> pdb=" O LYS y 175 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR y 181 " --> pdb=" O LYS y 177 " (cutoff:3.500A) Processing helix chain 'y' and resid 190 through 203 removed outlier: 3.566A 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: 4.480A pdb=" N ARG y 224 " --> pdb=" O PRO y 220 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ASP y 226 " --> pdb=" O VAL y 222 " (cutoff:3.500A) Processing helix chain 'y' and resid 227 through 239 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 removed outlier: 3.726A pdb=" N ALA y 303 " --> pdb=" O ALA y 299 " (cutoff:3.500A) Processing helix chain 'y' and resid 309 through 331 removed outlier: 3.552A pdb=" N PHE y 313 " --> pdb=" O SER y 309 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 removed outlier: 3.523A pdb=" N CYS 0 92 " --> pdb=" O GLU 0 88 " (cutoff:3.500A) Processing helix chain '0' and resid 96 through 101 removed outlier: 5.383A pdb=" N ILE 0 101 " --> pdb=" O PRO 0 97 " (cutoff:3.500A) Processing helix chain '0' and resid 123 through 146 removed outlier: 3.521A pdb=" N VAL 0 130 " --> pdb=" O CYS 0 126 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 72 removed outlier: 4.321A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 73 through 86 removed outlier: 3.515A pdb=" N GLN 2 77 " --> pdb=" O PRO 2 73 " (cutoff:3.500A) Processing helix chain '3' and resid 107 through 114 removed outlier: 3.863A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG 3 113 " --> pdb=" O ALA 3 109 " (cutoff:3.500A) Processing helix chain '3' and resid 132 through 137 removed outlier: 4.050A pdb=" N LYS 3 136 " --> pdb=" O LYS 3 132 " (cutoff:3.500A) removed outlier: 5.736A 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: 4.239A pdb=" N GLU 3 146 " --> pdb=" O LYS 3 142 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N PHE 3 147 " --> pdb=" O ARG 3 143 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 5.205A pdb=" N THR 3 163 " --> pdb=" O ASP 3 159 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 40 removed outlier: 5.342A pdb=" N LYS 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 47 through 52 removed outlier: 4.425A pdb=" N GLU 5 51 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE 5 52 " --> pdb=" O ARG 5 48 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 47 through 52' Processing helix chain '5' and resid 116 through 125 removed outlier: 3.615A pdb=" N TRP 5 122 " --> pdb=" O LYS 5 118 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 142 removed outlier: 3.648A pdb=" N LEU 5 139 " --> pdb=" O LYS 5 135 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL 5 140 " --> pdb=" O VAL 5 136 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASP 5 141 " --> pdb=" O LEU 5 137 " (cutoff:3.500A) removed outlier: 4.555A 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 Proline residue: 5 178 - end of helix removed outlier: 3.820A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU 5 184 " --> pdb=" O ILE 5 180 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLN 5 191 " --> pdb=" O LEU 5 187 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE 5 192 " --> pdb=" O CYS 5 188 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N LEU 5 193 " --> pdb=" O LYS 5 189 " (cutoff:3.500A) removed outlier: 5.612A 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: 3.947A pdb=" N THR 5 248 " --> pdb=" O GLU 5 244 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN 5 250 " --> pdb=" O GLU 5 246 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N HIS 5 251 " --> pdb=" O ALA 5 247 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N VAL 5 252 " --> pdb=" O THR 5 248 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 304 removed outlier: 5.271A 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: 4.204A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LYS 5 413 " --> pdb=" O GLU 5 409 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 49 removed outlier: 3.868A pdb=" N LEU 6 48 " --> pdb=" O ASN 6 44 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N GLU 6 49 " --> pdb=" O LEU 6 45 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 44 through 49' Processing helix chain '6' and resid 53 through 68 removed outlier: 3.634A pdb=" N TYR 6 57 " --> pdb=" O SER 6 53 " (cutoff:3.500A) removed outlier: 3.876A 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: 3.723A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 98 through 116 removed outlier: 3.539A 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: 3.768A pdb=" N ARG 6 141 " --> pdb=" O ALA 6 137 " (cutoff:3.500A) Processing helix chain '6' and resid 144 through 156 Processing helix chain '6' and resid 194 through 199 Processing helix chain '6' and resid 244 through 249 removed outlier: 3.805A pdb=" N GLY 6 248 " --> pdb=" O ARG 6 244 " (cutoff:3.500A) removed outlier: 5.566A 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: 3.585A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 333 removed outlier: 4.110A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) Processing helix chain '6' and resid 362 through 371 removed outlier: 4.898A pdb=" N LEU 6 366 " --> pdb=" O PRO 6 362 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASP 6 367 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG 6 368 " --> pdb=" O ARG 6 364 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ASP 6 371 " --> pdb=" O ASP 6 367 " (cutoff:3.500A) Processing helix chain '6' and resid 157 through 163 removed outlier: 4.083A pdb=" N PHE 6 162 " --> pdb=" O LEU 6 157 " (cutoff:3.500A) Processing helix chain '7' and resid 36 through 60 removed outlier: 4.005A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET 7 43 " --> pdb=" O GLU 7 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG 7 44 " --> pdb=" O LEU 7 40 " (cutoff:3.500A) removed outlier: 3.508A 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: 3.543A 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: 3.566A pdb=" N VAL 7 153 " --> pdb=" O MET 7 149 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU 7 155 " --> pdb=" O GLY 7 151 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ARG 7 156 " --> pdb=" O CYS 7 152 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 removed outlier: 3.786A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 222 through 231 removed outlier: 3.632A pdb=" N GLU 7 228 " --> pdb=" O LYS 7 224 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE 7 229 " --> pdb=" O VAL 7 225 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE 7 230 " --> pdb=" O ALA 7 226 " (cutoff:3.500A) Processing helix chain '7' and resid 233 through 248 removed outlier: 3.918A pdb=" N PHE 7 239 " --> pdb=" O TYR 7 235 " (cutoff:3.500A) Proline residue: 7 248 - end of helix Processing helix chain '7' and resid 309 through 323 removed outlier: 3.729A pdb=" N LYS 7 315 " --> pdb=" O THR 7 311 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS 7 322 " --> pdb=" O GLU 7 318 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N MET 7 323 " --> pdb=" O ARG 7 319 " (cutoff:3.500A) Processing helix chain '7' and resid 271 through 276 removed outlier: 3.705A pdb=" N CYS 7 275 " --> pdb=" O THR 7 272 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N PHE 7 276 " --> pdb=" O SER 7 273 " (cutoff:3.500A) Processing helix chain '8' and resid 107 through 154 removed outlier: 3.586A 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) Processing helix chain '8' and resid 155 through 164 removed outlier: 3.567A pdb=" N GLU 8 160 " --> pdb=" O LYS 8 156 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE 8 162 " --> pdb=" O HIS 8 158 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LYS 8 163 " --> pdb=" O ALA 8 159 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N ARG 8 164 " --> pdb=" O GLU 8 160 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 35 removed outlier: 5.508A pdb=" N GLY 9 35 " --> pdb=" O ARG 9 31 " (cutoff:3.500A) Processing helix chain '9' and resid 53 through 58 removed outlier: 3.531A 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 95 Processing helix chain '9' and resid 96 through 107 Processing helix chain '9' and resid 110 through 118 removed outlier: 4.114A pdb=" N LEU 9 114 " --> pdb=" O ASP 9 110 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLU 9 115 " --> pdb=" O PRO 9 111 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N LYS 9 116 " --> pdb=" O ASP 9 112 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR 9 117 " --> pdb=" O ASN 9 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 188 removed outlier: 3.788A pdb=" N LEU D 187 " --> pdb=" O PRO D 183 " (cutoff:3.500A) Proline residue: D 188 - end of helix No H-bonds generated for 'chain 'D' and resid 183 through 188' Processing helix chain 'D' and resid 259 through 267 removed outlier: 3.945A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 264 " --> pdb=" O ALA D 260 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLY D 267 " --> pdb=" O ASN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 285 removed outlier: 4.686A pdb=" N ARG D 284 " --> pdb=" O GLY D 280 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LYS D 285 " --> pdb=" O TRP D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'D' and resid 289 through 297 removed outlier: 4.191A pdb=" N SER D 294 " --> pdb=" O PRO D 290 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N TYR D 295 " --> pdb=" O PRO D 291 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL D 296 " --> pdb=" O MET D 292 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LYS D 297 " --> pdb=" O LYS D 293 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 83 Proline residue: E 59 - end of helix removed outlier: 3.951A pdb=" N LYS E 76 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LEU E 77 " --> pdb=" O LEU E 73 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N CYS E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) Proline residue: E 79 - end of helix removed outlier: 4.731A pdb=" N GLU E 83 " --> pdb=" O PRO E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.619A pdb=" N ASN E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 158 removed outlier: 4.196A pdb=" N LYS E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ALA E 158 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 158' Processing helix chain 'E' and resid 159 through 169 removed outlier: 3.531A pdb=" N LEU E 168 " --> pdb=" O PHE E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 194 through 199 removed outlier: 4.871A pdb=" N PHE E 198 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 5.300A 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: 4.467A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ARG F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 121 removed outlier: 6.423A pdb=" N ARG F 121 " --> pdb=" O ARG F 117 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 185 Processing helix chain 'F' and resid 199 through 211 removed outlier: 3.690A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 238 removed outlier: 4.220A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N LYS F 238 " --> pdb=" O THR F 234 " (cutoff:3.500A) Processing helix chain 'F' and resid 249 through 257 removed outlier: 4.950A pdb=" N GLN F 257 " --> pdb=" O MET F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 279 removed outlier: 3.536A pdb=" N TRP F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLN F 276 " --> pdb=" O LYS F 272 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASP F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG F 279 " --> pdb=" O TRP F 275 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 removed outlier: 3.701A pdb=" N ARG H 78 " --> pdb=" O HIS H 74 " (cutoff:3.500A) removed outlier: 4.531A 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: 4.153A 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 121 removed outlier: 4.237A pdb=" N ASN H 121 " --> pdb=" O SER H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 127 Processing helix chain 'H' and resid 133 through 149 Processing helix chain 'I' and resid 41 through 52 removed outlier: 3.817A 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 93 removed outlier: 3.664A pdb=" N ASN I 93 " --> pdb=" O VAL I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 120 removed outlier: 3.626A 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: 3.878A pdb=" N SER I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing helix chain 'I' and resid 143 through 148 removed outlier: 3.852A pdb=" N PHE I 147 " --> pdb=" O LEU I 143 " (cutoff:3.500A) removed outlier: 5.053A 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: 3.548A pdb=" N ARG I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE I 167 " --> pdb=" O GLU I 163 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR I 170 " --> pdb=" O ARG I 166 " (cutoff:3.500A) removed outlier: 4.678A 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 Processing helix chain 'J' and resid 45 through 58 Processing helix chain 'J' and resid 86 through 96 removed outlier: 3.504A pdb=" N PHE J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 125 removed outlier: 3.581A 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: 3.675A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG J 149 " --> pdb=" O ILE J 145 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER J 150 " --> pdb=" O GLY J 146 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU J 151 " --> pdb=" O SER J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 192 removed outlier: 4.110A pdb=" N ALA J 166 " --> pdb=" O GLU J 162 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE J 173 " --> pdb=" O LYS J 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.583A pdb=" N MET K 111 " --> pdb=" O ALA K 107 " (cutoff:3.500A) Proline residue: K 113 - end of helix Processing helix chain 'K' and resid 115 through 126 removed outlier: 4.669A pdb=" N ARG K 119 " --> pdb=" O ASN K 115 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU K 123 " --> pdb=" O ARG K 119 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N ARG K 124 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU K 125 " --> pdb=" O MET K 121 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N HIS K 126 " --> pdb=" O MET K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 removed outlier: 3.913A pdb=" N ASN K 140 " --> pdb=" O ASP K 136 " (cutoff:3.500A) removed outlier: 4.066A 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: 4.295A 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: 5.113A pdb=" N GLU L 131 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 142 removed outlier: 5.808A pdb=" N GLN L 142 " --> pdb=" O LEU L 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 6 through 20 removed outlier: 3.696A pdb=" N LEU M 13 " --> pdb=" O GLY M 9 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU M 15 " --> pdb=" O ARG M 11 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N LEU M 16 " --> pdb=" O ALA M 12 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) removed outlier: 3.978A 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 Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.647A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 91 removed outlier: 3.546A pdb=" N ARG M 90 " --> pdb=" O GLY M 86 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ARG M 91 " --> pdb=" O HIS M 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 86 through 91' Processing helix chain 'M' and resid 97 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 144 through 149 removed outlier: 6.061A pdb=" N THR M 149 " --> pdb=" O ALA M 145 " (cutoff:3.500A) Processing helix chain 'M' and resid 160 through 171 removed outlier: 3.716A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY M 171 " --> pdb=" O ILE M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 190 removed outlier: 3.608A 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: 3.925A pdb=" N ARG M 196 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 4.325A 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 Processing helix chain 'M' and resid 225 through 241 removed outlier: 3.881A pdb=" N PHE M 229 " --> pdb=" O ASP M 225 " (cutoff:3.500A) Proline residue: M 230 - end of helix Processing helix chain 'M' and resid 246 through 251 removed outlier: 4.082A pdb=" N ASP M 250 " --> pdb=" O ASP M 246 " (cutoff:3.500A) removed outlier: 5.491A 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 Processing helix chain 'N' and resid 98 through 113 Processing helix chain 'N' and resid 168 through 184 removed outlier: 3.830A 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: 4.977A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS N 182 " --> pdb=" O GLN N 178 " (cutoff:3.500A) removed outlier: 3.539A 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: 4.770A pdb=" N VAL N 229 " --> pdb=" O GLY N 225 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N SER N 231 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 232 through 238 removed outlier: 4.509A 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: 4.119A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP O 61 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) removed outlier: 4.064A 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: 4.260A pdb=" N ILE O 86 " --> pdb=" O GLU O 82 " (cutoff:3.500A) Proline residue: O 87 - end of helix removed outlier: 3.821A pdb=" N LEU O 93 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 5.482A 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: 4.593A pdb=" N LEU P 56 " --> pdb=" O ASN P 52 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLU P 57 " --> pdb=" O PRO P 53 " (cutoff:3.500A) Processing helix chain 'P' and resid 109 through 117 removed outlier: 4.550A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU P 116 " --> pdb=" O ILE P 112 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N TYR P 117 " --> pdb=" O LYS P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 140 removed outlier: 3.524A pdb=" N GLN P 134 " --> pdb=" O ARG P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 156 through 169 Processing helix chain 'Q' and resid 77 through 82 removed outlier: 4.213A 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 107 removed outlier: 4.008A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN Q 93 " --> pdb=" O PRO Q 89 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N HIS Q 107 " --> pdb=" O ARG Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 189 through 194 removed outlier: 5.108A pdb=" N LEU Q 194 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.101A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 262 removed outlier: 3.675A pdb=" N GLN Q 258 " --> pdb=" O MET Q 254 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LYS Q 259 " --> pdb=" O LYS Q 255 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N TRP Q 260 " --> pdb=" O GLU Q 256 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N ASN Q 261 " --> pdb=" O ALA Q 257 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N GLN Q 262 " --> pdb=" O GLN Q 258 " (cutoff:3.500A) Processing helix chain 'Q' and resid 263 through 268 removed outlier: 4.172A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 292 removed outlier: 3.919A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU Q 285 " --> pdb=" O ALA Q 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 29 removed outlier: 4.531A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA R 28 " --> pdb=" O VAL R 24 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 44 removed outlier: 4.201A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 46 through 64 removed outlier: 3.976A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS R 61 " --> pdb=" O ARG R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 80 removed outlier: 3.525A pdb=" N GLU R 78 " --> pdb=" O ALA R 74 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 removed outlier: 3.568A pdb=" N LYS R 92 " --> pdb=" O GLY R 88 " (cutoff:3.500A) removed outlier: 3.610A 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: 5.089A pdb=" N ASP R 134 " --> pdb=" O ALA R 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 69 through 90 removed outlier: 4.027A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 155 removed outlier: 3.756A pdb=" N VAL S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 5.470A 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: 3.773A pdb=" N LYS T 47 " --> pdb=" O ARG T 43 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN T 49 " --> pdb=" O TRP T 45 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS T 50 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ILE T 51 " --> pdb=" O LYS T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 77 through 89 removed outlier: 3.933A pdb=" N TYR T 83 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU T 84 " --> pdb=" O LYS T 80 " (cutoff:3.500A) Processing helix chain 'T' and resid 92 through 103 removed outlier: 3.694A pdb=" N PHE T 102 " --> pdb=" O ALA T 98 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 125 removed outlier: 4.100A pdb=" N LYS T 109 " --> pdb=" O LYS T 105 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'T' and resid 185 through 200 removed outlier: 3.603A 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: 5.117A 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: 5.763A pdb=" N TYR V 55 " --> pdb=" O ASP V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 116 through 121 removed outlier: 3.609A pdb=" N VAL V 120 " --> pdb=" O LEU V 116 " (cutoff:3.500A) removed outlier: 5.139A pdb=" N LYS V 121 " --> pdb=" O HIS V 117 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 116 through 121' Processing helix chain 'V' and resid 178 through 184 removed outlier: 3.815A 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: 3.964A pdb=" N ARG W 119 " --> pdb=" O ASP W 115 " (cutoff:3.500A) removed outlier: 3.522A 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: 3.726A pdb=" N TRP X 11 " --> pdb=" O PRO X 7 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LYS X 12 " --> pdb=" O VAL X 8 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N ARG X 13 " --> pdb=" O TRP X 9 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU X 16 " --> pdb=" O LYS X 12 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 25 Proline residue: X 25 - end of helix Processing helix chain 'X' and resid 26 through 34 Processing helix chain 'X' and resid 72 through 79 removed outlier: 4.165A pdb=" N GLN X 76 " --> pdb=" O PRO X 72 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ARG X 77 " --> pdb=" O PRO X 73 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLY X 78 " --> pdb=" O GLU X 74 " (cutoff:3.500A) removed outlier: 4.972A 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: 3.547A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LYS X 192 " --> pdb=" O TYR X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.717A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) removed outlier: 4.108A 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: 3.552A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 64 through 69 removed outlier: 4.632A pdb=" N PHE Y 68 " --> pdb=" O LEU Y 64 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ASP Y 69 " --> pdb=" O GLU Y 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 64 through 69' Processing helix chain 'Y' and resid 70 through 75 removed outlier: 5.816A pdb=" N GLY Y 75 " --> pdb=" O PRO Y 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 86 through 94 removed outlier: 4.036A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS Y 93 " --> pdb=" O GLN Y 89 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N SER Y 94 " --> pdb=" O LEU Y 90 " (cutoff:3.500A) Processing helix chain 'Y' and resid 95 through 123 removed outlier: 3.893A pdb=" N TYR Y 103 " --> pdb=" O HIS Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 158 removed outlier: 4.282A pdb=" N LEU Y 132 " --> pdb=" O SER Y 128 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 192 removed outlier: 5.889A pdb=" N LYS Y 192 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 193 through 198 removed outlier: 3.857A pdb=" N LYS Y 197 " --> pdb=" O ARG Y 193 " (cutoff:3.500A) removed outlier: 5.473A 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: 4.359A pdb=" N ASP Y 206 " --> pdb=" O LEU Y 202 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS Y 236 " --> pdb=" O LYS Y 232 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS Y 237 " --> pdb=" O ILE Y 233 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N PHE Y 238 " --> pdb=" O LEU Y 234 " (cutoff:3.500A) Proline residue: Y 239 - end of helix Processing helix chain 'Z' and resid 42 through 47 removed outlier: 4.236A pdb=" N PHE Z 46 " --> pdb=" O PRO Z 42 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N GLN Z 47 " --> pdb=" O GLU Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 47' Processing helix chain 'Z' and resid 49 through 57 removed outlier: 3.580A pdb=" N HIS Z 53 " --> pdb=" O SER Z 49 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) removed outlier: 3.914A 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: 3.503A pdb=" N LYS Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL Z 112 " --> pdb=" O ALA Z 108 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL Z 113 " --> pdb=" O LYS Z 109 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 135 removed outlier: 5.530A pdb=" N SER Z 135 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 117 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.629A pdb=" N TRP a 123 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.875A 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: 4.778A pdb=" N GLY b 20 " --> pdb=" O HIS b 16 " (cutoff:3.500A) removed outlier: 6.768A 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: 3.916A pdb=" N ARG b 41 " --> pdb=" O GLY b 37 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N GLY b 42 " --> pdb=" O ALA b 38 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA b 43 " --> pdb=" O SER b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 51 through 59 removed outlier: 3.656A pdb=" N ARG b 56 " --> pdb=" O ILE b 52 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG b 57 " --> pdb=" O ASP b 53 " (cutoff:3.500A) Proline residue: b 59 - end of helix Processing helix chain 'b' and resid 93 through 108 removed outlier: 5.990A pdb=" N SER b 108 " --> pdb=" O LEU b 104 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 137 removed outlier: 4.720A pdb=" N ASN b 135 " --> pdb=" O HIS b 131 " (cutoff:3.500A) removed outlier: 4.586A 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: 4.447A 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: 3.516A 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: 3.526A pdb=" N PHE c 75 " --> pdb=" O GLU c 71 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLY c 76 " --> pdb=" O ILE c 72 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS c 77 " --> pdb=" O GLN c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 94 removed outlier: 3.593A pdb=" N THR c 90 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N ASN c 94 " --> pdb=" O THR c 90 " (cutoff:3.500A) Processing helix chain 'c' and resid 95 through 109 removed outlier: 3.565A 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: 3.740A pdb=" N ASN c 172 " --> pdb=" O HIS c 168 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU c 173 " --> pdb=" O VAL c 169 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA c 174 " --> pdb=" O ALA c 170 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 removed outlier: 3.527A pdb=" N ILE c 199 " --> pdb=" O PHE c 195 " (cutoff:3.500A) Processing helix chain 'c' and resid 207 through 224 removed outlier: 3.649A pdb=" N LEU c 213 " --> pdb=" O GLU c 209 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE c 214 " --> pdb=" O ARG c 210 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE c 220 " --> pdb=" O ARG c 216 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N THR c 221 " --> pdb=" O ASP c 217 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N GLN c 222 " --> pdb=" O PHE c 218 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N MET c 223 " --> pdb=" O LEU c 219 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N THR c 224 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 233 removed outlier: 3.793A pdb=" N MET c 231 " --> pdb=" O GLU c 227 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N LYS c 233 " --> pdb=" O PHE c 229 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.573A pdb=" N GLU c 243 " --> pdb=" O GLY c 239 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 48 through 54 removed outlier: 4.724A pdb=" N THR d 52 " --> pdb=" O PRO d 48 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS d 54 " --> pdb=" O PHE d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 removed outlier: 3.570A pdb=" N ILE d 97 " --> pdb=" O GLY d 93 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER d 99 " --> pdb=" O ALA d 95 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N SER d 101 " --> pdb=" O ILE d 97 " (cutoff:3.500A) Processing helix chain 'd' and resid 102 through 115 removed outlier: 3.703A pdb=" N ILE d 106 " --> pdb=" O LYS d 102 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR d 109 " --> pdb=" O LEU d 105 " (cutoff:3.500A) Processing helix chain 'd' and resid 116 through 130 removed outlier: 3.693A pdb=" N ILE d 122 " --> pdb=" O SER d 118 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ARG d 123 " --> pdb=" O GLN d 119 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR d 128 " --> pdb=" O ARG d 124 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA d 130 " --> pdb=" O LYS d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 134 through 155 Proline residue: d 138 - end of helix removed outlier: 3.945A pdb=" N ASP d 143 " --> pdb=" O GLU d 139 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU d 152 " --> pdb=" O ALA d 148 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN d 153 " --> pdb=" O HIS d 149 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ASN d 154 " --> pdb=" O LEU d 150 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 3.607A pdb=" N HIS d 161 " --> pdb=" O HIS d 157 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) removed outlier: 3.618A 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: 5.129A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) removed outlier: 4.370A 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: 3.561A pdb=" N MET e 123 " --> pdb=" O ASP e 119 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N LYS e 132 " --> pdb=" O PHE e 128 " (cutoff:3.500A) Processing helix chain 'e' and resid 138 through 144 removed outlier: 3.562A pdb=" N GLU e 142 " --> pdb=" O THR e 138 " (cutoff:3.500A) Processing helix chain 'e' and resid 183 through 195 removed outlier: 3.828A pdb=" N ALA e 188 " --> pdb=" O LEU e 184 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU e 192 " --> pdb=" O ALA e 188 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ALA e 193 " --> pdb=" O GLU e 189 " (cutoff:3.500A) Processing helix chain 'e' and resid 256 through 264 removed outlier: 4.381A pdb=" N GLY e 261 " --> pdb=" O LYS e 257 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ASP e 262 " --> pdb=" O ASP e 258 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N TYR e 263 " --> pdb=" O GLU e 259 " (cutoff:3.500A) Processing helix chain 'e' and resid 266 through 277 removed outlier: 3.849A pdb=" N GLN e 271 " --> pdb=" O LYS e 267 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ARG e 274 " --> pdb=" O ALA e 270 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE e 275 " --> pdb=" O GLN e 271 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N SER e 277 " --> pdb=" O ARG e 273 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 64 removed outlier: 3.548A pdb=" N ILE f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 99 through 118 removed outlier: 3.576A pdb=" N ALA f 103 " --> pdb=" O ASP f 99 " (cutoff:3.500A) Processing helix chain 'f' and resid 164 through 178 removed outlier: 3.815A pdb=" N GLU f 168 " --> pdb=" O ALA f 164 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE f 169 " --> pdb=" O THR f 165 " (cutoff:3.500A) Processing helix chain 'f' and resid 200 through 212 Processing helix chain 'g' and resid 44 through 52 removed outlier: 4.226A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 132 removed outlier: 3.667A 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: 3.675A 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: 4.610A pdb=" N HIS h 118 " --> pdb=" O ASN h 114 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLN h 119 " --> pdb=" O SER h 115 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N MET h 120 " --> pdb=" O ARG h 116 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N CYS h 121 " --> pdb=" O LEU h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.942A pdb=" N VAL h 132 " --> pdb=" O ASP h 128 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 147 removed outlier: 5.369A 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 75 removed outlier: 3.737A pdb=" N LEU i 73 " --> pdb=" O HIS i 69 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE i 74 " --> pdb=" O PRO i 70 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG i 75 " --> pdb=" O LYS i 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 69 through 75' 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 removed outlier: 3.546A pdb=" N GLY j 32 " --> pdb=" O ARG j 28 " (cutoff:3.500A) Processing helix chain 'j' and resid 36 through 41 removed outlier: 4.507A pdb=" N TYR j 40 " --> pdb=" O ASN j 36 " (cutoff:3.500A) removed outlier: 5.446A 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 109 removed outlier: 3.723A pdb=" N GLN j 102 " --> pdb=" O LEU j 98 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG j 103 " --> pdb=" O GLN j 99 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLN j 105 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU j 106 " --> pdb=" O GLN j 102 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASN j 107 " --> pdb=" O ARG j 103 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALA j 108 " --> pdb=" O LYS j 104 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU j 109 " --> pdb=" O GLN j 105 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 9 removed outlier: 3.557A pdb=" N ARG k 7 " --> pdb=" O ALA k 3 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU k 8 " --> pdb=" O ALA k 4 " (cutoff:3.500A) Processing helix chain 'k' and resid 27 through 39 removed outlier: 3.713A pdb=" N SER k 39 " --> pdb=" O GLN k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 40 through 47 removed outlier: 3.647A pdb=" N THR k 45 " --> pdb=" O LYS k 41 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASN k 46 " --> pdb=" O VAL k 42 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU k 47 " --> pdb=" O ARG k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 102 removed outlier: 3.504A pdb=" N ARG k 95 " --> pdb=" O ALA k 91 " (cutoff:3.500A) Processing helix chain 'l' and resid 64 through 71 Processing helix chain 'l' and resid 88 through 93 removed outlier: 3.829A 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: 4.519A pdb=" N GLU l 98 " --> pdb=" O GLU l 94 " (cutoff:3.500A) removed outlier: 4.427A 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: 5.441A pdb=" N ASP l 111 " --> pdb=" O LEU l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 136 removed outlier: 3.714A pdb=" N TRP l 118 " --> pdb=" O SER l 114 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN l 135 " --> pdb=" O ARG l 131 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N LYS l 136 " --> pdb=" O LEU l 132 " (cutoff:3.500A) Processing helix chain 'm' and resid 34 through 39 removed outlier: 4.906A pdb=" N ALA m 38 " --> pdb=" O ASP m 34 " (cutoff:3.500A) removed outlier: 4.021A 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: 3.549A pdb=" N LYS o 32 " --> pdb=" O SER o 28 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR o 47 " --> pdb=" O ALA o 43 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N SER o 50 " --> pdb=" O HIS o 46 " (cutoff:3.500A) removed outlier: 4.352A 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: 3.584A pdb=" N ILE o 74 " --> pdb=" O ALA o 70 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS o 81 " --> pdb=" O ALA o 77 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 100 removed outlier: 3.778A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N ASN o 96 " --> pdb=" O LEU o 92 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N VAL o 97 " --> pdb=" O ASP o 93 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N THR o 98 " --> pdb=" O HIS o 94 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS o 99 " --> pdb=" O LEU o 95 " (cutoff:3.500A) removed outlier: 5.899A 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: 4.102A pdb=" N LEU p 77 " --> pdb=" O PRO p 73 " (cutoff:3.500A) removed outlier: 5.293A 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 Processing helix chain 'p' and resid 142 through 164 removed outlier: 3.595A pdb=" N THR p 164 " --> pdb=" O GLU p 160 " (cutoff:3.500A) Processing helix chain 'p' and resid 173 through 190 removed outlier: 4.326A pdb=" N ARG p 177 " --> pdb=" O VAL p 173 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE p 178 " --> pdb=" O LYS p 174 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE p 180 " --> pdb=" O HIS p 176 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG p 189 " --> pdb=" O ARG p 185 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N GLN p 190 " --> pdb=" O GLU p 186 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 3.625A pdb=" N THR p 57 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ALA p 58 " --> pdb=" O SER p 55 " (cutoff:3.500A) removed outlier: 5.449A 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: 4.226A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 4.063A 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: 4.524A pdb=" N LEU q 75 " --> pdb=" O VAL q 71 " (cutoff:3.500A) removed outlier: 4.659A 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: 3.587A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 163 removed outlier: 3.571A pdb=" N LYS q 127 " --> pdb=" O GLU q 123 " (cutoff:3.500A) Proline residue: q 129 - end of helix removed outlier: 3.509A pdb=" N ALA q 160 " --> pdb=" O LEU q 156 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLN q 161 " --> pdb=" O GLN q 157 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 76 removed outlier: 3.596A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.984A 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: 3.787A pdb=" N ILE r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 5.915A 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: 3.533A pdb=" N LYS r 114 " --> pdb=" O GLU r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 183 removed outlier: 4.181A pdb=" N ARG r 182 " --> pdb=" O SER r 178 " (cutoff:3.500A) removed outlier: 5.325A 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 73 removed outlier: 3.578A pdb=" N THR s 69 " --> pdb=" O ARG s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.907A pdb=" N TYR s 108 " --> pdb=" O ARG s 104 " (cutoff:3.500A) Processing helix chain 's' and resid 138 through 155 removed outlier: 3.776A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N HIS s 154 " --> pdb=" O LEU s 150 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 169 removed outlier: 4.819A pdb=" N SER s 169 " --> pdb=" O ARG s 165 " (cutoff:3.500A) Processing helix chain 's' and resid 171 through 193 Proline residue: s 175 - end of helix removed outlier: 3.697A pdb=" N GLY s 186 " --> pdb=" O SER s 182 " (cutoff:3.500A) Proline residue: s 190 - end of helix Proline residue: s 193 - end of helix Processing helix chain 's' and resid 267 through 272 removed outlier: 4.802A 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: 3.544A pdb=" N ARG s 313 " --> pdb=" O GLU s 309 " (cutoff:3.500A) Processing helix chain 's' and resid 317 through 344 removed outlier: 4.860A pdb=" N GLU s 321 " --> pdb=" O ALA s 317 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY s 344 " --> pdb=" O ALA s 340 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 387 removed outlier: 5.299A pdb=" N ASN s 386 " --> pdb=" O GLN s 382 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN s 387 " --> pdb=" O ALA s 383 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.668A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'u' and resid 107 through 114 removed outlier: 3.552A pdb=" N ASP u 108 " --> pdb=" O SER u 128 " (cutoff:3.500A) removed outlier: 4.866A pdb=" N ASP u 122 " --> pdb=" O VAL u 114 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL u 176 " --> pdb=" O TYR u 123 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY u 129 " --> pdb=" O MET u 180 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'x' and resid 130 through 133 removed outlier: 5.274A pdb=" N ARG x 130 " --> pdb=" O VAL x 77 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU x 154 " --> pdb=" O ASN x 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'x' and resid 230 through 236 removed outlier: 3.817A pdb=" N TRP x 236 " --> pdb=" O ASP x 204 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG x 251 " --> pdb=" O ILE x 176 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASP x 255 " --> pdb=" O LEU x 180 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N ASP x 250 " --> pdb=" O GLY x 302 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY x 303 " --> pdb=" O ARG x 382 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N SER x 311 " --> pdb=" O PRO x 374 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N LYS x 379 " --> pdb=" O GLU x 339 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'x' and resid 361 through 365 Processing sheet with id= 5, first strand: chain '0' and resid 107 through 111 removed outlier: 4.468A pdb=" N HIS 0 115 " --> pdb=" O CYS 0 110 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain '0' and resid 155 through 161 Processing sheet with id= 7, first strand: chain '1' and resid 16 through 22 removed outlier: 5.915A pdb=" N PHE 1 28 " --> pdb=" O SER 1 22 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain '1' and resid 41 through 46 removed outlier: 6.358A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 58 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain '4' and resid 66 through 70 removed outlier: 3.539A pdb=" N LYS 4 67 " --> pdb=" O LYS 4 99 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N HIS 4 98 " --> pdb=" O CYS 4 92 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N CYS 4 92 " --> pdb=" O HIS 4 98 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N TRP 4 88 " --> pdb=" O GLN 4 102 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain '5' and resid 126 through 130 removed outlier: 5.234A pdb=" N VAL 5 351 " --> pdb=" O ASP 5 348 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N ARG 5 200 " --> pdb=" O LYS 5 233 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain '5' and resid 208 through 214 removed outlier: 4.528A pdb=" N LEU 5 219 " --> pdb=" O ALA 5 103 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain '6' and resid 183 through 187 removed outlier: 3.677A pdb=" N ASP 6 183 " --> pdb=" O VAL 6 179 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain '6' and resid 231 through 234 removed outlier: 6.636A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '6' and resid 311 through 314 removed outlier: 6.657A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '6' and resid 213 through 220 removed outlier: 3.962A pdb=" N LEU 6 213 " --> pdb=" O GLN 6 275 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain '7' and resid 64 through 69 removed outlier: 4.423A pdb=" N THR 7 77 " --> pdb=" O HIS 7 69 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain '7' and resid 104 through 107 Processing sheet with id= 18, first strand: chain '7' and resid 178 through 184 removed outlier: 7.081A pdb=" N GLN 7 298 " --> pdb=" O SER 7 281 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain '7' and resid 216 through 221 Processing sheet with id= 20, first strand: chain '7' and resid 282 through 286 removed outlier: 3.828A pdb=" N ALA 7 282 " --> pdb=" O GLN 7 298 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE 7 294 " --> pdb=" O LEU 7 286 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain '9' and resid 42 through 45 removed outlier: 3.662A pdb=" N ARG 9 49 " --> pdb=" O THR 9 45 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'D' and resid 128 through 131 removed outlier: 6.591A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N ASP D 161 " --> pdb=" O VAL D 126 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'D' and resid 214 through 217 removed outlier: 6.649A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'D' and resid 139 through 144 Processing sheet with id= 25, first strand: chain 'E' and resid 98 through 101 Processing sheet with id= 26, first strand: chain 'E' and resid 105 through 111 removed outlier: 3.862A pdb=" N GLY E 105 " --> pdb=" O LEU E 121 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N GLN E 115 " --> pdb=" O THR E 111 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N ASN E 281 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLU E 330 " --> pdb=" O THR E 278 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'E' and resid 126 through 129 removed outlier: 7.115A pdb=" N ASP E 126 " --> pdb=" O LYS E 150 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR E 144 " --> pdb=" O THR E 133 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS E 131 " --> pdb=" O SER E 146 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'E' and resid 142 through 149 removed outlier: 3.678A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'F' and resid 46 through 50 Processing sheet with id= 30, first strand: chain 'F' and resid 186 through 189 Processing sheet with id= 31, first strand: chain 'H' and resid 55 through 58 removed outlier: 7.088A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'H' and resid 94 through 97 Processing sheet with id= 33, first strand: chain 'I' and resid 121 through 125 removed outlier: 5.690A pdb=" N HIS I 150 " --> pdb=" O ASN I 101 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N MET I 95 " --> pdb=" O SER I 156 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLY I 178 " --> pdb=" O VAL I 98 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'J' and resid 18 through 24 Processing sheet with id= 35, first strand: chain 'K' and resid 55 through 60 removed outlier: 3.531A pdb=" N GLU K 143 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ASP K 22 " --> pdb=" O LEU K 145 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 38 through 41 removed outlier: 7.948A pdb=" N LEU L 107 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS L 83 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASP L 71 " --> pdb=" O ILE L 86 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N LEU L 74 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG L 56 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'L' and resid 87 through 90 removed outlier: 3.634A pdb=" N GLY L 88 " --> pdb=" O ASN L 104 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N CYS L 90 " --> pdb=" O SER L 102 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N SER L 102 " --> pdb=" O CYS L 90 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 93 through 96 Processing sheet with id= 39, first strand: chain 'M' and resid 273 through 277 Processing sheet with id= 40, first strand: chain 'N' and resid 93 through 96 removed outlier: 3.605A pdb=" N HIS N 149 " --> pdb=" O ILE N 131 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 118 through 123 removed outlier: 5.590A pdb=" N VAL N 160 " --> pdb=" O ARG N 123 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA N 186 " --> pdb=" O LEU N 92 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.325A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N TYR O 104 " --> pdb=" O LYS O 126 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'P' and resid 80 through 85 removed outlier: 6.521A pdb=" N VAL P 90 " --> pdb=" O THR P 107 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'Q' and resid 130 through 136 removed outlier: 6.413A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Q' and resid 139 through 143 removed outlier: 4.063A pdb=" N GLN Q 139 " --> pdb=" O ILE Q 150 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ARG Q 143 " --> pdb=" O GLY Q 146 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'S' and resid 105 through 109 removed outlier: 7.064A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N PHE S 141 " --> pdb=" O ALA S 138 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'S' and resid 111 through 117 removed outlier: 4.033A pdb=" N ASP S 112 " --> pdb=" O ILE S 195 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLU S 126 " --> pdb=" O VAL S 160 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'S' and resid 162 through 165 removed outlier: 3.754A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'S' and resid 168 through 175 removed outlier: 3.957A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'T' and resid 65 through 72 removed outlier: 4.655A pdb=" N ALA T 65 " --> pdb=" O GLU T 174 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N LYS T 171 " --> pdb=" O ALA T 137 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 138 through 144 removed outlier: 4.920A pdb=" N TYR T 165 " --> pdb=" O GLY T 144 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 146 through 153 No H-bonds generated for sheet with id= 52 Processing sheet with id= 53, first strand: chain 'U' and resid 26 through 29 removed outlier: 4.710A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ASP U 38 " --> pdb=" O LEU U 99 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) removed outlier: 5.538A pdb=" N LYS U 88 " --> pdb=" O ASN U 77 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ASN U 77 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N GLY U 75 " --> pdb=" O PRO U 90 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA U 67 " --> pdb=" O GLN U 98 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'V' and resid 60 through 65 removed outlier: 4.303A pdb=" N ASP V 60 " --> pdb=" O VAL V 76 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL V 76 " --> pdb=" O ASP V 60 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS V 72 " --> pdb=" O ILE V 64 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'V' and resid 78 through 81 removed outlier: 4.006A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'V' and resid 92 through 97 removed outlier: 6.096A pdb=" N ASN V 92 " --> pdb=" O ALA V 113 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'W' and resid 67 through 70 removed outlier: 3.807A pdb=" N GLN W 70 " --> pdb=" O LYS W 87 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N LYS W 87 " --> pdb=" O GLN W 70 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N CYS W 88 " --> pdb=" O GLY W 84 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 97 through 103 Processing sheet with id= 59, first strand: chain 'X' and resid 49 through 53 removed outlier: 5.366A pdb=" N LYS X 49 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN X 58 " --> pdb=" O ASN X 53 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'X' and resid 85 through 92 removed outlier: 5.498A pdb=" N LYS X 99 " --> pdb=" O ALA X 92 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'Y' and resid 165 through 170 Processing sheet with id= 62, first strand: chain 'Z' and resid 97 through 101 removed outlier: 5.402A pdb=" N LEU Z 66 " --> pdb=" O LEU Z 122 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU Z 116 " --> pdb=" O ILE Z 72 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'a' and resid 45 through 52 removed outlier: 6.305A pdb=" N THR a 57 " --> pdb=" O THR a 52 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'b' and resid 61 through 68 removed outlier: 3.887A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N SER b 88 " --> pdb=" O PRO b 73 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL b 75 " --> pdb=" O GLU b 86 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU b 86 " --> pdb=" O VAL b 75 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA b 77 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL b 84 " --> pdb=" O ALA b 77 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N TYR b 79 " --> pdb=" O GLY b 82 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'c' and resid 254 through 257 Processing sheet with id= 66, first strand: chain 'c' and resid 269 through 274 removed outlier: 3.998A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'd' and resid 212 through 219 removed outlier: 6.714A pdb=" N TYR d 245 " --> pdb=" O LYS d 264 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS d 264 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'e' and resid 174 through 178 removed outlier: 6.131A pdb=" N LEU e 47 " --> pdb=" O TRP e 178 " (cutoff:3.500A) removed outlier: 10.547A pdb=" N LEU e 51 " --> pdb=" O VAL e 161 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N VAL e 161 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.732A pdb=" N LEU e 53 " --> pdb=" O LEU e 159 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ARG e 155 " --> pdb=" O PRO e 57 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'e' and resid 211 through 216 removed outlier: 3.695A pdb=" N GLY e 211 " --> pdb=" O PHE e 233 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'f' and resid 144 through 147 removed outlier: 7.145A pdb=" N VAL f 134 " --> pdb=" O ASP f 147 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N THR f 129 " --> pdb=" O THR f 152 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR f 152 " --> pdb=" O THR f 129 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'g' and resid 95 through 101 removed outlier: 5.440A pdb=" N VAL g 137 " --> pdb=" O LYS g 150 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'k' and resid 49 through 54 removed outlier: 4.134A pdb=" N PHE k 20 " --> pdb=" O ASP k 54 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'm' and resid 62 through 66 removed outlier: 4.631A pdb=" N SER m 62 " --> pdb=" O LYS m 58 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'p' and resid 79 through 83 Processing sheet with id= 75, first strand: chain 'r' and resid 35 through 42 removed outlier: 3.579A pdb=" N PHE r 35 " --> pdb=" O THR r 54 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 's' and resid 90 through 93 removed outlier: 4.157A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP s 227 " --> pdb=" O GLU s 214 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N GLU s 214 " --> pdb=" O ASP s 227 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS s 204 " --> pdb=" O PRO s 237 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 's' and resid 112 through 116 removed outlier: 6.611A pdb=" N ASN s 391 " --> pdb=" O ASN s 375 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N ASN s 375 " --> pdb=" O ASN s 391 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N CYS s 393 " --> pdb=" O GLN s 373 " (cutoff:3.500A) removed outlier: 7.197A pdb=" N GLN s 373 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N GLY s 395 " --> pdb=" O CYS s 371 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N CYS s 371 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N GLN s 397 " --> pdb=" O PHE s 369 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N PHE s 369 " --> pdb=" O GLN s 397 " (cutoff:3.500A) removed outlier: 8.637A pdb=" N LYS s 365 " --> pdb=" O LEU s 401 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N TYR s 366 " --> pdb=" O ASP s 363 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 's' and resid 198 through 202 2818 hydrogen bonds defined for protein. 8352 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 794 hydrogen bonds 1360 hydrogen bond angles 0 basepair planarities 332 basepair parallelities 834 stacking parallelities Total time for adding SS restraints: 73.04 Time building geometry restraints manager: 38.80 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: 44873 1.41 - 1.61: 66485 1.61 - 1.80: 1479 1.80 - 2.00: 102 2.00 - 2.20: 4 Bond restraints: 112943 Sorted by residual: bond pdb=" C34 PM8 w 200 " pdb=" N36 PM8 w 200 " ideal model delta sigma weight residual 1.451 1.326 0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" C39 PM8 w 200 " pdb=" N41 PM8 w 200 " ideal model delta sigma weight residual 1.452 1.337 0.115 2.00e-02 2.50e+03 3.29e+01 bond pdb=" C28 PM8 w 200 " pdb=" O27 PM8 w 200 " ideal model delta sigma weight residual 1.399 1.459 -0.060 2.00e-02 2.50e+03 9.06e+00 bond pdb=" C1 PM8 w 200 " pdb=" S1 PM8 w 200 " ideal model delta sigma weight residual 1.817 1.761 0.056 2.00e-02 2.50e+03 7.77e+00 bond pdb=" O23 PM8 w 200 " pdb=" P24 PM8 w 200 " ideal model delta sigma weight residual 1.510 1.563 -0.053 2.00e-02 2.50e+03 7.00e+00 ... (remaining 112938 not shown) Histogram of bond angle deviations from ideal: 74.82 - 86.65: 2 86.65 - 98.49: 0 98.49 - 110.33: 39516 110.33 - 122.17: 98757 122.17 - 134.00: 21658 Bond angle restraints: 159933 Sorted by residual: angle pdb=" C LYS M 54 " pdb=" CA LYS M 54 " pdb=" CB LYS M 54 " ideal model delta sigma weight residual 115.79 109.80 5.99 1.19e+00 7.06e-01 2.53e+01 angle pdb=" C ASP s 407 " pdb=" CA ASP s 407 " pdb=" CB ASP s 407 " ideal model delta sigma weight residual 117.23 110.69 6.54 1.36e+00 5.41e-01 2.31e+01 angle pdb=" N VAL I 130 " pdb=" CA VAL I 130 " pdb=" C VAL I 130 " ideal model delta sigma weight residual 112.96 108.65 4.31 1.00e+00 1.00e+00 1.86e+01 angle pdb=" N VAL P 61 " pdb=" CA VAL P 61 " pdb=" C VAL P 61 " ideal model delta sigma weight residual 113.47 109.53 3.94 1.01e+00 9.80e-01 1.52e+01 angle pdb=" N ILE 7 85 " pdb=" CA ILE 7 85 " pdb=" C ILE 7 85 " ideal model delta sigma weight residual 111.62 108.70 2.92 7.90e-01 1.60e+00 1.37e+01 ... (remaining 159928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 64488 35.92 - 71.84: 850 71.84 - 107.76: 68 107.76 - 143.69: 5 143.69 - 179.61: 21 Dihedral angle restraints: 65432 sinusoidal: 38483 harmonic: 26949 Sorted by residual: dihedral pdb=" O4' U A3071 " pdb=" C1' U A3071 " pdb=" N1 U A3071 " pdb=" C2 U A3071 " ideal model delta sinusoidal sigma weight residual 200.00 20.63 179.37 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U A2898 " pdb=" C1' U A2898 " pdb=" N1 U A2898 " pdb=" C2 U A2898 " ideal model delta sinusoidal sigma weight residual 200.00 21.71 178.29 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 31.97 168.03 1 1.50e+01 4.44e-03 8.44e+01 ... (remaining 65429 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 15545 0.037 - 0.074: 2162 0.074 - 0.111: 765 0.111 - 0.148: 128 0.148 - 0.185: 2 Chirality restraints: 18602 Sorted by residual: chirality pdb=" C3' U A2030 " pdb=" C4' U A2030 " pdb=" O3' U A2030 " pdb=" C2' U A2030 " both_signs ideal model delta sigma weight residual False -2.74 -2.56 -0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" C1' U A2499 " pdb=" O4' U A2499 " pdb=" C2' U A2499 " pdb=" N1 U A2499 " both_signs ideal model delta sigma weight residual False 2.47 2.29 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" C32 PM8 w 200 " pdb=" C29 PM8 w 200 " pdb=" C34 PM8 w 200 " pdb=" O33 PM8 w 200 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.06e-01 ... (remaining 18599 not shown) Planarity restraints: 15032 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' N A3241 " 0.409 2.00e-02 2.50e+03 4.22e-01 3.56e+03 pdb=" C2' N A3241 " 0.431 2.00e-02 2.50e+03 pdb=" C3' N A3241 " 0.502 2.00e-02 2.50e+03 pdb=" C4' N A3241 " -0.385 2.00e-02 2.50e+03 pdb=" C5' N A3241 " -0.103 2.00e-02 2.50e+03 pdb=" O2' N A3241 " -0.795 2.00e-02 2.50e+03 pdb=" O3' N A3241 " 0.087 2.00e-02 2.50e+03 pdb=" O4' N A3241 " -0.146 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N A3243 " 0.397 2.00e-02 2.50e+03 4.21e-01 3.55e+03 pdb=" C2' N A3243 " 0.425 2.00e-02 2.50e+03 pdb=" C3' N A3243 " 0.507 2.00e-02 2.50e+03 pdb=" C4' N A3243 " -0.378 2.00e-02 2.50e+03 pdb=" C5' N A3243 " -0.116 2.00e-02 2.50e+03 pdb=" O2' N A3243 " -0.800 2.00e-02 2.50e+03 pdb=" O3' N A3243 " 0.094 2.00e-02 2.50e+03 pdb=" O4' N A3243 " -0.131 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' N A3242 " 0.396 2.00e-02 2.50e+03 4.20e-01 3.54e+03 pdb=" C2' N A3242 " 0.428 2.00e-02 2.50e+03 pdb=" C3' N A3242 " 0.505 2.00e-02 2.50e+03 pdb=" C4' N A3242 " -0.378 2.00e-02 2.50e+03 pdb=" C5' N A3242 " -0.114 2.00e-02 2.50e+03 pdb=" O2' N A3242 " -0.798 2.00e-02 2.50e+03 pdb=" O3' N A3242 " 0.093 2.00e-02 2.50e+03 pdb=" O4' N A3242 " -0.130 2.00e-02 2.50e+03 ... (remaining 15029 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.60: 1271 2.60 - 3.23: 97369 3.23 - 3.87: 226303 3.87 - 4.50: 318462 4.50 - 5.14: 457472 Nonbonded interactions: 1100877 Sorted by model distance: nonbonded pdb=" OP2 U A2037 " pdb="MG MG A3344 " model vdw 1.963 2.170 nonbonded pdb=" O4 U A2475 " pdb="MG MG A3332 " model vdw 1.976 2.170 nonbonded pdb=" OP1 A A2509 " pdb="MG MG A3333 " model vdw 1.984 2.170 nonbonded pdb=" OP2 C A2474 " pdb="MG MG A3332 " model vdw 2.010 2.170 nonbonded pdb=" OP1 A A2503 " pdb="MG MG A3309 " model vdw 2.014 2.170 ... (remaining 1100872 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians K 2 8.98 5 Fe 2 7.16 5 Zn 2 6.06 5 P 1521 5.49 5 Mg 97 5.21 5 S 329 5.16 5 C 62347 2.51 5 N 19392 2.21 5 O 23772 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.100 Extract box with map and model: 26.500 Check model and map are aligned: 1.230 Convert atoms to be neutral: 0.720 Process input model: 323.900 Find NCS groups from input model: 3.310 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:11.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 371.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.002 0.125 112943 Z= 0.131 Angle : 0.405 8.875 159933 Z= 0.225 Chirality : 0.031 0.185 18602 Planarity : 0.019 0.422 15032 Dihedral : 11.097 179.607 47984 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.10 % Favored : 98.89 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.96 (0.09), residues: 9112 helix: 0.89 (0.09), residues: 3090 sheet: 0.35 (0.15), residues: 1233 loop : 0.73 (0.09), residues: 4789 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1833 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1797 time to evaluate : 7.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 9 residues processed: 1824 average time/residue: 1.8703 time to fit residues: 4662.9053 Evaluate side-chains 905 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 896 time to evaluate : 7.748 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 8 residues processed: 2 average time/residue: 0.7939 time to fit residues: 12.8281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 890 optimal weight: 10.0000 chunk 798 optimal weight: 5.9990 chunk 443 optimal weight: 0.9980 chunk 272 optimal weight: 7.9990 chunk 538 optimal weight: 6.9990 chunk 426 optimal weight: 8.9990 chunk 826 optimal weight: 8.9990 chunk 319 optimal weight: 8.9990 chunk 502 optimal weight: 10.0000 chunk 614 optimal weight: 6.9990 chunk 957 optimal weight: 9.9990 overall best weight: 5.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 19 GLN v 63 ASN ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 172 GLN x 230 GLN ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 122 GLN y 123 GLN y 192 GLN y 195 ASN y 235 GLN y 255 GLN y 284 GLN 1 31 ASN 3 185 ASN 5 165 GLN 5 191 GLN 5 266 HIS ** 6 275 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 320 GLN 6 359 HIS 7 84 ASN 7 232 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 290 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN D 249 ASN F 63 GLN F 103 GLN F 105 ASN F 228 GLN H 148 GLN ** I 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN L 52 HIS L 142 GLN M 170 ASN N 98 HIS N 117 ASN N 209 ASN N 237 HIS O 27 HIS O 69 ASN ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 147 GLN O 158 GLN P 55 ASN P 79 HIS P 87 GLN P 142 ASN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 77 GLN S 91 GLN S 118 ASN T 103 ASN T 195 GLN U 4 ASN U 27 GLN U 74 HIS V 195 GLN X 53 ASN X 236 GLN Y 99 HIS Y 179 HIS Z 64 HIS Z 148 GLN a 111 GLN c 65 ASN c 236 ASN c 310 ASN ** d 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 212 HIS ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN k 15 GLN l 82 GLN l 124 GLN l 129 HIS m 65 HIS p 123 HIS p 146 ASN q 107 GLN q 137 GLN q 147 GLN r 96 HIS r 146 GLN s 239 ASN s 240 GLN s 343 GLN s 358 GLN Total number of N/Q/H flips: 81 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.134 112943 Z= 0.466 Angle : 0.796 14.645 159933 Z= 0.438 Chirality : 0.045 0.328 18602 Planarity : 0.008 0.120 15032 Dihedral : 12.963 177.299 28436 Min Nonbonded Distance : 1.778 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.00 % Favored : 97.99 % Rotamer Outliers : 4.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.66 (0.08), residues: 9112 helix: 0.86 (0.09), residues: 3176 sheet: 0.05 (0.14), residues: 1216 loop : 0.41 (0.09), residues: 4720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 335 poor density : 954 time to evaluate : 7.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 335 outliers final: 131 residues processed: 1191 average time/residue: 1.7487 time to fit residues: 2929.0069 Evaluate side-chains 954 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 823 time to evaluate : 7.759 Switching outliers to nearest non-outliers outliers start: 131 outliers final: 97 residues processed: 36 average time/residue: 0.9951 time to fit residues: 70.7672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 531 optimal weight: 0.0670 chunk 297 optimal weight: 5.9990 chunk 796 optimal weight: 0.9990 chunk 651 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 chunk 958 optimal weight: 40.0000 chunk 1035 optimal weight: 0.5980 chunk 853 optimal weight: 20.0000 chunk 950 optimal weight: 9.9990 chunk 326 optimal weight: 7.9990 chunk 769 optimal weight: 0.9990 overall best weight: 1.5324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 322 GLN 5 353 HIS 6 243 ASN 6 249 GLN 6 275 GLN 7 232 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN E 281 ASN F 98 GLN ** I 36 HIS ** 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 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN K 74 GLN N 98 HIS N 117 ASN O 69 ASN ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 55 ASN P 134 GLN ** Q 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 4 ASN V 92 ASN X 53 ASN X 236 GLN Y 157 GLN Z 62 ASN d 217 HIS ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 GLN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN o 94 HIS p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 146 GLN s 240 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.120 112943 Z= 0.190 Angle : 0.657 13.421 159933 Z= 0.375 Chirality : 0.037 0.338 18602 Planarity : 0.007 0.109 15032 Dihedral : 12.901 179.164 28436 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.49 % Favored : 98.50 % Rotamer Outliers : 3.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.91 (0.09), residues: 9112 helix: 1.18 (0.09), residues: 3191 sheet: 0.04 (0.14), residues: 1210 loop : 0.52 (0.09), residues: 4711 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 280 poor density : 947 time to evaluate : 7.805 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: 280 outliers final: 136 residues processed: 1147 average time/residue: 1.7265 time to fit residues: 2822.6248 Evaluate side-chains 966 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 830 time to evaluate : 7.693 Switching outliers to nearest non-outliers outliers start: 136 outliers final: 111 residues processed: 28 average time/residue: 1.1594 time to fit residues: 63.2945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 947 optimal weight: 10.0000 chunk 720 optimal weight: 10.0000 chunk 497 optimal weight: 30.0000 chunk 106 optimal weight: 4.9990 chunk 457 optimal weight: 10.0000 chunk 643 optimal weight: 6.9990 chunk 962 optimal weight: 50.0000 chunk 1018 optimal weight: 5.9990 chunk 502 optimal weight: 30.0000 chunk 912 optimal weight: 0.0770 chunk 274 optimal weight: 8.9990 overall best weight: 5.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 69 HIS 7 232 HIS ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 ASN E 125 GLN F 98 GLN F 188 HIS F 228 GLN ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN N 98 HIS N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 55 ASN Q 239 ASN T 103 ASN X 53 ASN X 76 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 150 HIS a 90 GLN ** d 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 219 GLN e 226 ASN e 252 HIS ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN h 147 ASN l 125 ASN l 129 HIS p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 164 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.154 112943 Z= 0.444 Angle : 0.777 13.705 159933 Z= 0.428 Chirality : 0.044 0.283 18602 Planarity : 0.008 0.109 15032 Dihedral : 13.200 176.713 28436 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.22 % Favored : 97.77 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.50 (0.09), residues: 9112 helix: 0.88 (0.09), residues: 3206 sheet: -0.15 (0.14), residues: 1238 loop : 0.23 (0.09), residues: 4668 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1226 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 368 poor density : 858 time to evaluate : 7.606 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: 368 outliers final: 184 residues processed: 1125 average time/residue: 1.6888 time to fit residues: 2718.9599 Evaluate side-chains 996 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 812 time to evaluate : 7.269 Switching outliers to nearest non-outliers outliers start: 184 outliers final: 141 residues processed: 45 average time/residue: 1.1629 time to fit residues: 93.9278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 848 optimal weight: 1.9990 chunk 578 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 758 optimal weight: 4.9990 chunk 420 optimal weight: 4.9990 chunk 869 optimal weight: 8.9990 chunk 704 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 520 optimal weight: 1.9990 chunk 914 optimal weight: 8.9990 chunk 257 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN 7 198 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 252 HIS ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 HIS I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN Q 261 ASN T 195 GLN U 4 ASN X 76 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS Y 157 GLN Y 189 HIS ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 192 GLN d 149 HIS d 196 GLN d 217 HIS ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN h 147 ASN p 96 ASN p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 194 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.142 112943 Z= 0.246 Angle : 0.685 17.256 159933 Z= 0.387 Chirality : 0.038 0.349 18602 Planarity : 0.007 0.109 15032 Dihedral : 13.158 177.818 28436 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 1.91 % Favored : 98.08 % Rotamer Outliers : 3.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.66 (0.09), residues: 9112 helix: 1.07 (0.09), residues: 3199 sheet: -0.16 (0.14), residues: 1234 loop : 0.30 (0.09), residues: 4679 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1194 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 888 time to evaluate : 7.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 306 outliers final: 167 residues processed: 1109 average time/residue: 1.6476 time to fit residues: 2620.8817 Evaluate side-chains 967 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 800 time to evaluate : 7.774 Switching outliers to nearest non-outliers outliers start: 167 outliers final: 140 residues processed: 30 average time/residue: 1.1238 time to fit residues: 64.5643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 342 optimal weight: 10.0000 chunk 917 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 chunk 598 optimal weight: 5.9990 chunk 251 optimal weight: 20.0000 chunk 1019 optimal weight: 0.9990 chunk 846 optimal weight: 7.9990 chunk 472 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 337 optimal weight: 10.0000 chunk 535 optimal weight: 20.0000 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN 7 49 ASN 7 198 ASN 7 246 GLN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 137 ASN ** F 241 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 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN I 193 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 117 ASN ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 134 GLN P 162 GLN T 103 ASN U 4 ASN X 53 ASN X 76 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS d 217 HIS ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 94 HIS f 153 HIS ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN h 147 ASN l 129 HIS ** o 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.143 112943 Z= 0.370 Angle : 0.743 16.343 159933 Z= 0.413 Chirality : 0.041 0.368 18602 Planarity : 0.007 0.109 15032 Dihedral : 13.281 176.860 28436 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.51 % Favored : 97.48 % Rotamer Outliers : 4.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.51 (0.09), residues: 9112 helix: 0.99 (0.09), residues: 3161 sheet: -0.17 (0.14), residues: 1221 loop : 0.16 (0.09), residues: 4730 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1185 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 338 poor density : 847 time to evaluate : 7.857 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: 338 outliers final: 197 residues processed: 1106 average time/residue: 1.6880 time to fit residues: 2680.6360 Evaluate side-chains 997 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 800 time to evaluate : 7.600 Switching outliers to nearest non-outliers outliers start: 197 outliers final: 163 residues processed: 38 average time/residue: 1.0355 time to fit residues: 76.3065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 983 optimal weight: 7.9990 chunk 114 optimal weight: 10.0000 chunk 581 optimal weight: 0.8980 chunk 744 optimal weight: 0.9990 chunk 577 optimal weight: 10.0000 chunk 858 optimal weight: 0.2980 chunk 569 optimal weight: 6.9990 chunk 1015 optimal weight: 1.9990 chunk 635 optimal weight: 1.9990 chunk 619 optimal weight: 6.9990 chunk 469 optimal weight: 8.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN 7 198 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 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 128 ASN I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN I 193 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 162 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS ** Y 157 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 222 GLN ** d 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS ** d 262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN l 129 HIS p 96 ASN p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.235 112943 Z= 0.429 Angle : 0.799 106.092 159933 Z= 0.429 Chirality : 0.039 0.379 18602 Planarity : 0.007 0.143 15032 Dihedral : 13.282 176.930 28436 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.55 % Favored : 97.44 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.88 % 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: 0.52 (0.09), residues: 9112 helix: 1.01 (0.09), residues: 3166 sheet: -0.19 (0.14), residues: 1221 loop : 0.17 (0.09), residues: 4725 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1077 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 808 time to evaluate : 7.839 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: 269 outliers final: 200 residues processed: 1027 average time/residue: 1.6693 time to fit residues: 2467.7667 Evaluate side-chains 995 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 795 time to evaluate : 7.845 Switching outliers to nearest non-outliers outliers start: 200 outliers final: 185 residues processed: 20 average time/residue: 1.2956 time to fit residues: 50.8056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 628 optimal weight: 8.9990 chunk 405 optimal weight: 2.9990 chunk 606 optimal weight: 8.9990 chunk 306 optimal weight: 10.0000 chunk 199 optimal weight: 7.9990 chunk 196 optimal weight: 0.9990 chunk 645 optimal weight: 0.9980 chunk 692 optimal weight: 10.0000 chunk 502 optimal weight: 4.9990 chunk 94 optimal weight: 0.9990 chunk 798 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 102 GLN ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 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 128 ASN I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN N 98 HIS N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 162 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS Y 157 GLN ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 138 GLN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN h 147 ASN p 96 ASN p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 1.059 112943 Z= 0.389 Angle : 0.773 105.883 159933 Z= 0.418 Chirality : 0.039 0.395 18602 Planarity : 0.007 0.134 15032 Dihedral : 13.270 177.118 28436 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.37 % Favored : 97.62 % Rotamer Outliers : 3.26 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.88 % 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: 0.58 (0.09), residues: 9112 helix: 1.04 (0.09), residues: 3170 sheet: -0.17 (0.14), residues: 1214 loop : 0.21 (0.09), residues: 4728 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1096 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 830 time to evaluate : 7.809 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: 266 outliers final: 204 residues processed: 1048 average time/residue: 1.6554 time to fit residues: 2498.4665 Evaluate side-chains 996 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 792 time to evaluate : 7.851 Switching outliers to nearest non-outliers outliers start: 204 outliers final: 179 residues processed: 31 average time/residue: 1.1362 time to fit residues: 68.0725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 924 optimal weight: 9.9990 chunk 973 optimal weight: 9.9990 chunk 887 optimal weight: 8.9990 chunk 946 optimal weight: 5.9990 chunk 972 optimal weight: 0.8980 chunk 569 optimal weight: 3.9990 chunk 412 optimal weight: 0.8980 chunk 743 optimal weight: 8.9990 chunk 290 optimal weight: 30.0000 chunk 855 optimal weight: 20.0000 chunk 895 optimal weight: 0.2980 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 GLN ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 102 GLN ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 228 GLN ** F 241 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 128 ASN I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN I 193 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 162 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS Y 157 GLN d 217 HIS ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 138 GLN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN ** o 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 96 ASN p 123 HIS ** p 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.3177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.020 112943 Z= 0.481 Angle : 0.806 106.094 159933 Z= 0.429 Chirality : 0.039 0.378 18602 Planarity : 0.007 0.133 15032 Dihedral : 13.265 177.213 28436 Min Nonbonded Distance : 1.856 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.36 % Favored : 97.63 % Rotamer Outliers : 3.05 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 9112 helix: 1.04 (0.09), residues: 3169 sheet: -0.17 (0.14), residues: 1212 loop : 0.21 (0.09), residues: 4731 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1048 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 799 time to evaluate : 7.865 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: 249 outliers final: 213 residues processed: 1006 average time/residue: 1.6733 time to fit residues: 2431.4487 Evaluate side-chains 1001 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 788 time to evaluate : 7.918 Switching outliers to nearest non-outliers outliers start: 213 outliers final: 192 residues processed: 28 average time/residue: 1.2143 time to fit residues: 65.0032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 943 optimal weight: 20.0000 chunk 621 optimal weight: 1.9990 chunk 1001 optimal weight: 8.9990 chunk 610 optimal weight: 9.9990 chunk 474 optimal weight: 0.7980 chunk 695 optimal weight: 7.9990 chunk 1050 optimal weight: 0.1980 chunk 966 optimal weight: 5.9990 chunk 836 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 645 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 46 GLN ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 102 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 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 128 ASN I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN I 193 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 98 HIS N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 162 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 138 GLN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN p 96 ASN p 123 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.020 112943 Z= 0.482 Angle : 0.812 106.100 159933 Z= 0.434 Chirality : 0.039 0.378 18602 Planarity : 0.007 0.216 15032 Dihedral : 13.265 177.213 28436 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.36 % Favored : 97.63 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 9112 helix: 1.04 (0.09), residues: 3169 sheet: -0.17 (0.14), residues: 1212 loop : 0.21 (0.09), residues: 4731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18224 Ramachandran restraints generated. 9112 Oldfield, 0 Emsley, 9112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 790 time to evaluate : 7.690 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: 191 outliers final: 192 residues processed: 975 average time/residue: 1.6797 time to fit residues: 2366.3307 Evaluate side-chains 975 residues out of total 8166 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 783 time to evaluate : 7.799 Switching outliers to nearest non-outliers outliers start: 192 outliers final: 192 residues processed: 7 average time/residue: 1.0983 time to fit residues: 22.7663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 512 optimal weight: 1.9990 chunk 664 optimal weight: 0.9980 chunk 890 optimal weight: 7.9990 chunk 256 optimal weight: 10.0000 chunk 770 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 232 optimal weight: 7.9990 chunk 837 optimal weight: 3.9990 chunk 350 optimal weight: 7.9990 chunk 859 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** u 178 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 314 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 316 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 102 GLN ** 5 384 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN ** D 195 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 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 128 ASN I 142 ASN ** I 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 189 GLN I 193 ASN ** K 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN ** O 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 158 GLN P 162 GLN ** X 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 99 HIS ** Z 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 217 HIS ** e 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 138 GLN ** h 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 147 ASN p 96 ASN p 123 HIS ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.125790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.096067 restraints weight = 228475.898| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.65 r_work: 0.3471 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 1.58 restraints_weight: 0.2500 r_work: 0.3436 rms_B_bonded: 1.72 restraints_weight: 0.1250 r_work: 0.3416 rms_B_bonded: 1.94 restraints_weight: 0.0625 r_work: 0.3394 rms_B_bonded: 2.24 restraints_weight: 0.0312 r_work: 0.3367 rms_B_bonded: 2.66 restraints_weight: 0.0156 r_work: 0.3334 rms_B_bonded: 3.22 restraints_weight: 0.0078 r_work: 0.3293 rms_B_bonded: 4.01 restraints_weight: 0.0039 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.3175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 1.020 112943 Z= 0.482 Angle : 0.812 106.100 159933 Z= 0.434 Chirality : 0.039 0.378 18602 Planarity : 0.007 0.216 15032 Dihedral : 13.265 177.213 28436 Min Nonbonded Distance : 1.760 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 2.36 % Favored : 97.63 % Rotamer Outliers : 2.35 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 2.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 9112 helix: 1.04 (0.09), residues: 3169 sheet: -0.17 (0.14), residues: 1212 loop : 0.21 (0.09), residues: 4731 =============================================================================== Job complete usr+sys time: 36623.60 seconds wall clock time: 627 minutes 23.19 seconds (37643.19 seconds total)