Starting phenix.real_space_refine on Tue Nov 21 20:28:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/11_2023/8bjq_16090.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/11_2023/8bjq_16090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/11_2023/8bjq_16090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/11_2023/8bjq_16090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/11_2023/8bjq_16090.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/11_2023/8bjq_16090.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3580 5.49 5 Mg 206 5.21 5 S 172 5.16 5 C 75216 2.51 5 N 25748 2.21 5 O 36457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "LE ASP 137": "OD1" <-> "OD2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 515": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 141384 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1612 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 184} Chain: "B" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6536 Classifications: {'peptide': 796} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 776} Chain: "C4" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "C3" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "LA" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1899 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LB" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Chain: "LC" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "LD" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LE" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1305 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "LF" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "LG" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LH" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "LI" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "LJ" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1350 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LL" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "LM" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "LN" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "LO" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "LP" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "LQ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "LR" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LS" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "LT" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "LU" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "LV" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "LW" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 538 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LX" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LY" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LZ" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "La" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "Lb" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Lc" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Ld" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 880 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Le" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1017 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Lf" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "Lg" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Lh" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Li" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lj" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "Lk" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Ll" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "Ln" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 229 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Lo" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Lp" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "1" Number of atoms: 70586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3301, 70586 Classifications: {'RNA': 3301} Modifications used: {'rna2p_pur': 333, 'rna2p_pyr': 219, 'rna3p_pur': 1483, 'rna3p_pyr': 1266} Link IDs: {'rna2p': 552, 'rna3p': 2748} Chain breaks: 3 Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 571 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "D" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6536 Classifications: {'peptide': 796} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 776} Chain: "C4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "La" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 195 Unusual residues: {' MG': 195} Classifications: {'undetermined': 195} Link IDs: {None: 194} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57351 SG CYSLg 47 89.225 175.502 73.683 1.00117.34 S ATOM 57604 SG CYSLg 81 89.741 178.491 71.910 1.00126.28 S ATOM 57623 SG CYSLg 84 86.214 176.122 72.595 1.00117.22 S ATOM 59734 SG CYSLj 19 92.241 164.192 132.198 1.00104.18 S ATOM 59759 SG CYSLj 22 93.883 162.744 135.248 1.00106.83 S ATOM 59859 SG CYSLj 34 92.791 160.482 132.411 1.00101.40 S ATOM 59877 SG CYSLj 37 90.101 162.158 134.479 1.00100.07 S ATOM 61466 SG CYSLm 96 160.014 70.577 129.691 1.00129.51 S ATOM 61492 SG CYSLm 99 161.593 72.745 130.066 1.00126.38 S ATOM 61579 SG CYSLm 110 162.955 70.888 131.865 1.00128.15 S ATOM 61625 SG CYSLm 115 160.112 71.947 133.874 1.00127.10 S ATOM 62052 SG CYSLo 12 50.210 80.088 149.915 1.00139.72 S ATOM 62087 SG CYSLo 17 46.711 78.622 151.274 1.00145.97 S ATOM 62551 SG CYSLo 74 47.932 78.239 147.404 1.00139.03 S ATOM 62573 SG CYSLo 77 46.960 80.802 149.483 1.00143.74 S ATOM 63096 SG CYSLp 39 88.731 160.303 64.737 1.00116.21 S ATOM 63119 SG CYSLp 42 90.448 161.921 63.329 1.00116.67 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N AVALLO 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 3 " occ=0.50 residue: pdb=" N AGLULO 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLULO 4 " occ=0.50 residue: pdb=" N APROLO 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APROLO 5 " occ=0.50 residue: pdb=" N AVALLO 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 6 " occ=0.50 residue: pdb=" N AVALLO 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 7 " occ=0.50 residue: pdb=" N AVALLO 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 8 " occ=0.50 residue: pdb=" N AILELO 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILELO 9 " occ=0.50 residue: pdb=" N AASPLO 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASPLO 10 " occ=0.50 residue: pdb=" N AGLYLO 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLYLO 11 " occ=0.50 residue: pdb=" N ALYSLO 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYSLO 12 " occ=0.50 residue: pdb=" N AGLYLO 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLYLO 13 " occ=0.50 residue: pdb=" N AHISLO 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHISLO 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 52.48, per 1000 atoms: 0.37 Number of scatterers: 141384 At special positions: 0 Unit cell: (238.26, 281.105, 246.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 172 16.00 P 3580 15.00 Mg 206 11.99 O 36457 8.00 N 25748 7.00 C 75216 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 Atom "ATOM A05GP O5' A 12092 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.35 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLg 201 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 47 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 84 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 81 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 17 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 74 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb=" ZNLp 501 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 42 " Number of angles added : 18 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15212 Finding SS restraints... Secondary structure from input PDB file: 346 helices and 68 sheets defined 47.4% alpha, 12.4% beta 1149 base pairs and 1743 stacking pairs defined. Time for finding SS restraints: 47.22 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.543A pdb=" N LEU A 12 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 28 through 39 removed outlier: 3.615A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.600A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.625A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 removed outlier: 4.170A pdb=" N CYS B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.640A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 90 through 105 removed outlier: 3.551A pdb=" N LEU B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.721A pdb=" N SER B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 144 through 163 removed outlier: 4.017A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 185 removed outlier: 3.594A pdb=" N ILE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 245 through 259 Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.532A pdb=" N LYS B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.799A pdb=" N LEU B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.161A pdb=" N LYS B 324 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.728A pdb=" N TYR B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.592A pdb=" N TYR B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 398 through 412 removed outlier: 4.229A pdb=" N PHE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 removed outlier: 3.664A pdb=" N ASN B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.618A pdb=" N TRP B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.754A pdb=" N ALA B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 470 through 476 removed outlier: 3.556A pdb=" N SER B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 508 through 523 Proline residue: B 514 - end of helix removed outlier: 3.647A pdb=" N PHE B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 542 removed outlier: 3.636A pdb=" N ILE B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 559 removed outlier: 3.568A pdb=" N THR B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 580 removed outlier: 3.935A pdb=" N THR B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.829A pdb=" N ILE B 593 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 603 removed outlier: 4.160A pdb=" N ASN B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 4.903A pdb=" N TYR B 610 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 631 removed outlier: 3.518A pdb=" N GLU B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.875A pdb=" N LEU B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 678 removed outlier: 3.549A pdb=" N PHE B 672 " --> pdb=" O PHE B 668 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 674 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 699 through 719 removed outlier: 4.270A pdb=" N SER B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 742 Processing helix chain 'B' and resid 743 through 762 removed outlier: 3.560A pdb=" N LEU B 753 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 772 Processing helix chain 'B' and resid 778 through 795 removed outlier: 3.966A pdb=" N ILE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'LA' and resid 5 through 10 Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 103 through 107 removed outlier: 3.843A pdb=" N VALLA 107 " --> pdb=" O LEULA 104 " (cutoff:3.500A) Processing helix chain 'LA' and resid 173 through 177 removed outlier: 3.702A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Processing helix chain 'LA' and resid 181 through 191 removed outlier: 4.022A pdb=" N LEULA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 204 Processing helix chain 'LB' and resid 13 through 17 removed outlier: 3.516A pdb=" N PHELB 16 " --> pdb=" O HISLB 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEULB 17 " --> pdb=" O LEULB 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 13 through 17' Processing helix chain 'LB' and resid 111 through 116 removed outlier: 3.521A pdb=" N LYSLB 115 " --> pdb=" O SERLB 111 " (cutoff:3.500A) Processing helix chain 'LB' and resid 117 through 119 No H-bonds generated for 'chain 'LB' and resid 117 through 119' Processing helix chain 'LB' and resid 130 through 135 Processing helix chain 'LB' and resid 141 through 154 removed outlier: 3.873A pdb=" N ARGLB 146 " --> pdb=" O ALALB 142 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLULB 147 " --> pdb=" O GLYLB 143 " (cutoff:3.500A) Processing helix chain 'LB' and resid 165 through 169 Processing helix chain 'LB' and resid 187 through 198 Processing helix chain 'LB' and resid 204 through 208 Processing helix chain 'LB' and resid 228 through 234 Processing helix chain 'LB' and resid 372 through 381 Processing helix chain 'LC' and resid 31 through 43 Processing helix chain 'LC' and resid 114 through 130 removed outlier: 4.271A pdb=" N ALALC 130 " --> pdb=" O ILELC 126 " (cutoff:3.500A) Processing helix chain 'LC' and resid 131 through 138 Processing helix chain 'LC' and resid 154 through 159 Processing helix chain 'LC' and resid 161 through 173 Processing helix chain 'LC' and resid 174 through 184 Processing helix chain 'LC' and resid 190 through 195 removed outlier: 4.183A pdb=" N LYSLC 193 " --> pdb=" O GLYLC 190 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 221 removed outlier: 4.494A pdb=" N ASNLC 221 " --> pdb=" O LYSLC 217 " (cutoff:3.500A) Processing helix chain 'LC' and resid 234 through 239 Processing helix chain 'LC' and resid 240 through 243 Processing helix chain 'LC' and resid 252 through 263 removed outlier: 4.680A pdb=" N ASPLC 259 " --> pdb=" O PHELC 255 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLNLC 260 " --> pdb=" O THRLC 256 " (cutoff:3.500A) Processing helix chain 'LC' and resid 285 through 291 removed outlier: 3.605A pdb=" N ILELC 289 " --> pdb=" O ASPLC 285 " (cutoff:3.500A) Processing helix chain 'LC' and resid 293 through 299 Processing helix chain 'LC' and resid 320 through 328 removed outlier: 3.628A pdb=" N LEULC 324 " --> pdb=" O ASNLC 320 " (cutoff:3.500A) Processing helix chain 'LC' and resid 330 through 338 Processing helix chain 'LC' and resid 339 through 342 removed outlier: 3.686A pdb=" N LYSLC 342 " --> pdb=" O LEULC 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 339 through 342' Processing helix chain 'LC' and resid 352 through 361 Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 4.312A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 82 through 87 Processing helix chain 'LD' and resid 94 through 113 Processing helix chain 'LD' and resid 158 through 170 Processing helix chain 'LD' and resid 191 through 200 Processing helix chain 'LD' and resid 201 through 215 removed outlier: 4.049A pdb=" N TYRLD 207 " --> pdb=" O HISLD 203 " (cutoff:3.500A) Processing helix chain 'LD' and resid 215 through 222 Processing helix chain 'LD' and resid 223 through 229 removed outlier: 3.525A pdb=" N LEULD 227 " --> pdb=" O PHELD 223 " (cutoff:3.500A) Processing helix chain 'LD' and resid 234 through 250 removed outlier: 4.403A pdb=" N ASPLD 238 " --> pdb=" O ASPLD 234 " (cutoff:3.500A) Processing helix chain 'LD' and resid 261 through 273 removed outlier: 3.774A pdb=" N GLULD 268 " --> pdb=" O GLNLD 264 " (cutoff:3.500A) Processing helix chain 'LD' and resid 278 through 294 Processing helix chain 'LE' and resid 80 through 82 No H-bonds generated for 'chain 'LE' and resid 80 through 82' Processing helix chain 'LE' and resid 131 through 150 removed outlier: 3.736A pdb=" N ALALE 147 " --> pdb=" O LYSLE 143 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLULE 148 " --> pdb=" O ALALE 144 " (cutoff:3.500A) Processing helix chain 'LE' and resid 154 through 161 Processing helix chain 'LF' and resid 27 through 72 Processing helix chain 'LF' and resid 96 through 106 Processing helix chain 'LF' and resid 120 through 130 removed outlier: 4.124A pdb=" N GLULF 125 " --> pdb=" O LYSLF 121 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEULF 126 " --> pdb=" O ALALF 122 " (cutoff:3.500A) Processing helix chain 'LF' and resid 140 through 151 Processing helix chain 'LF' and resid 165 through 174 removed outlier: 4.250A pdb=" N ILELF 169 " --> pdb=" O ASPLF 165 " (cutoff:3.500A) Processing helix chain 'LF' and resid 180 through 190 Processing helix chain 'LF' and resid 194 through 202 Processing helix chain 'LF' and resid 222 through 226 Processing helix chain 'LF' and resid 235 through 244 removed outlier: 3.588A pdb=" N LEULF 239 " --> pdb=" O PHELF 235 " (cutoff:3.500A) Processing helix chain 'LG' and resid 46 through 50 removed outlier: 3.568A pdb=" N VALLG 50 " --> pdb=" O SERLG 47 " (cutoff:3.500A) Processing helix chain 'LG' and resid 53 through 69 removed outlier: 4.107A pdb=" N LYSLG 63 " --> pdb=" O GLNLG 59 " (cutoff:3.500A) Processing helix chain 'LG' and resid 83 through 96 removed outlier: 3.972A pdb=" N LYSLG 96 " --> pdb=" O LYSLG 92 " (cutoff:3.500A) Processing helix chain 'LG' and resid 101 through 119 Processing helix chain 'LG' and resid 135 through 145 Processing helix chain 'LG' and resid 159 through 163 Processing helix chain 'LG' and resid 165 through 174 Processing helix chain 'LG' and resid 182 through 190 Processing helix chain 'LG' and resid 204 through 206 No H-bonds generated for 'chain 'LG' and resid 204 through 206' Processing helix chain 'LG' and resid 207 through 222 removed outlier: 3.907A pdb=" N ALALG 220 " --> pdb=" O SERLG 216 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASNLG 221 " --> pdb=" O THRLG 217 " (cutoff:3.500A) Processing helix chain 'LG' and resid 225 through 230 Processing helix chain 'LG' and resid 239 through 254 removed outlier: 4.219A pdb=" N LYSLG 245 " --> pdb=" O LYSLG 241 " (cutoff:3.500A) Processing helix chain 'LH' and resid 61 through 84 removed outlier: 3.595A pdb=" N LEULH 68 " --> pdb=" O HISLH 64 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARGLH 69 " --> pdb=" O VALLH 65 " (cutoff:3.500A) Processing helix chain 'LH' and resid 116 through 120 Processing helix chain 'LH' and resid 150 through 164 Processing helix chain 'LI' and resid 5 through 10 removed outlier: 3.926A pdb=" N ARGLI 10 " --> pdb=" O ARGLI 7 " (cutoff:3.500A) Processing helix chain 'LI' and resid 62 through 80 Processing helix chain 'LI' and resid 107 through 111 Processing helix chain 'LI' and resid 144 through 157 removed outlier: 3.595A pdb=" N GLULI 150 " --> pdb=" O ASPLI 146 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYRLI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 178 through 187 removed outlier: 3.983A pdb=" N ALALI 187 " --> pdb=" O LYSLI 183 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 212 Processing helix chain 'LI' and resid 213 through 218 removed outlier: 4.107A pdb=" N PHELI 217 " --> pdb=" O PHELI 213 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 27 through 41 Processing helix chain 'LJ' and resid 73 through 87 removed outlier: 3.588A pdb=" N VALLJ 86 " --> pdb=" O ARGLJ 82 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 92 through 96 Processing helix chain 'LJ' and resid 108 through 112 Processing helix chain 'LJ' and resid 135 through 140 removed outlier: 3.720A pdb=" N VALLJ 138 " --> pdb=" O GLYLJ 135 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 149 through 153 Processing helix chain 'LJ' and resid 155 through 166 removed outlier: 3.531A pdb=" N SERLJ 161 " --> pdb=" O GLULJ 157 " (cutoff:3.500A) Processing helix chain 'LL' and resid 17 through 20 Processing helix chain 'LL' and resid 27 through 46 Processing helix chain 'LL' and resid 77 through 84 Processing helix chain 'LL' and resid 86 through 92 removed outlier: 3.502A pdb=" N THRLL 92 " --> pdb=" O ALALL 88 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 122 Processing helix chain 'LL' and resid 140 through 145 removed outlier: 3.556A pdb=" N THRLL 144 " --> pdb=" O SERLL 140 " (cutoff:3.500A) Processing helix chain 'LL' and resid 167 through 179 Processing helix chain 'LL' and resid 179 through 192 removed outlier: 3.801A pdb=" N GLULL 192 " --> pdb=" O ARGLL 188 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 88 Processing helix chain 'LM' and resid 89 through 96 removed outlier: 3.778A pdb=" N LYSLM 93 " --> pdb=" O ALALM 89 " (cutoff:3.500A) Processing helix chain 'LM' and resid 97 through 112 removed outlier: 3.599A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 135 Processing helix chain 'LN' and resid 3 through 12 removed outlier: 3.509A pdb=" N ARGLN 12 " --> pdb=" O GLULN 8 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 33 removed outlier: 3.597A pdb=" N TRPLN 28 " --> pdb=" O ARGLN 24 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 75 through 79 Processing helix chain 'LN' and resid 83 through 87 Processing helix chain 'LN' and resid 97 through 110 Processing helix chain 'LN' and resid 139 through 144 Processing helix chain 'LN' and resid 148 through 157 Proline residue: LN 154 - end of helix removed outlier: 3.561A pdb=" N LYSLN 157 " --> pdb=" O PROLN 154 " (cutoff:3.500A) Processing helix chain 'LN' and resid 158 through 163 Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 177 through 181 Processing helix chain 'LN' and resid 186 through 195 Processing helix chain 'LO' and resid 15 through 29 Processing helix chain 'LO' and resid 37 through 40 Processing helix chain 'LO' and resid 46 through 60 removed outlier: 4.013A pdb=" N ALYSLO 60 " --> pdb=" O AASPLO 56 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 69 removed outlier: 3.646A pdb=" N AGLYLO 69 " --> pdb=" O ALYSLO 66 " (cutoff:3.500A) Processing helix chain 'LO' and resid 75 through 86 Processing helix chain 'LO' and resid 92 through 101 Processing helix chain 'LO' and resid 120 through 123 Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 138 through 146 Processing helix chain 'LO' and resid 149 through 186 Processing helix chain 'LO' and resid 188 through 197 Processing helix chain 'LP' and resid 10 through 12 No H-bonds generated for 'chain 'LP' and resid 10 through 12' Processing helix chain 'LP' and resid 25 through 35 Processing helix chain 'LP' and resid 40 through 53 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 3.510A pdb=" N GLYLP 73 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLULP 75 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 132 through 134 No H-bonds generated for 'chain 'LP' and resid 132 through 134' Processing helix chain 'LP' and resid 169 through 183 Processing helix chain 'LQ' and resid 23 through 41 removed outlier: 4.393A pdb=" N ASPLQ 41 " --> pdb=" O ALALQ 37 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 42 through 54 removed outlier: 3.760A pdb=" N LYSLQ 46 " --> pdb=" O ALALQ 42 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHELQ 53 " --> pdb=" O LEULQ 49 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEULQ 54 " --> pdb=" O LYSLQ 50 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 64 through 72 Processing helix chain 'LQ' and resid 107 through 117 Processing helix chain 'LQ' and resid 123 through 131 Processing helix chain 'LQ' and resid 148 through 153 Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 28 through 35 Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 72 Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 removed outlier: 3.529A pdb=" N VALLR 122 " --> pdb=" O HISLR 118 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 172 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 52 through 54 No H-bonds generated for 'chain 'LS' and resid 52 through 54' Processing helix chain 'LS' and resid 98 through 115 Processing helix chain 'LS' and resid 117 through 119 No H-bonds generated for 'chain 'LS' and resid 117 through 119' Processing helix chain 'LS' and resid 137 through 142 Processing helix chain 'LS' and resid 143 through 145 No H-bonds generated for 'chain 'LS' and resid 143 through 145' Processing helix chain 'LT' and resid 27 through 32 Processing helix chain 'LT' and resid 54 through 58 Processing helix chain 'LT' and resid 99 through 121 removed outlier: 3.864A pdb=" N GLNLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALALT 121 " --> pdb=" O ALALT 117 " (cutoff:3.500A) Processing helix chain 'LU' and resid 19 through 24 removed outlier: 3.652A pdb=" N THRLU 23 " --> pdb=" O VALLU 19 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLULU 24 " --> pdb=" O SERLU 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 19 through 24' Processing helix chain 'LU' and resid 29 through 41 Processing helix chain 'LU' and resid 72 through 87 Processing helix chain 'LV' and resid 119 through 126 removed outlier: 3.501A pdb=" N LEULV 125 " --> pdb=" O GLULV 121 " (cutoff:3.500A) Processing helix chain 'LV' and resid 126 through 133 Processing helix chain 'LW' and resid 33 through 42 Processing helix chain 'LW' and resid 45 through 49 Processing helix chain 'LW' and resid 52 through 59 Processing helix chain 'LX' and resid 58 through 62 Processing helix chain 'LX' and resid 69 through 80 removed outlier: 3.915A pdb=" N ASNLX 80 " --> pdb=" O VALLX 76 " (cutoff:3.500A) Processing helix chain 'LX' and resid 91 through 104 Processing helix chain 'LX' and resid 131 through 140 removed outlier: 3.545A pdb=" N ASNLX 137 " --> pdb=" O LEULX 133 " (cutoff:3.500A) Processing helix chain 'LY' and resid 11 through 21 Processing helix chain 'LY' and resid 23 through 31 removed outlier: 3.778A pdb=" N VALLY 29 " --> pdb=" O SERLY 25 " (cutoff:3.500A) Processing helix chain 'LY' and resid 36 through 44 Processing helix chain 'LY' and resid 74 through 78 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 122 Processing helix chain 'LZ' and resid 60 through 66 Processing helix chain 'LZ' and resid 103 through 124 removed outlier: 3.895A pdb=" N ARGLZ 107 " --> pdb=" O GLNLZ 103 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 127 through 132 Processing helix chain 'La' and resid 2 through 5 removed outlier: 3.518A pdb=" N PHELa 5 " --> pdb=" O PROLa 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 2 through 5' Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.904A pdb=" N LYSLa 10 " --> pdb=" O THRLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 41 through 49 Processing helix chain 'La' and resid 83 through 93 removed outlier: 4.001A pdb=" N ASPLa 88 " --> pdb=" O GLULa 84 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLNLa 89 " --> pdb=" O ASPLa 85 " (cutoff:3.500A) Processing helix chain 'La' and resid 104 through 108 Processing helix chain 'La' and resid 131 through 141 Processing helix chain 'Lb' and resid 11 through 19 removed outlier: 4.082A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 59 removed outlier: 3.511A pdb=" N ASNLb 42 " --> pdb=" O LYSLb 38 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HISLb 45 " --> pdb=" O ARGLb 41 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 10 through 21 Processing helix chain 'Lc' and resid 26 through 36 Processing helix chain 'Lc' and resid 49 through 64 Processing helix chain 'Lc' and resid 73 through 81 Processing helix chain 'Ld' and resid 16 through 20 Processing helix chain 'Ld' and resid 24 through 26 No H-bonds generated for 'chain 'Ld' and resid 24 through 26' Processing helix chain 'Ld' and resid 27 through 45 Processing helix chain 'Ld' and resid 52 through 61 Processing helix chain 'Le' and resid 54 through 58 Processing helix chain 'Le' and resid 78 through 83 removed outlier: 3.552A pdb=" N LEULe 82 " --> pdb=" O ASNLe 78 " (cutoff:3.500A) Processing helix chain 'Le' and resid 84 through 86 No H-bonds generated for 'chain 'Le' and resid 84 through 86' Processing helix chain 'Le' and resid 101 through 116 Processing helix chain 'Lf' and resid 37 through 42 Processing helix chain 'Lf' and resid 43 through 45 No H-bonds generated for 'chain 'Lf' and resid 43 through 45' Processing helix chain 'Lg' and resid 15 through 18 Processing helix chain 'Lg' and resid 58 through 65 removed outlier: 3.555A pdb=" N VALLg 65 " --> pdb=" O TYRLg 62 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 67 through 71 Processing helix chain 'Lg' and resid 81 through 113 removed outlier: 3.591A pdb=" N LYSLg 113 " --> pdb=" O THRLg 109 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.900A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 36 removed outlier: 3.722A pdb=" N GLNLh 34 " --> pdb=" O GLULh 30 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEULh 36 " --> pdb=" O LYSLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 43 through 70 removed outlier: 3.697A pdb=" N VALLh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 77 through 81 removed outlier: 3.533A pdb=" N ARGLh 81 " --> pdb=" O LYSLh 78 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 85 through 91 Processing helix chain 'Lh' and resid 93 through 99 Processing helix chain 'Lh' and resid 101 through 111 Processing helix chain 'Li' and resid 34 through 49 Processing helix chain 'Li' and resid 51 through 64 Processing helix chain 'Li' and resid 64 through 77 removed outlier: 4.673A pdb=" N ARGLi 68 " --> pdb=" O SERLi 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALALi 69 " --> pdb=" O GLYLi 65 " (cutoff:3.500A) Processing helix chain 'Li' and resid 79 through 100 Processing helix chain 'Lj' and resid 4 through 9 removed outlier: 3.596A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 Processing helix chain 'Lj' and resid 69 through 76 Processing helix chain 'Lk' and resid 7 through 15 Processing helix chain 'Lk' and resid 58 through 69 Processing helix chain 'Ll' and resid 6 through 20 Processing helix chain 'Ll' and resid 24 through 30 Processing helix chain 'Lm' and resid 80 through 91 removed outlier: 3.880A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Ln' and resid 2 through 24 removed outlier: 4.123A pdb=" N SERLn 24 " --> pdb=" O VALLn 20 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 37 through 48 Processing helix chain 'Lp' and resid 8 through 15 removed outlier: 3.848A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.905A pdb=" N GLNLp 32 " --> pdb=" O LYSLp 28 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 91 Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'D' and resid 2 through 16 removed outlier: 4.227A pdb=" N ARG D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 32 Processing helix chain 'D' and resid 35 through 50 removed outlier: 3.964A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 54 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 90 through 105 removed outlier: 3.811A pdb=" N LEU D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'D' and resid 138 through 141 Processing helix chain 'D' and resid 144 through 163 removed outlier: 4.213A pdb=" N TYR D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.576A pdb=" N ASN D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 263 through 277 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 295 through 311 removed outlier: 3.919A pdb=" N LEU D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 removed outlier: 4.298A pdb=" N LYS D 324 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 338 through 342 removed outlier: 3.546A pdb=" N ILE D 342 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.621A pdb=" N LEU D 403 " --> pdb=" O CYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 433 Processing helix chain 'D' and resid 438 through 452 Processing helix chain 'D' and resid 454 through 463 removed outlier: 3.543A pdb=" N HIS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing helix chain 'D' and resid 470 through 476 removed outlier: 3.695A pdb=" N SER D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.564A pdb=" N SER D 481 " --> pdb=" O TYR D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 492 through 497 Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 508 through 523 Proline residue: D 514 - end of helix Processing helix chain 'D' and resid 525 through 541 removed outlier: 3.827A pdb=" N ILE D 529 " --> pdb=" O SER D 525 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 559 Processing helix chain 'D' and resid 563 through 580 removed outlier: 3.641A pdb=" N THR D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 603 removed outlier: 3.624A pdb=" N ASN D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 5.116A pdb=" N TYR D 610 " --> pdb=" O ILE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 631 Processing helix chain 'D' and resid 637 through 647 removed outlier: 3.550A pdb=" N LEU D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 660 Processing helix chain 'D' and resid 661 through 678 Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 700 through 719 Processing helix chain 'D' and resid 724 through 761 removed outlier: 4.885A pdb=" N ASP D 743 " --> pdb=" O ARG D 739 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 761 " --> pdb=" O TYR D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 772 Processing helix chain 'D' and resid 779 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.045A pdb=" N PHE A 44 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 61 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU A 48 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 59 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER A 60 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 83 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR A 62 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL A 81 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 64 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 117 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA A 80 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 12.728A pdb=" N LYS A 119 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 14.768A pdb=" N THR A 82 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 164 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG A 139 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 166 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N CYS A 188 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 139 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LA' and resid 73 through 77 removed outlier: 3.639A pdb=" N GLNLA 47 " --> pdb=" O LYSLA 60 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VALLA 62 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VALLA 45 " --> pdb=" O VALLA 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LA' and resid 155 through 158 removed outlier: 6.682A pdb=" N ARGLA 149 " --> pdb=" O ILELA 136 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILELA 136 " --> pdb=" O ARGLA 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LA' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'LB' and resid 356 through 359 removed outlier: 6.829A pdb=" N VALLB 57 " --> pdb=" O LYSLB 357 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILELB 359 " --> pdb=" O THRLB 55 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THRLB 55 " --> pdb=" O ILELB 359 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILELB 335 " --> pdb=" O VALLB 220 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VALLB 220 " --> pdb=" O ILELB 335 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILELB 215 " --> pdb=" O ASNLB 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASNLB 279 " --> pdb=" O ILELB 215 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYSLB 281 " --> pdb=" O LYSLB 325 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N METLB 323 " --> pdb=" O TYRLB 283 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VALLB 285 " --> pdb=" O PHELB 321 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHELB 321 " --> pdb=" O VALLB 285 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASPLB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYSLB 50 " --> pdb=" O ASPLB 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LB' and resid 100 through 105 removed outlier: 7.360A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THRLB 104 " --> pdb=" O VALLB 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VALLB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VALLB 86 " --> pdb=" O HISLB 163 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N HISLB 163 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLYLB 88 " --> pdb=" O LEULB 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'LB' and resid 100 through 105 removed outlier: 7.360A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THRLB 104 " --> pdb=" O VALLB 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VALLB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYSLB 201 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'LB' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'LC' and resid 19 through 20 removed outlier: 4.594A pdb=" N VALLC 151 " --> pdb=" O THRLC 7 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEULC 150 " --> pdb=" O VALLC 248 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEULC 206 " --> pdb=" O ILELC 249 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THRLC 251 " --> pdb=" O LEULC 206 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VALLC 208 " --> pdb=" O THRLC 251 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VALLC 207 " --> pdb=" O ALALC 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'LC' and resid 63 through 64 Processing sheet with id=AB2, first strand: chain 'LC' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'LD' and resid 71 through 79 removed outlier: 6.567A pdb=" N ILELD 64 " --> pdb=" O LEULD 75 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALALD 77 " --> pdb=" O CYSLD 62 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYSLD 62 " --> pdb=" O ALALD 77 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYRLD 79 " --> pdb=" O ILELD 60 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILELD 60 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LE' and resid 77 through 79 removed outlier: 3.605A pdb=" N LYSLE 56 " --> pdb=" O LEULE 64 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THRLE 66 " --> pdb=" O TYRLE 54 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYRLE 54 " --> pdb=" O THRLE 66 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THRLE 38 " --> pdb=" O TYRLE 54 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VALLE 39 " --> pdb=" O THRLE 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'LF' and resid 75 through 77 Processing sheet with id=AB6, first strand: chain 'LF' and resid 205 through 206 removed outlier: 4.349A pdb=" N SERLF 113 " --> pdb=" O ARGLF 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'LF' and resid 153 through 156 Processing sheet with id=AB8, first strand: chain 'LG' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'LG' and resid 133 through 134 removed outlier: 6.685A pdb=" N VALLG 151 " --> pdb=" O ALALG 178 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VALLG 180 " --> pdb=" O VALLG 151 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILELG 153 " --> pdb=" O VALLG 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'LH' and resid 6 through 11 removed outlier: 3.631A pdb=" N GLNLH 8 " --> pdb=" O VALLH 55 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALLH 55 " --> pdb=" O GLNLH 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LH' and resid 32 through 37 removed outlier: 3.612A pdb=" N LYSLH 36 " --> pdb=" O VALLH 25 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VALLH 18 " --> pdb=" O ILELM 6 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LH' and resid 132 through 135 removed outlier: 6.925A pdb=" N LYSLH 87 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYSLH 184 " --> pdb=" O LYSLH 87 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYSLH 89 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LH' and resid 100 through 104 Processing sheet with id=AC5, first strand: chain 'LI' and resid 35 through 37 removed outlier: 6.393A pdb=" N LEULI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SERLI 137 " --> pdb=" O VALLI 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VALLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARGLI 139 " --> pdb=" O LEULI 48 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEULI 48 " --> pdb=" O ARGLI 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'LI' and resid 58 through 61 removed outlier: 3.704A pdb=" N GLULI 58 " --> pdb=" O VALLI 129 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILELI 99 " --> pdb=" O PROLI 122 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLYLI 124 " --> pdb=" O LEULI 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LI' and resid 170 through 171 removed outlier: 5.737A pdb=" N LEULI 176 " --> pdb=" O TRPLI 171 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'LI' and resid 190 through 192 Processing sheet with id=AC9, first strand: chain 'LJ' and resid 46 through 48 removed outlier: 3.542A pdb=" N ALALJ 66 " --> pdb=" O SERLJ 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASNLJ 132 " --> pdb=" O LYSLJ 13 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VALLJ 130 " --> pdb=" O GLULJ 15 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEULJ 17 " --> pdb=" O TYRLJ 128 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYRLJ 128 " --> pdb=" O LEULJ 17 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEULJ 19 " --> pdb=" O ASPLJ 126 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASPLJ 126 " --> pdb=" O LEULJ 19 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'LJ' and resid 90 through 91 removed outlier: 3.519A pdb=" N LEULJ 91 " --> pdb=" O ASPLJ 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'LL' and resid 22 through 24 removed outlier: 6.075A pdb=" N LYSLL 23 " --> pdb=" O LEULN 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'LL' and resid 57 through 59 Processing sheet with id=AD4, first strand: chain 'LL' and resid 123 through 125 Processing sheet with id=AD5, first strand: chain 'LM' and resid 53 through 59 removed outlier: 4.621A pdb=" N GLYLM 48 " --> pdb=" O PROLM 54 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYSLM 43 " --> pdb=" O ILELM 38 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILELM 38 " --> pdb=" O LYSLM 43 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEULM 45 " --> pdb=" O VALLM 36 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARGLM 19 " --> pdb=" O ILELM 35 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VALLM 20 " --> pdb=" O THRLM 66 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.433A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYRLN 127 " --> pdb=" O GLNLN 123 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLNLN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VALLN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VALLN 115 " --> pdb=" O VALLN 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LO' and resid 6 through 10 removed outlier: 5.915A pdb=" N AVALLO 7 " --> pdb=" O AVALLO 34 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N AVALLO 36 " --> pdb=" O AVALLO 7 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N AILELO 9 " --> pdb=" O AVALLO 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LO' and resid 42 through 44 Processing sheet with id=AD9, first strand: chain 'LP' and resid 14 through 22 removed outlier: 3.648A pdb=" N TYRLP 21 " --> pdb=" O SERLP 144 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SERLP 144 " --> pdb=" O TYRLP 21 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THRLP 151 " --> pdb=" O VALLP 114 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VALLP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'LP' and resid 125 through 131 removed outlier: 3.760A pdb=" N GLNLP 125 " --> pdb=" O SERLP 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LQ' and resid 62 through 63 removed outlier: 3.667A pdb=" N LEULQ 104 " --> pdb=" O VALLQ 83 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLYLQ 85 " --> pdb=" O LEULQ 104 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHELQ 106 " --> pdb=" O GLYLQ 85 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VALLQ 87 " --> pdb=" O PHELQ 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VALLQ 101 " --> pdb=" O ILELQ 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LQ' and resid 62 through 63 Processing sheet with id=AE5, first strand: chain 'LR' and resid 23 through 24 removed outlier: 3.585A pdb=" N VALLR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LS' and resid 56 through 63 removed outlier: 5.211A pdb=" N ILELS 58 " --> pdb=" O ARGLS 12 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARGLS 12 " --> pdb=" O ILELS 58 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SERLS 60 " --> pdb=" O ILELS 10 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LS' and resid 87 through 96 removed outlier: 3.516A pdb=" N LYSLS 125 " --> pdb=" O TRPLS 78 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARGLS 80 " --> pdb=" O ILELS 123 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILELS 123 " --> pdb=" O ARGLS 80 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASPLS 82 " --> pdb=" O ILELS 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILELS 121 " --> pdb=" O ASPLS 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LT' and resid 83 through 92 removed outlier: 5.987A pdb=" N ILELT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VALLT 64 " --> pdb=" O ILELT 75 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYSLT 97 " --> pdb=" O ASPLT 41 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LU' and resid 54 through 58 Processing sheet with id=AF1, first strand: chain 'LU' and resid 42 through 43 Processing sheet with id=AF2, first strand: chain 'LV' and resid 17 through 18 Processing sheet with id=AF3, first strand: chain 'LV' and resid 22 through 25 removed outlier: 6.498A pdb=" N METLV 59 " --> pdb=" O ILELV 37 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VALLV 39 " --> pdb=" O METLV 57 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N METLV 57 " --> pdb=" O VALLV 39 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALALV 99 " --> pdb=" O VALLV 79 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLYLV 100 " --> pdb=" O ILELV 22 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASNLV 24 " --> pdb=" O GLYLV 100 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILELV 102 " --> pdb=" O ASNLV 24 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LV' and resid 85 through 86 removed outlier: 6.465A pdb=" N PHELV 92 " --> pdb=" O LEULW 20 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VALLW 22 " --> pdb=" O PHELV 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYRLV 94 " --> pdb=" O VALLW 22 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'LW' and resid 4 through 5 Processing sheet with id=AF6, first strand: chain 'LX' and resid 63 through 66 removed outlier: 4.060A pdb=" N GLNLX 65 " --> pdb=" O GLNLX 85 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYSLX 120 " --> pdb=" O VALLX 86 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'LY' and resid 32 through 34 Processing sheet with id=AF8, first strand: chain 'LY' and resid 94 through 99 removed outlier: 10.061A pdb=" N VALLY 95 " --> pdb=" O LYSLY 84 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYSLY 84 " --> pdb=" O VALLY 95 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILELY 97 " --> pdb=" O VALLY 82 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VALLY 82 " --> pdb=" O ILELY 97 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLNLY 81 " --> pdb=" O SERLY 71 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYSLY 69 " --> pdb=" O ASPLY 83 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VALLY 85 " --> pdb=" O GLULY 67 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N GLULY 67 " --> pdb=" O VALLY 85 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLULY 55 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'LZ' and resid 69 through 72 removed outlier: 6.555A pdb=" N LYSLZ 69 " --> pdb=" O GLULZ 47 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILELZ 46 " --> pdb=" O LYSLZ 22 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VALLZ 10 " --> pdb=" O THRLZ 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'LZ' and resid 28 through 29 Processing sheet with id=AG2, first strand: chain 'La' and resid 72 through 74 removed outlier: 5.963A pdb=" N LEULa 73 " --> pdb=" O LEULa 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'La' and resid 101 through 103 removed outlier: 6.479A pdb=" N VALLa 125 " --> pdb=" O GLULa 146 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Lc' and resid 22 through 25 removed outlier: 7.086A pdb=" N THRLc 24 " --> pdb=" O ILELc 92 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILELc 92 " --> pdb=" O THRLc 24 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEULc 41 " --> pdb=" O ILELc 92 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILELc 42 " --> pdb=" O TYRLc 68 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Ld' and resid 49 through 51 Processing sheet with id=AG6, first strand: chain 'Le' and resid 72 through 76 Processing sheet with id=AG7, first strand: chain 'Lf' and resid 8 through 18 removed outlier: 9.867A pdb=" N VALLf 9 " --> pdb=" O ILELf 32 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILELf 32 " --> pdb=" O VALLf 9 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLYLf 11 " --> pdb=" O ILELf 30 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILELf 30 " --> pdb=" O GLYLf 11 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N HISLf 13 " --> pdb=" O SERLf 28 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N SERLf 28 " --> pdb=" O HISLf 13 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N SERLf 15 " --> pdb=" O ASNLf 26 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASNLf 26 " --> pdb=" O SERLf 15 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLNLf 17 " --> pdb=" O ASNLf 24 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASNLf 26 " --> pdb=" O PHELf 85 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHELf 85 " --> pdb=" O ASNLf 26 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARGLf 73 " --> pdb=" O ARGLf 82 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THRLf 84 " --> pdb=" O VALLf 71 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VALLf 71 " --> pdb=" O THRLf 84 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARGLf 48 " --> pdb=" O PHELf 101 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VALLf 52 " --> pdb=" O SERLf 97 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SERLf 97 " --> pdb=" O VALLf 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AG9, first strand: chain 'Lj' and resid 16 through 17 removed outlier: 3.606A pdb=" N THRLj 33 " --> pdb=" O HISLj 28 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.425A pdb=" N VALLk 55 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THRLk 22 " --> pdb=" O ARGLk 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AH3, first strand: chain 'Lo' and resid 7 through 12 removed outlier: 4.415A pdb=" N VALLo 68 " --> pdb=" O LEULo 85 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Lp' and resid 37 through 38 removed outlier: 6.849A pdb=" N ILELp 54 " --> pdb=" O GLYLp 50 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 2 through 6 removed outlier: 3.627A pdb=" N GLY C 61 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU C 48 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 59 " --> pdb=" O GLU C 48 " (cutoff:3.500A) 2887 hydrogen bonds defined for protein. 8130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2814 hydrogen bonds 4468 hydrogen bond angles 0 basepair planarities 1149 basepair parallelities 1743 stacking parallelities Total time for adding SS restraints: 203.22 Time building geometry restraints manager: 64.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27001 1.33 - 1.45: 55999 1.45 - 1.58: 61063 1.58 - 1.70: 7151 1.70 - 1.82: 272 Bond restraints: 151486 Sorted by residual: bond pdb=" O3' C 12094 " pdb=" P G 12095 " ideal model delta sigma weight residual 1.607 1.404 0.203 1.50e-02 4.44e+03 1.83e+02 bond pdb=" O3' U 11950 " pdb=" P C 11951 " ideal model delta sigma weight residual 1.607 1.429 0.178 1.50e-02 4.44e+03 1.41e+02 bond pdb=" N SER D 16 " pdb=" CA SER D 16 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" CZ ARG D 161 " pdb=" NH2 ARG D 161 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.84e+00 bond pdb=" CD2 HIS D 364 " pdb=" NE2 HIS D 364 " ideal model delta sigma weight residual 1.374 1.408 -0.034 1.10e-02 8.26e+03 9.35e+00 ... (remaining 151481 not shown) Histogram of bond angle deviations from ideal: 77.02 - 92.88: 2 92.88 - 108.73: 46678 108.73 - 124.59: 159713 124.59 - 140.45: 15580 140.45 - 156.31: 1 Bond angle restraints: 221974 Sorted by residual: angle pdb=" O3' U 11950 " pdb=" P C 11951 " pdb=" O5' C 11951 " ideal model delta sigma weight residual 104.00 156.31 -52.31 1.50e+00 4.44e-01 1.22e+03 angle pdb=" O3' U 11950 " pdb=" P C 11951 " pdb=" OP2 C 11951 " ideal model delta sigma weight residual 108.00 77.02 30.98 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C3' U 11950 " pdb=" O3' U 11950 " pdb=" P C 11951 " ideal model delta sigma weight residual 120.20 106.03 14.17 1.50e+00 4.44e-01 8.92e+01 angle pdb=" C ARG D 15 " pdb=" N SER D 16 " pdb=" CA SER D 16 " ideal model delta sigma weight residual 121.54 135.67 -14.13 1.91e+00 2.74e-01 5.47e+01 angle pdb=" O3' U 11950 " pdb=" P C 11951 " pdb=" OP1 C 11951 " ideal model delta sigma weight residual 108.00 87.69 20.31 3.00e+00 1.11e-01 4.58e+01 ... (remaining 221969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 80783 35.98 - 71.96: 2394 71.96 - 107.95: 214 107.95 - 143.93: 23 143.93 - 179.91: 53 Dihedral angle restraints: 83467 sinusoidal: 59911 harmonic: 23556 Sorted by residual: dihedral pdb=" CA APROLO 110 " pdb=" C APROLO 110 " pdb=" N APROLO 111 " pdb=" CA APROLO 111 " ideal model delta harmonic sigma weight residual -180.00 -118.24 -61.76 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" C4' U 12501 " pdb=" C3' U 12501 " pdb=" C2' U 12501 " pdb=" C1' U 12501 " ideal model delta sinusoidal sigma weight residual -35.00 31.85 -66.85 1 8.00e+00 1.56e-02 9.10e+01 dihedral pdb=" O4' U 12846 " pdb=" C1' U 12846 " pdb=" N1 U 12846 " pdb=" C2 U 12846 " ideal model delta sinusoidal sigma weight residual 200.00 31.65 168.35 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 83464 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 25795 0.076 - 0.153: 1666 0.153 - 0.229: 162 0.229 - 0.305: 15 0.305 - 0.381: 5 Chirality restraints: 27643 Sorted by residual: chirality pdb=" CA SER D 16 " pdb=" N SER D 16 " pdb=" C SER D 16 " pdb=" CB SER D 16 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB ILELh 118 " pdb=" CA ILELh 118 " pdb=" CG1 ILELh 118 " pdb=" CG2 ILELh 118 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ASPLG 158 " pdb=" N ASPLG 158 " pdb=" C ASPLG 158 " pdb=" CB ASPLG 158 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 27640 not shown) Planarity restraints: 14813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 574 " -0.127 2.00e-02 2.50e+03 6.41e-02 1.03e+02 pdb=" CG TRP D 574 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 574 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 574 " 0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP D 574 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP D 574 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP D 574 " 0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 574 " -0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 574 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 574 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 502 " -0.093 2.00e-02 2.50e+03 7.13e-02 7.63e+01 pdb=" CG HIS D 502 " 0.088 2.00e-02 2.50e+03 pdb=" ND1 HIS D 502 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 HIS D 502 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS D 502 " -0.070 2.00e-02 2.50e+03 pdb=" NE2 HIS D 502 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 56 " -0.103 2.00e-02 2.50e+03 5.74e-02 6.60e+01 pdb=" CG TYR D 56 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 56 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR D 56 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 56 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR D 56 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 56 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 56 " -0.090 2.00e-02 2.50e+03 ... (remaining 14810 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 14 1.79 - 2.57: 1816 2.57 - 3.35: 176882 3.35 - 4.12: 440853 4.12 - 4.90: 656867 Nonbonded interactions: 1276432 Sorted by model distance: nonbonded pdb=" CE MET C 1 " pdb=" O ILE D 333 " model vdw 1.017 3.460 nonbonded pdb=" CB ILELR 143 " pdb=" OP2 A 12093 " model vdw 1.236 3.470 nonbonded pdb=" O2' U 11763 " pdb=" CE1 PHE D 105 " model vdw 1.359 3.340 nonbonded pdb=" O MET C 49 " pdb=" CD1 ILE D 333 " model vdw 1.400 3.460 nonbonded pdb=" CZ PHE D 18 " pdb=" CB GLN D 49 " model vdw 1.431 3.740 ... (remaining 1276427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.720 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: 0.170 Extract box with map and model: 18.260 Check model and map are aligned: 1.540 Set scattering table: 0.990 Process input model: 485.890 Find NCS groups from input model: 3.410 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 518.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 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 : 0.005 0.203 151486 Z= 0.285 Angle : 0.687 52.305 221974 Z= 0.401 Chirality : 0.039 0.381 27643 Planarity : 0.006 0.098 14813 Dihedral : 15.157 179.910 68255 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.35 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 7994 helix: 0.66 (0.09), residues: 3202 sheet: -0.34 (0.17), residues: 888 loop : -0.63 (0.10), residues: 3904 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2460 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2449 time to evaluate : 7.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash 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: 11 outliers final: 2 residues processed: 2456 average time/residue: 1.4072 time to fit residues: 5929.8636 Evaluate side-chains 1397 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1395 time to evaluate : 7.300 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 1.0657 time to fit residues: 12.8681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 966 optimal weight: 20.0000 chunk 867 optimal weight: 20.0000 chunk 481 optimal weight: 8.9990 chunk 296 optimal weight: 20.0000 chunk 584 optimal weight: 30.0000 chunk 463 optimal weight: 8.9990 chunk 896 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 545 optimal weight: 6.9990 chunk 667 optimal weight: 0.6980 chunk 1038 optimal weight: 20.0000 overall best weight: 6.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: