Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 29 00:08:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bip_16086/04_2023/8bip_16086.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bip_16086/04_2023/8bip_16086.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bip_16086/04_2023/8bip_16086.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bip_16086/04_2023/8bip_16086.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bip_16086/04_2023/8bip_16086.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bip_16086/04_2023/8bip_16086.pdb" } resolution = 3.1 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= 0.011 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 137 5.16 5 C 70712 2.51 5 N 24610 2.21 5 O 35142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "LB GLU 7": "OE1" <-> "OE2" Residue "LB PHE 321": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LD PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LE GLU 59": "OE1" <-> "OE2" Residue "LE GLU 136": "OE1" <-> "OE2" Residue "LG GLU 161": "OE1" <-> "OE2" Residue "LG GLU 208": "OE1" <-> "OE2" Residue "LH GLU 105": "OE1" <-> "OE2" Residue "LJ GLU 81": "OE1" <-> "OE2" Residue "LN GLU 8": "OE1" <-> "OE2" Residue "LQ PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LT GLU 86": "OE1" <-> "OE2" Residue "LT GLU 94": "OE1" <-> "OE2" Residue "LT GLU 104": "OE1" <-> "OE2" Residue "LT GLU 107": "OE1" <-> "OE2" Residue "LU GLU 44": "OE1" <-> "OE2" Residue "LU GLU 58": "OE1" <-> "OE2" Residue "LV GLU 68": "OE1" <-> "OE2" Residue "LV GLU 121": "OE1" <-> "OE2" Residue "LY GLU 67": "OE1" <-> "OE2" Residue "LY GLU 88": "OE1" <-> "OE2" Residue "LZ PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LZ GLU 99": "OE1" <-> "OE2" Residue "LZ GLU 119": "OE1" <-> "OE2" Residue "LZ GLU 120": "OE1" <-> "OE2" Residue "Lc GLU 55": "OE1" <-> "OE2" Residue "Ld ASP 6": "OD1" <-> "OD2" Residue "Ld GLU 54": "OE1" <-> "OE2" Residue "Ld GLU 94": "OE1" <-> "OE2" Residue "Le GLU 30": "OE1" <-> "OE2" Residue "Le GLU 83": "OE1" <-> "OE2" Residue "Lg TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Lg GLU 97": "OE1" <-> "OE2" Residue "Lh GLU 96": "OE1" <-> "OE2" Residue "Li GLU 66": "OE1" <-> "OE2" Residue "Li GLU 89": "OE1" <-> "OE2" Residue "Lo GLU 96": "OE1" <-> "OE2" Residue "B PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 134392 Number of models: 1 Model: "" Number of chains: 62 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: 3 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': 332, 'rna2p_pyr': 219, 'rna3p_pur': 1484, 'rna3p_pyr': 1266} Link IDs: {'rna2p': 551, 'rna3p': 2749} Chain breaks: 3 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: "8" Number of atoms: 115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 115 Classifications: {'peptide': 23} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 22} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 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: "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: 196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 196 Unusual residues: {' MG': 196} Classifications: {'undetermined': 196} Link IDs: {None: 195} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 49185 SG CYSLg 44 86.731 174.663 75.599 1.00108.78 S ATOM 49203 SG CYSLg 47 88.971 173.407 73.238 1.00110.43 S ATOM 49475 SG CYSLg 84 84.948 173.074 72.406 1.00109.92 S ATOM 51586 SG CYSLj 19 93.107 164.099 132.090 1.00 96.49 S ATOM 51611 SG CYSLj 22 94.904 162.878 135.134 1.00 97.16 S ATOM 51711 SG CYSLj 34 93.942 160.412 132.391 1.00 92.62 S ATOM 51729 SG CYSLj 37 91.178 161.986 134.469 1.00 92.25 S ATOM 53318 SG CYSLm 96 168.116 75.521 132.045 1.00121.10 S ATOM 53344 SG CYSLm 99 169.291 79.024 132.326 1.00117.70 S ATOM 53431 SG CYSLm 110 171.312 76.332 133.933 1.00120.37 S ATOM 53477 SG CYSLm 115 168.114 77.249 135.580 1.00116.99 S ATOM 53904 SG CYSLo 12 58.261 77.272 152.868 1.00132.82 S ATOM 53939 SG CYSLo 17 55.394 75.212 154.310 1.00136.59 S ATOM 54403 SG CYSLo 74 56.006 75.474 150.444 1.00132.36 S ATOM 54425 SG CYSLo 77 54.644 78.340 152.433 1.00139.00 S ATOM 54948 SG CYSLp 39 89.758 158.033 64.890 1.00111.88 S ATOM 54971 SG CYSLp 42 90.933 159.721 63.646 1.00112.16 S ATOM 55080 SG CYSLp 57 92.074 158.801 66.307 1.00113.90 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: 49.20, per 1000 atoms: 0.37 Number of scatterers: 134392 At special positions: 0 Unit cell: (237.215, 277.97, 248.71, 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 137 16.00 P 3580 15.00 Mg 206 11.99 O 35142 8.00 N 24610 7.00 C 70712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.96 Conformation dependent library (CDL) restraints added in 6.5 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 44 " 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 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 74 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 17 " pdb=" ZNLp 501 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 42 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 57 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 39 " Number of angles added : 18 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13580 Finding SS restraints... Secondary structure from input PDB file: 289 helices and 67 sheets defined 43.4% alpha, 13.5% beta 1154 base pairs and 1735 stacking pairs defined. Time for finding SS restraints: 38.74 Creating SS restraints... 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: 3.817A pdb=" N VALLA 107 " --> pdb=" O LEULA 104 " (cutoff:3.500A) Processing helix chain 'LA' and resid 173 through 177 removed outlier: 3.671A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Processing helix chain 'LA' and resid 181 through 191 removed outlier: 3.939A 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: 3.755A pdb=" N LEULB 17 " --> pdb=" O LEULB 14 " (cutoff:3.500A) Processing helix chain 'LB' and resid 111 through 116 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: 3.953A 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) removed outlier: 3.584A pdb=" N TYRLB 154 " --> pdb=" O ARGLB 150 " (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 44 through 46 No H-bonds generated for 'chain 'LC' and resid 44 through 46' Processing helix chain 'LC' and resid 114 through 130 removed outlier: 4.212A 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: 4.238A pdb=" N LYSLC 193 " --> pdb=" O GLYLC 190 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 221 removed outlier: 4.425A 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: 4.545A pdb=" N ASPLC 259 " --> pdb=" O PHELC 255 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLNLC 260 " --> pdb=" O THRLC 256 " (cutoff:3.500A) Processing helix chain 'LC' and resid 285 through 291 removed outlier: 3.560A pdb=" N ILELC 289 " --> pdb=" O ASPLC 285 " (cutoff:3.500A) Processing helix chain 'LC' and resid 293 through 299 removed outlier: 3.753A pdb=" N ALALC 298 " --> pdb=" O GLULC 294 " (cutoff:3.500A) Processing helix chain 'LC' and resid 320 through 328 removed outlier: 3.528A pdb=" N LEULC 324 " --> pdb=" O ASNLC 320 " (cutoff:3.500A) Processing helix chain 'LC' and resid 329 through 337 removed outlier: 4.343A pdb=" N VALLC 333 " --> pdb=" O PROLC 329 " (cutoff:3.500A) Processing helix chain 'LC' and resid 338 through 342 removed outlier: 3.683A pdb=" N LYSLC 342 " --> pdb=" O LEULC 339 " (cutoff:3.500A) Processing helix chain 'LC' and resid 352 through 361 Processing helix chain 'LD' and resid 9 through 15 Processing helix chain 'LD' and resid 21 through 26 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 4.233A 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 removed outlier: 3.551A pdb=" N ALALD 162 " --> pdb=" O ARGLD 158 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEULD 163 " --> pdb=" O VALLD 159 " (cutoff:3.500A) Processing helix chain 'LD' and resid 191 through 200 Processing helix chain 'LD' and resid 201 through 215 removed outlier: 3.904A 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 Processing helix chain 'LD' and resid 232 through 250 removed outlier: 4.181A pdb=" N GLULD 237 " --> pdb=" O ALALD 233 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ASPLD 238 " --> pdb=" O ASPLD 234 " (cutoff:3.500A) Processing helix chain 'LD' and resid 261 through 273 removed outlier: 3.515A 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: 3.635A pdb=" N LYSLE 143 " --> pdb=" O LYSLE 139 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ALALE 147 " --> pdb=" O LYSLE 143 " (cutoff:3.500A) removed outlier: 4.235A 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: 3.894A pdb=" N GLULF 125 " --> pdb=" O LYSLF 121 " (cutoff:3.500A) removed outlier: 4.436A 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: 4.225A 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 Processing helix chain 'LG' and resid 46 through 50 removed outlier: 3.579A pdb=" N VALLG 50 " --> pdb=" O SERLG 47 " (cutoff:3.500A) Processing helix chain 'LG' and resid 53 through 69 removed outlier: 4.068A pdb=" N LYSLG 63 " --> pdb=" O GLNLG 59 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILELG 67 " --> pdb=" O LYSLG 63 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEULG 69 " --> pdb=" O LEULG 65 " (cutoff:3.500A) Processing helix chain 'LG' and resid 83 through 96 removed outlier: 3.840A 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 removed outlier: 3.518A pdb=" N ALALG 141 " --> pdb=" O ASNLG 137 " (cutoff:3.500A) 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: 3.927A pdb=" N ALALG 220 " --> pdb=" O SERLG 216 " (cutoff:3.500A) removed outlier: 3.696A 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: 4.318A pdb=" N LYSLG 245 " --> pdb=" O LYSLG 241 " (cutoff:3.500A) Processing helix chain 'LH' and resid 61 through 84 removed outlier: 3.568A pdb=" N LEULH 68 " --> pdb=" O HISLH 64 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARGLH 69 " --> pdb=" O VALLH 65 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THRLH 70 " --> pdb=" O ALALH 66 " (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: 3.943A pdb=" N ARGLI 10 " --> pdb=" O ARGLI 7 " (cutoff:3.500A) Processing helix chain 'LI' and resid 62 through 80 removed outlier: 3.675A pdb=" N TYRLI 75 " --> pdb=" O CYSLI 71 " (cutoff:3.500A) Processing helix chain 'LI' and resid 107 through 111 Processing helix chain 'LI' and resid 141 through 143 No H-bonds generated for 'chain 'LI' and resid 141 through 143' Processing helix chain 'LI' and resid 144 through 157 removed outlier: 4.064A pdb=" N TYRLI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 177 through 186 Processing helix chain 'LI' and resid 205 through 212 removed outlier: 3.506A pdb=" N GLULI 212 " --> pdb=" O ASNLI 208 " (cutoff:3.500A) Processing helix chain 'LI' and resid 213 through 218 removed outlier: 3.963A pdb=" N PHELI 217 " --> pdb=" O PHELI 213 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 27 through 41 removed outlier: 3.514A pdb=" N VALLJ 36 " --> pdb=" O ARGLJ 32 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEULJ 37 " --> pdb=" O ALALJ 33 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLULJ 38 " --> pdb=" O SERLJ 34 " (cutoff:3.500A) 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 108 through 112 removed outlier: 3.503A pdb=" N ASPLJ 111 " --> pdb=" O GLULJ 108 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEULJ 112 " --> pdb=" O HISLJ 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'LJ' and resid 108 through 112' Processing helix chain 'LJ' and resid 135 through 140 removed outlier: 3.756A 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: 3.989A 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 76 through 84 removed outlier: 3.717A pdb=" N VALLL 80 " --> pdb=" O THRLL 76 " (cutoff:3.500A) Processing helix chain 'LL' and resid 86 through 92 removed outlier: 3.513A pdb=" N THRLL 92 " --> pdb=" O ALALL 88 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 123 removed outlier: 3.558A pdb=" N ALALL 111 " --> pdb=" O GLULL 107 " (cutoff:3.500A) Processing helix chain 'LL' and resid 140 through 145 removed outlier: 3.540A 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: 4.016A pdb=" N GLULL 192 " --> pdb=" O ARGLL 188 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 89 Processing helix chain 'LM' and resid 90 through 96 Processing helix chain 'LM' and resid 97 through 112 removed outlier: 3.688A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 115 through 135 removed outlier: 3.720A pdb=" N GLNLM 119 " --> pdb=" O PHELM 115 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N METLM 121 " --> pdb=" O ARGLM 117 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N THRLM 130 " --> pdb=" O GLNLM 126 " (cutoff:3.500A) Processing helix chain 'LN' and resid 3 through 12 removed outlier: 3.516A pdb=" N ARGLN 12 " --> pdb=" O GLULN 8 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 33 removed outlier: 3.638A 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 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 removed outlier: 3.504A pdb=" N PHELN 180 " --> pdb=" O GLYLN 177 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASNLN 181 " --> pdb=" O HISLN 178 " (cutoff:3.500A) No H-bonds generated for '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: 4.027A pdb=" N ALYSLO 60 " --> pdb=" O AASPLO 56 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 69 removed outlier: 3.597A 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 145 Processing helix chain 'LO' and resid 149 through 186 removed outlier: 3.918A pdb=" N AGLULO 166 " --> pdb=" O AVALLO 162 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ATYRLO 167 " --> pdb=" O ASERLO 163 " (cutoff:3.500A) Processing helix chain 'LO' and resid 188 through 198 removed outlier: 3.511A pdb=" N AGLNLO 193 " --> pdb=" O AASPLO 189 " (cutoff:3.500A) 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: 3.532A pdb=" N GLYLP 73 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 3.933A 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 40 removed outlier: 3.592A pdb=" N PHELQ 35 " --> pdb=" O LYSLQ 31 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARGLQ 38 " --> pdb=" O THRLQ 34 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 42 through 54 removed outlier: 3.828A pdb=" N LYSLQ 46 " --> pdb=" O ALALQ 42 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHELQ 53 " --> pdb=" O LEULQ 49 " (cutoff:3.500A) removed outlier: 3.755A 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 removed outlier: 3.593A pdb=" N GLNLR 34 " --> pdb=" O SERLR 30 " (cutoff:3.500A) Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 73 Processing helix chain 'LR' and resid 77 through 81 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 128 Processing helix chain 'LR' and resid 134 through 172 Processing helix chain 'LS' and resid 33 through 47 removed outlier: 3.514A pdb=" N LYSLS 47 " --> pdb=" O TYRLS 43 " (cutoff:3.500A) 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: 3.845A pdb=" N GLNLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALALT 121 " --> pdb=" O ALALT 117 " (cutoff:3.500A) Processing helix chain 'LU' and resid 19 through 24 removed outlier: 3.538A pdb=" N THRLU 23 " --> pdb=" O VALLU 19 " (cutoff:3.500A) removed outlier: 3.982A 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 removed outlier: 3.507A pdb=" N ILELU 38 " --> pdb=" O ALALU 34 " (cutoff:3.500A) Processing helix chain 'LU' and resid 72 through 87 Processing helix chain 'LV' and resid 66 through 70 Processing helix chain 'LV' and resid 119 through 126 Processing helix chain 'LV' and resid 126 through 133 removed outlier: 3.546A pdb=" N ASNLV 132 " --> pdb=" O ARGLV 128 " (cutoff:3.500A) 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 78 Processing helix chain 'LX' and resid 91 through 103 Processing helix chain 'LX' and resid 131 through 140 Processing helix chain 'LY' and resid 11 through 21 Processing helix chain 'LY' and resid 23 through 31 removed outlier: 3.784A 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 123 Processing helix chain 'LZ' and resid 60 through 66 Processing helix chain 'LZ' and resid 103 through 105 No H-bonds generated for 'chain 'LZ' and resid 103 through 105' Processing helix chain 'LZ' and resid 106 through 124 Processing helix chain 'LZ' and resid 127 through 132 Processing helix chain 'La' and resid 2 through 5 Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.900A 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: 3.924A pdb=" N ASPLa 88 " --> pdb=" O GLULa 84 " (cutoff:3.500A) removed outlier: 4.473A 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: 4.095A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 59 removed outlier: 3.675A 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 removed outlier: 3.602A pdb=" N GLULc 57 " --> pdb=" O LYSLc 53 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 73 through 81 Processing helix chain 'Ld' and resid 17 through 19 No H-bonds generated for 'chain 'Ld' and resid 17 through 19' 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 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 removed outlier: 3.559A pdb=" N VALLe 107 " --> pdb=" O LYSLe 103 " (cutoff:3.500A) 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 64 Processing helix chain 'Lg' and resid 67 through 71 Processing helix chain 'Lg' and resid 81 through 113 removed outlier: 3.542A pdb=" N ILELg 100 " --> pdb=" O GLULg 96 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N LYSLg 113 " --> pdb=" O THRLg 109 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.835A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 36 removed outlier: 3.657A pdb=" N GLULh 27 " --> pdb=" O ASPLh 23 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEULh 28 " --> pdb=" O LEULh 24 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LEULh 36 " --> pdb=" O LYSLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 42 through 70 removed outlier: 4.350A pdb=" N THRLh 46 " --> pdb=" O PROLh 42 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VALLh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 77 through 81 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: 4.609A pdb=" N ARGLi 68 " --> pdb=" O SERLi 64 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ALALi 69 " --> pdb=" O GLYLi 65 " (cutoff:3.500A) Processing helix chain 'Li' and resid 79 through 100 removed outlier: 3.709A pdb=" N VALLi 87 " --> pdb=" O ALALi 83 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLULi 88 " --> pdb=" O LYSLi 84 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLULi 89 " --> pdb=" O ALALi 85 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 4 through 9 removed outlier: 3.610A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 removed outlier: 3.562A pdb=" N HISLj 57 " --> pdb=" O ALALj 53 " (cutoff:3.500A) 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 removed outlier: 3.582A pdb=" N SERLk 68 " --> pdb=" O LYSLk 64 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 6 through 20 removed outlier: 3.626A pdb=" N LYSLl 15 " --> pdb=" O GLNLl 11 " (cutoff:3.500A) Processing helix chain 'Ll' and resid 24 through 28 Processing helix chain 'Lm' and resid 80 through 91 removed outlier: 3.559A pdb=" N ALALm 84 " --> pdb=" O PROLm 80 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEULm 85 " --> pdb=" O SERLm 81 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Ln' and resid 2 through 24 removed outlier: 4.184A 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: 3.768A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.926A pdb=" N GLNLp 32 " --> pdb=" O LYSLp 28 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 92 removed outlier: 3.808A pdb=" N ALALp 92 " --> pdb=" O GLULp 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 28 through 39 removed outlier: 3.697A pdb=" N PHE A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 4.107A 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 74 removed outlier: 3.564A pdb=" N TRP A 74 " --> pdb=" O THR A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 88 removed outlier: 3.673A pdb=" N ARG A 88 " --> pdb=" O PRO A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.620A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) 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: 3.584A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 32 removed outlier: 3.812A pdb=" N TYR B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ALA B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.807A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) 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: 3.535A pdb=" N VAL B 97 " --> pdb=" O GLU B 93 " (cutoff:3.500A) removed outlier: 4.435A 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: 3.572A pdb=" N SER B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 144 through 163 removed outlier: 3.826A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 185 removed outlier: 3.771A 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 244 Processing helix chain 'B' and resid 245 through 259 Processing helix chain 'B' and resid 263 through 277 Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.922A pdb=" N LEU B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.116A pdb=" N LYS B 324 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.726A pdb=" N TYR B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 354 Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 385 through 391 removed outlier: 4.273A pdb=" N GLU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LYS B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 398 through 412 removed outlier: 4.297A pdb=" N PHE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 removed outlier: 3.512A pdb=" N ASN B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 453 removed outlier: 3.791A pdb=" N TRP B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 466 removed outlier: 3.563A pdb=" N HIS B 461 " --> pdb=" O ASP B 457 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE B 463 " --> pdb=" O TYR B 459 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ASN B 464 " --> pdb=" O PHE B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 476 removed outlier: 4.169A pdb=" N ASP B 473 " --> pdb=" O ASN B 469 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 479 No H-bonds generated for 'chain 'B' and resid 477 through 479' Processing helix chain 'B' and resid 482 through 486 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 512 through 523 removed outlier: 3.731A pdb=" N TYR B 516 " --> pdb=" O ASN B 512 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL B 519 " --> pdb=" O ARG B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 541 removed outlier: 3.552A pdb=" N ILE B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N GLY B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ARG B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS B 541 " --> pdb=" O ASP B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 559 removed outlier: 3.730A pdb=" N THR B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 579 Processing helix chain 'B' and resid 597 through 603 removed outlier: 4.121A pdb=" N ASN B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 5.166A pdb=" N TYR B 610 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 634 removed outlier: 3.563A pdb=" N GLU B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Proline residue: B 632 - end of helix Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.605A pdb=" N ASN B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 677 removed outlier: 3.595A pdb=" N PHE B 671 " --> pdb=" O SER B 667 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 672 " --> pdb=" O PHE B 668 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE B 674 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 698 Processing helix chain 'B' and resid 699 through 719 removed outlier: 4.294A pdb=" N SER B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 762 removed outlier: 3.732A pdb=" N LYS B 732 " --> pdb=" O GLN B 728 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU B 737 " --> pdb=" O ASN B 733 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 742 " --> pdb=" O LEU B 738 " (cutoff:3.500A) removed outlier: 5.000A pdb=" N ASP B 743 " --> pdb=" O ARG B 739 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASP B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N PHE B 746 " --> pdb=" O CYS B 742 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA B 756 " --> pdb=" O ALA B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 773 Processing helix chain 'B' and resid 778 through 796 removed outlier: 4.688A pdb=" N ILE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN B 795 " --> pdb=" O LYS B 791 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LEU B 796 " --> pdb=" O SER B 792 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'LA' and resid 73 through 77 removed outlier: 3.640A pdb=" N GLNLA 47 " --> pdb=" O LYSLA 60 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N VALLA 62 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N VALLA 45 " --> pdb=" O VALLA 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LA' and resid 155 through 159 removed outlier: 6.765A pdb=" N LYSLA 145 " --> pdb=" O HISLA 139 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N HISLA 139 " --> pdb=" O LYSLA 145 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N ARGLA 147 " --> pdb=" O ILELA 137 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LA' and resid 224 through 225 Processing sheet with id=AA4, first strand: chain 'LB' and resid 356 through 359 removed outlier: 6.887A pdb=" N VALLB 57 " --> pdb=" O LYSLB 357 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ILELB 359 " --> pdb=" O THRLB 55 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N THRLB 55 " --> pdb=" O ILELB 359 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILELB 335 " --> pdb=" O VALLB 220 " (cutoff:3.500A) removed outlier: 5.085A pdb=" N VALLB 220 " --> pdb=" O ILELB 335 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILELB 215 " --> pdb=" O ASNLB 279 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASNLB 279 " --> pdb=" O ILELB 215 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LYSLB 281 " --> pdb=" O LYSLB 325 " (cutoff:3.500A) removed outlier: 7.313A pdb=" N METLB 323 " --> pdb=" O TYRLB 283 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VALLB 285 " --> pdb=" O PHELB 321 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHELB 321 " --> pdb=" O VALLB 285 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASPLB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N LYSLB 50 " --> pdb=" O ASPLB 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'LB' and resid 100 through 105 removed outlier: 7.350A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THRLB 104 " --> pdb=" O VALLB 89 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VALLB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N VALLB 86 " --> pdb=" O HISLB 163 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N HISLB 163 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLYLB 88 " --> pdb=" O LEULB 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LB' and resid 100 through 105 removed outlier: 7.350A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N THRLB 104 " --> pdb=" O VALLB 89 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VALLB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N LYSLB 201 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'LB' and resid 226 through 227 Processing sheet with id=AA8, first strand: chain 'LC' and resid 15 through 20 removed outlier: 4.954A pdb=" N VALLC 8 " --> pdb=" O THRLC 16 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N ASNLC 18 " --> pdb=" O VALLC 6 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VALLC 6 " --> pdb=" O ASNLC 18 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VALLC 151 " --> pdb=" O THRLC 7 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEULC 150 " --> pdb=" O VALLC 248 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VALLC 207 " --> pdb=" O ALALC 228 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'LC' and resid 63 through 64 Processing sheet with id=AB1, first strand: chain 'LC' and resid 186 through 187 Processing sheet with id=AB2, first strand: chain 'LD' and resid 71 through 79 removed outlier: 6.609A pdb=" N ILELD 64 " --> pdb=" O LEULD 75 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ALALD 77 " --> pdb=" O CYSLD 62 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N CYSLD 62 " --> pdb=" O ALALD 77 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N TYRLD 79 " --> pdb=" O ILELD 60 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILELD 60 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'LD' and resid 183 through 184 removed outlier: 3.903A pdb=" N GLULD 189 " --> pdb=" O ASPLD 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LE' and resid 77 through 79 removed outlier: 6.638A pdb=" N THRLE 66 " --> pdb=" O TYRLE 54 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N TYRLE 54 " --> pdb=" O THRLE 66 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THRLE 38 " --> pdb=" O TYRLE 54 " (cutoff:3.500A) removed outlier: 4.840A 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: 4.410A 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: 6.772A pdb=" N VALLG 151 " --> pdb=" O ALALG 178 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N VALLG 180 " --> pdb=" O VALLG 151 " (cutoff:3.500A) removed outlier: 5.672A 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: 3.590A pdb=" N VALLH 55 " --> pdb=" O GLNLH 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALALH 56 " --> pdb=" O THRLH 44 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LH' and resid 32 through 37 removed outlier: 3.691A pdb=" N LYSLH 36 " --> pdb=" O VALLH 25 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VALLH 25 " --> pdb=" O LYSLH 36 " (cutoff:3.500A) removed outlier: 6.176A 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: 6.938A pdb=" N LYSLH 87 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYSLH 184 " --> pdb=" O LYSLH 87 " (cutoff:3.500A) removed outlier: 6.839A 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: 6.344A pdb=" N LEULI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N SERLI 137 " --> pdb=" O VALLI 50 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VALLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ARGLI 139 " --> pdb=" O LEULI 48 " (cutoff:3.500A) removed outlier: 6.877A 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: 3.780A pdb=" N GLULI 58 " --> pdb=" O VALLI 129 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N ILELI 99 " --> pdb=" O PROLI 122 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLYLI 124 " --> pdb=" O LEULI 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LI' and resid 190 through 192 Processing sheet with id=AC8, first strand: chain 'LJ' and resid 46 through 48 removed outlier: 3.690A pdb=" N ALALJ 66 " --> pdb=" O SERLJ 48 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N ILELJ 14 " --> pdb=" O ASNLJ 132 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASNLJ 132 " --> pdb=" O ILELJ 14 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N LYSLJ 16 " --> pdb=" O VALLJ 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'LJ' and resid 90 through 91 Processing sheet with id=AD1, first strand: chain 'LL' and resid 22 through 24 removed outlier: 6.280A pdb=" N LYSLL 23 " --> pdb=" O LEULN 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'LL' and resid 57 through 59 Processing sheet with id=AD3, first strand: chain 'LL' and resid 124 through 125 Processing sheet with id=AD4, first strand: chain 'LL' and resid 156 through 157 removed outlier: 7.444A pdb=" N LYSLa 126 " --> pdb=" O PROLa 100 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILELa 102 " --> pdb=" O LYSLa 126 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VALLa 125 " --> pdb=" O GLULa 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'LM' and resid 53 through 59 removed outlier: 4.636A pdb=" N GLYLM 48 " --> pdb=" O PROLM 54 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N LYSLM 43 " --> pdb=" O ILELM 38 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILELM 38 " --> pdb=" O LYSLM 43 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEULM 45 " --> pdb=" O VALLM 36 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ARGLM 19 " --> pdb=" O ILELM 35 " (cutoff:3.500A) removed outlier: 4.632A 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: 4.415A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYRLN 127 " --> pdb=" O GLNLN 123 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLNLN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VALLN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.595A 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: 5.868A pdb=" N AVALLO 7 " --> pdb=" O AVALLO 34 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N AVALLO 36 " --> pdb=" O AVALLO 7 " (cutoff:3.500A) removed outlier: 6.280A 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: 3.647A 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: 6.594A pdb=" N THRLP 151 " --> pdb=" O VALLP 114 " (cutoff:3.500A) removed outlier: 5.418A 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: 3.981A pdb=" N GLNLP 125 " --> pdb=" O SERLP 141 " (cutoff:3.500A) removed outlier: 3.694A 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: 3.739A pdb=" N LEULQ 104 " --> pdb=" O VALLQ 83 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLYLQ 85 " --> pdb=" O LEULQ 104 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N PHELQ 106 " --> pdb=" O GLYLQ 85 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VALLQ 87 " --> pdb=" O PHELQ 106 " (cutoff:3.500A) removed outlier: 6.287A 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: 3.517A 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: 5.243A pdb=" N ILELS 58 " --> pdb=" O ARGLS 12 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ARGLS 12 " --> pdb=" O ILELS 58 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.546A pdb=" N LYSLS 125 " --> pdb=" O TRPLS 78 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ARGLS 80 " --> pdb=" O ILELS 123 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ILELS 123 " --> pdb=" O ARGLS 80 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASPLS 82 " --> pdb=" O ILELS 121 " (cutoff:3.500A) removed outlier: 6.858A 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: 6.126A pdb=" N ILELT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 6.024A pdb=" N VALLT 64 " --> pdb=" O ILELT 75 " (cutoff:3.500A) removed outlier: 8.588A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) removed outlier: 3.979A 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 'LV' and resid 17 through 18 Processing sheet with id=AF2, first strand: chain 'LV' and resid 22 through 25 removed outlier: 6.565A pdb=" N METLV 59 " --> pdb=" O ILELV 37 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N VALLV 39 " --> pdb=" O METLV 57 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N METLV 57 " --> pdb=" O VALLV 39 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N ALALV 99 " --> pdb=" O VALLV 79 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N GLYLV 100 " --> pdb=" O ILELV 22 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ASNLV 24 " --> pdb=" O GLYLV 100 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N ILELV 102 " --> pdb=" O ASNLV 24 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LV' and resid 85 through 86 removed outlier: 6.319A pdb=" N PHELV 92 " --> pdb=" O LEULW 20 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N VALLW 22 " --> pdb=" O PHELV 92 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N TYRLV 94 " --> pdb=" O VALLW 22 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LV' and resid 117 through 118 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: 4.100A pdb=" N GLNLX 65 " --> pdb=" O GLNLX 85 " (cutoff:3.500A) removed outlier: 3.813A 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: 10.325A pdb=" N VALLY 95 " --> pdb=" O LYSLY 84 " (cutoff:3.500A) removed outlier: 8.660A pdb=" N LYSLY 84 " --> pdb=" O VALLY 95 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILELY 97 " --> pdb=" O VALLY 82 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N VALLY 82 " --> pdb=" O ILELY 97 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLNLY 81 " --> pdb=" O SERLY 71 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LYSLY 69 " --> pdb=" O ASPLY 83 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N VALLY 85 " --> pdb=" O GLULY 67 " (cutoff:3.500A) removed outlier: 9.874A pdb=" N GLULY 67 " --> pdb=" O VALLY 85 " (cutoff:3.500A) removed outlier: 6.456A 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: 6.518A pdb=" N LYSLZ 69 " --> pdb=" O GLULZ 47 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILELZ 46 " --> pdb=" O LYSLZ 22 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 5.089A 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: 5.968A pdb=" N LEULa 73 " --> pdb=" O LEULa 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Lc' and resid 22 through 25 removed outlier: 7.171A pdb=" N THRLc 24 " --> pdb=" O ILELc 92 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILELc 92 " --> pdb=" O THRLc 24 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEULc 41 " --> pdb=" O ILELc 92 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILELc 42 " --> pdb=" O TYRLc 68 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Ld' and resid 49 through 51 Processing sheet with id=AG5, first strand: chain 'Le' and resid 72 through 76 Processing sheet with id=AG6, first strand: chain 'Lf' and resid 8 through 18 removed outlier: 9.902A pdb=" N VALLf 9 " --> pdb=" O ILELf 32 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILELf 32 " --> pdb=" O VALLf 9 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N GLYLf 11 " --> pdb=" O ILELf 30 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N ILELf 30 " --> pdb=" O GLYLf 11 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N HISLf 13 " --> pdb=" O SERLf 28 " (cutoff:3.500A) removed outlier: 9.850A pdb=" N SERLf 28 " --> pdb=" O HISLf 13 " (cutoff:3.500A) removed outlier: 11.462A pdb=" N SERLf 15 " --> pdb=" O ASNLf 26 " (cutoff:3.500A) removed outlier: 8.825A pdb=" N ASNLf 26 " --> pdb=" O SERLf 15 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLNLf 17 " --> pdb=" O ASNLf 24 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N ASNLf 26 " --> pdb=" O PHELf 85 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N PHELf 85 " --> pdb=" O ASNLf 26 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARGLf 73 " --> pdb=" O ARGLf 82 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N THRLf 84 " --> pdb=" O VALLf 71 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VALLf 71 " --> pdb=" O THRLf 84 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ARGLf 48 " --> pdb=" O PHELf 101 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N VALLf 52 " --> pdb=" O SERLf 97 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SERLf 97 " --> pdb=" O VALLf 52 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AG8, first strand: chain 'Lj' and resid 16 through 17 removed outlier: 3.629A pdb=" N THRLj 33 " --> pdb=" O HISLj 28 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'Lk' and resid 3 through 4 removed outlier: 5.018A pdb=" N THRLk 22 " --> pdb=" O ARGLk 46 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AH2, first strand: chain 'Lo' and resid 7 through 11 Processing sheet with id=AH3, first strand: chain 'Lp' and resid 47 through 51 removed outlier: 6.864A pdb=" N ILELp 54 " --> pdb=" O GLYLp 50 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'A' and resid 2 through 6 removed outlier: 7.234A pdb=" N PHE A 44 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N TYR A 62 " --> pdb=" O PHE A 44 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N SER A 46 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 7.444A pdb=" N TYR A 62 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL A 81 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N MET A 64 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N PHE A 117 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N ALA A 80 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 12.866A pdb=" N LYS A 119 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ALA A 164 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N ARG A 139 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ASP A 166 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS A 188 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ARG A 139 " --> pdb=" O CYS A 188 " (cutoff:3.500A) 2382 hydrogen bonds defined for protein. 6657 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2830 hydrogen bonds 4506 hydrogen bond angles 0 basepair planarities 1154 basepair parallelities 1735 stacking parallelities Total time for adding SS restraints: 254.21 Time building geometry restraints manager: 60.66 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: 23789 1.33 - 1.45: 54566 1.45 - 1.57: 58620 1.57 - 1.70: 7155 1.70 - 1.82: 216 Bond restraints: 144346 Sorted by residual: bond pdb=" CA ARGLD 21 " pdb=" C ARGLD 21 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.34e-02 5.57e+03 4.49e+00 bond pdb=" CA SERLD 9 " pdb=" C SERLD 9 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.30e-02 5.92e+03 3.49e+00 bond pdb=" N ARGLD 21 " pdb=" CA ARGLD 21 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.09e+00 bond pdb=" CB PROLJ 118 " pdb=" CG PROLJ 118 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C ARGLD 21 " pdb=" O ARGLD 21 " ideal model delta sigma weight residual 1.235 1.216 0.019 1.26e-02 6.30e+03 2.36e+00 ... (remaining 144341 not shown) Histogram of bond angle deviations from ideal: 95.33 - 103.08: 7050 103.08 - 110.82: 71087 110.82 - 118.57: 57667 118.57 - 126.31: 65115 126.31 - 134.05: 11432 Bond angle restraints: 212351 Sorted by residual: angle pdb=" N GLULC 294 " pdb=" CA GLULC 294 " pdb=" C GLULC 294 " ideal model delta sigma weight residual 112.90 98.87 14.03 1.31e+00 5.83e-01 1.15e+02 angle pdb=" C THRLD 18 " pdb=" N PROLD 19 " pdb=" CA PROLD 19 " ideal model delta sigma weight residual 120.21 129.86 -9.65 9.60e-01 1.09e+00 1.01e+02 angle pdb=" N GLYLD 26 " pdb=" CA GLYLD 26 " pdb=" C GLYLD 26 " ideal model delta sigma weight residual 114.46 105.03 9.43 1.81e+00 3.05e-01 2.71e+01 angle pdb=" N PHELD 20 " pdb=" CA PHELD 20 " pdb=" C PHELD 20 " ideal model delta sigma weight residual 110.97 116.02 -5.05 1.09e+00 8.42e-01 2.14e+01 angle pdb=" C PHELZ 101 " pdb=" N GLULZ 102 " pdb=" CA GLULZ 102 " ideal model delta sigma weight residual 121.54 129.47 -7.93 1.91e+00 2.74e-01 1.72e+01 ... (remaining 212346 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 76503 35.97 - 71.93: 2322 71.93 - 107.90: 216 107.90 - 143.86: 18 143.86 - 179.83: 53 Dihedral angle restraints: 79112 sinusoidal: 58071 harmonic: 21041 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 -121.30 -58.70 0 5.00e+00 4.00e-02 1.38e+02 dihedral pdb=" O4' U 12137 " pdb=" C1' U 12137 " pdb=" N1 U 12137 " pdb=" C2 U 12137 " ideal model delta sinusoidal sigma weight residual 200.00 33.37 166.63 1 1.50e+01 4.44e-03 8.42e+01 dihedral pdb=" O4' UC3 125 " pdb=" C1' UC3 125 " pdb=" N1 UC3 125 " pdb=" C2 UC3 125 " ideal model delta sinusoidal sigma weight residual 200.00 37.58 162.42 1 1.50e+01 4.44e-03 8.33e+01 ... (remaining 79109 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 25342 0.077 - 0.153: 1156 0.153 - 0.230: 71 0.230 - 0.307: 8 0.307 - 0.383: 3 Chirality restraints: 26580 Sorted by residual: chirality pdb=" CA SERLC 293 " pdb=" N SERLC 293 " pdb=" C SERLC 293 " pdb=" CB SERLC 293 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+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 2.13 0.38 2.00e-01 2.50e+01 3.67e+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 2.28 0.37 2.00e-01 2.50e+01 3.36e+00 ... (remaining 26577 not shown) Planarity restraints: 13600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASPLJ 117 " 0.068 5.00e-02 4.00e+02 1.02e-01 1.66e+01 pdb=" N PROLJ 118 " -0.176 5.00e-02 4.00e+02 pdb=" CA PROLJ 118 " 0.053 5.00e-02 4.00e+02 pdb=" CD PROLJ 118 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C APROLO 110 " -0.060 5.00e-02 4.00e+02 9.06e-02 1.31e+01 pdb=" N APROLO 111 " 0.157 5.00e-02 4.00e+02 pdb=" CA APROLO 111 " -0.049 5.00e-02 4.00e+02 pdb=" CD APROLO 111 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' GC3 39 " 0.047 2.00e-02 2.50e+03 1.99e-02 1.19e+01 pdb=" N9 GC3 39 " -0.047 2.00e-02 2.50e+03 pdb=" C8 GC3 39 " -0.005 2.00e-02 2.50e+03 pdb=" N7 GC3 39 " 0.001 2.00e-02 2.50e+03 pdb=" C5 GC3 39 " -0.000 2.00e-02 2.50e+03 pdb=" C6 GC3 39 " 0.006 2.00e-02 2.50e+03 pdb=" O6 GC3 39 " 0.012 2.00e-02 2.50e+03 pdb=" N1 GC3 39 " 0.004 2.00e-02 2.50e+03 pdb=" C2 GC3 39 " -0.003 2.00e-02 2.50e+03 pdb=" N2 GC3 39 " -0.000 2.00e-02 2.50e+03 pdb=" N3 GC3 39 " -0.009 2.00e-02 2.50e+03 pdb=" C4 GC3 39 " -0.007 2.00e-02 2.50e+03 ... (remaining 13597 not shown) Histogram of nonbonded interaction distances: 1.79 - 2.42: 909 2.42 - 3.04: 77164 3.04 - 3.66: 250548 3.66 - 4.28: 371008 4.28 - 4.90: 520456 Nonbonded interactions: 1220085 Sorted by model distance: nonbonded pdb=" O4 U 12875 " pdb=" C UNK 8 23 " model vdw 1.794 3.270 nonbonded pdb=" CD1 ILELC 299 " pdb=" O ARGLQ 39 " model vdw 1.826 3.460 nonbonded pdb=" CB CYSLg 81 " pdb="ZN ZNLg 201 " model vdw 1.896 2.630 nonbonded pdb=" OE1 GLNLj 30 " pdb="MG MG 13409 " model vdw 1.929 2.170 nonbonded pdb=" O6 G 1 644 " pdb="MG MG 13506 " model vdw 1.942 2.170 ... (remaining 1220080 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 3.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 21.150 Check model and map are aligned: 1.430 Set scattering table: 0.860 Process input model: 510.390 Find NCS groups from input model: 2.490 Set up NCS constraints: 0.290 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:2.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 541.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.085 144346 Z= 0.203 Angle : 0.535 14.025 212351 Z= 0.287 Chirality : 0.034 0.383 26580 Planarity : 0.004 0.102 13600 Dihedral : 15.183 179.829 65532 Min Nonbonded Distance : 1.794 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.65 % Favored : 95.28 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.76 % Twisted General : 0.01 % 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: -0.06 (0.10), residues: 7134 helix: 0.81 (0.10), residues: 2611 sheet: -0.22 (0.17), residues: 873 loop : -0.57 (0.10), residues: 3650 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1360 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1353 time to evaluate : 6.851 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 outliers start: 7 outliers final: 3 residues processed: 1359 average time/residue: 1.1579 time to fit residues: 2768.7669 Evaluate side-chains 1129 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1126 time to evaluate : 6.793 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.9231 time to fit residues: 13.3089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 895 optimal weight: 10.0000 chunk 804 optimal weight: 20.0000 chunk 446 optimal weight: 9.9990 chunk 274 optimal weight: 20.0000 chunk 542 optimal weight: 7.9990 chunk 429 optimal weight: 3.9990 chunk 831 optimal weight: 50.0000 chunk 321 optimal weight: 9.9990 chunk 505 optimal weight: 5.9990 chunk 618 optimal weight: 0.7980 chunk 963 optimal weight: 4.9990 overall best weight: 4.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 132 ASN LB 319 ASN ** LC 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 296 GLN ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 97 ASN LF 25 GLN LF 104 GLN LF 225 GLN LG 41 GLN LG 59 GLN LJ 43 GLN LL 28 GLN LL 129 ASN LN 117 ASN LN 123 GLN LO 50 ASN A LQ 126 GLN LX 85 GLN ** LZ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 33 GLN Lg 34 HIS Lg 61 GLN Lh 76 GLN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Ll 11 GLN Lo 22 GLN Lo 47 GLN Lp 32 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 438 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 681 ASN B 698 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.0887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 144346 Z= 0.256 Angle : 0.562 11.097 212351 Z= 0.296 Chirality : 0.036 0.301 26580 Planarity : 0.005 0.094 13600 Dihedral : 14.638 179.607 51010 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.17 % Favored : 94.74 % Rotamer Outliers : 1.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.06 (0.10), residues: 7134 helix: 0.84 (0.10), residues: 2701 sheet: -0.37 (0.17), residues: 921 loop : -0.57 (0.10), residues: 3512 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1325 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1213 time to evaluate : 6.929 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: 112 outliers final: 71 residues processed: 1251 average time/residue: 1.2142 time to fit residues: 2693.3162 Evaluate side-chains 1196 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1125 time to evaluate : 6.837 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 1 residues processed: 71 average time/residue: 1.0376 time to fit residues: 149.5286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 535 optimal weight: 10.0000 chunk 299 optimal weight: 5.9990 chunk 801 optimal weight: 10.0000 chunk 656 optimal weight: 20.0000 chunk 265 optimal weight: 0.6980 chunk 965 optimal weight: 50.0000 chunk 1042 optimal weight: 20.0000 chunk 859 optimal weight: 10.0000 chunk 957 optimal weight: 20.0000 chunk 329 optimal weight: 10.0000 chunk 774 optimal weight: 10.0000 overall best weight: 7.3394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 132 ASN LB 121 ASN LB 243 HIS LB 371 GLN LC 58 HIS ** LC 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 97 ASN LF 104 GLN LG 59 GLN LH 157 ASN ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 50 ASN A LP 54 HIS ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN LY 42 GLN ** LZ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 61 GLN Lh 59 ASN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 67 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 657 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 144346 Z= 0.369 Angle : 0.603 9.140 212351 Z= 0.316 Chirality : 0.038 0.306 26580 Planarity : 0.005 0.099 13600 Dihedral : 14.738 179.733 51010 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.22 (0.10), residues: 7134 helix: 0.74 (0.10), residues: 2724 sheet: -0.48 (0.17), residues: 925 loop : -0.69 (0.10), residues: 3485 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1272 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1154 time to evaluate : 6.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 70 residues processed: 1200 average time/residue: 1.1650 time to fit residues: 2471.3495 Evaluate side-chains 1160 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1090 time to evaluate : 6.844 Switching outliers to nearest non-outliers outliers start: 70 outliers final: 1 residues processed: 70 average time/residue: 1.0067 time to fit residues: 142.5888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 953 optimal weight: 10.0000 chunk 725 optimal weight: 10.0000 chunk 500 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 chunk 460 optimal weight: 8.9990 chunk 648 optimal weight: 30.0000 chunk 968 optimal weight: 40.0000 chunk 1025 optimal weight: 7.9990 chunk 506 optimal weight: 9.9990 chunk 918 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 110 ASN LC 296 GLN LE 97 ASN LG 59 GLN LI 144 ASN LM 27 GLN LO 50 ASN A ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 134 GLN LV 24 ASN ** LZ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 59 ASN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lm 90 ASN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 144346 Z= 0.338 Angle : 0.589 8.887 212351 Z= 0.309 Chirality : 0.038 0.289 26580 Planarity : 0.005 0.099 13600 Dihedral : 14.766 179.529 51010 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.54 % Favored : 94.38 % Rotamer Outliers : 2.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.24 (0.10), residues: 7134 helix: 0.76 (0.10), residues: 2723 sheet: -0.55 (0.16), residues: 923 loop : -0.73 (0.10), residues: 3488 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1149 time to evaluate : 6.951 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: 124 outliers final: 79 residues processed: 1208 average time/residue: 1.2694 time to fit residues: 2727.9410 Evaluate side-chains 1179 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1100 time to evaluate : 6.832 Switching outliers to nearest non-outliers outliers start: 79 outliers final: 1 residues processed: 79 average time/residue: 1.0238 time to fit residues: 162.1903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 854 optimal weight: 10.0000 chunk 582 optimal weight: 0.0870 chunk 14 optimal weight: 10.0000 chunk 763 optimal weight: 10.0000 chunk 423 optimal weight: 2.9990 chunk 875 optimal weight: 40.0000 chunk 708 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 523 optimal weight: 0.9980 chunk 920 optimal weight: 10.0000 chunk 258 optimal weight: 5.9990 overall best weight: 4.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 296 GLN LE 97 ASN LF 225 GLN LG 59 GLN ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 119 GLN LO 50 ASN A LP 28 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN ** LZ 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** La 120 ASN Le 35 GLN Le 104 ASN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 61 GLN Lh 59 ASN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 32 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 364 HIS ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.095 144346 Z= 0.222 Angle : 0.550 15.430 212351 Z= 0.289 Chirality : 0.035 0.289 26580 Planarity : 0.004 0.095 13600 Dihedral : 14.714 179.933 51010 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.06 % Favored : 94.86 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.15 (0.10), residues: 7134 helix: 0.85 (0.10), residues: 2727 sheet: -0.55 (0.16), residues: 924 loop : -0.68 (0.10), residues: 3483 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1304 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1219 time to evaluate : 6.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 85 outliers final: 48 residues processed: 1259 average time/residue: 1.1724 time to fit residues: 2610.1666 Evaluate side-chains 1189 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1141 time to evaluate : 6.371 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 1 residues processed: 48 average time/residue: 0.9672 time to fit residues: 96.1011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 345 optimal weight: 6.9990 chunk 923 optimal weight: 10.0000 chunk 202 optimal weight: 5.9990 chunk 602 optimal weight: 3.9990 chunk 253 optimal weight: 6.9990 chunk 1026 optimal weight: 9.9990 chunk 852 optimal weight: 10.0000 chunk 475 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 538 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN LG 41 GLN LG 59 GLN ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 117 ASN LO 50 ASN A LP 28 ASN ** LP 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 127 GLN LV 24 ASN La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 59 ASN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 32 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 ASN ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.075 144346 Z= 0.275 Angle : 0.565 15.791 212351 Z= 0.297 Chirality : 0.036 0.270 26580 Planarity : 0.004 0.097 13600 Dihedral : 14.711 179.719 51010 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.18 (0.10), residues: 7134 helix: 0.83 (0.10), residues: 2742 sheet: -0.53 (0.16), residues: 930 loop : -0.71 (0.11), residues: 3462 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1265 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1161 time to evaluate : 6.810 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: 104 outliers final: 69 residues processed: 1207 average time/residue: 1.1541 time to fit residues: 2460.4673 Evaluate side-chains 1182 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1113 time to evaluate : 6.855 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 1 residues processed: 69 average time/residue: 0.9730 time to fit residues: 134.7970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 989 optimal weight: 50.0000 chunk 115 optimal weight: 3.9990 chunk 584 optimal weight: 5.9990 chunk 749 optimal weight: 30.0000 chunk 580 optimal weight: 4.9990 chunk 864 optimal weight: 10.0000 chunk 573 optimal weight: 5.9990 chunk 1022 optimal weight: 8.9990 chunk 639 optimal weight: 10.0000 chunk 623 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LB 3 HIS ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 97 ASN LF 225 GLN LG 59 GLN ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 50 ASN A LP 28 ASN LP 137 ASN ** LR 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 112 ASN LT 127 GLN LV 24 ASN La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 59 ASN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Ll 4 GLN ** Ll 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 32 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.071 144346 Z= 0.290 Angle : 0.577 14.193 212351 Z= 0.302 Chirality : 0.037 0.314 26580 Planarity : 0.004 0.097 13600 Dihedral : 14.727 179.622 51010 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.33 % Favored : 94.59 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.19 (0.10), residues: 7134 helix: 0.82 (0.10), residues: 2742 sheet: -0.53 (0.16), residues: 930 loop : -0.73 (0.10), residues: 3462 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1163 time to evaluate : 6.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 46 residues processed: 1195 average time/residue: 1.2006 time to fit residues: 2532.7587 Evaluate side-chains 1159 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1113 time to evaluate : 6.804 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 1 residues processed: 46 average time/residue: 0.9936 time to fit residues: 96.0615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 632 optimal weight: 10.0000 chunk 408 optimal weight: 6.9990 chunk 610 optimal weight: 0.8980 chunk 308 optimal weight: 0.9980 chunk 200 optimal weight: 7.9990 chunk 198 optimal weight: 0.0370 chunk 650 optimal weight: 10.0000 chunk 696 optimal weight: 10.0000 chunk 505 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 803 optimal weight: 20.0000 overall best weight: 2.9862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 97 ASN LF 225 GLN LG 59 GLN LM 27 GLN ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 50 ASN A LP 92 GLN ** LR 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 16 GLN LT 127 GLN LZ 123 GLN La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 59 ASN Lj 76 ASN Ll 4 GLN ** Ll 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 32 GLN ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.051 144346 Z= 0.180 Angle : 0.547 17.221 212351 Z= 0.286 Chirality : 0.035 0.262 26580 Planarity : 0.004 0.094 13600 Dihedral : 14.674 179.975 51010 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.86 % Favored : 95.05 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.12 (0.10), residues: 7134 helix: 0.86 (0.10), residues: 2751 sheet: -0.41 (0.17), residues: 908 loop : -0.68 (0.11), residues: 3475 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1236 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 1189 time to evaluate : 6.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 23 residues processed: 1209 average time/residue: 1.1986 time to fit residues: 2608.5071 Evaluate side-chains 1155 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1132 time to evaluate : 6.805 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 1 residues processed: 23 average time/residue: 0.9978 time to fit residues: 52.0984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 930 optimal weight: 10.0000 chunk 979 optimal weight: 40.0000 chunk 893 optimal weight: 10.0000 chunk 952 optimal weight: 10.0000 chunk 573 optimal weight: 7.9990 chunk 415 optimal weight: 9.9990 chunk 748 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 861 optimal weight: 10.0000 chunk 901 optimal weight: 10.0000 chunk 949 optimal weight: 20.0000 overall best weight: 8.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 296 GLN LE 97 ASN LF 225 GLN LG 41 GLN LH 163 GLN ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 50 ASN A ** LO 55 HIS A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 127 GLN LZ 123 GLN La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 59 ASN Lk 67 GLN Ll 4 GLN ** Ll 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.080 144346 Z= 0.414 Angle : 0.643 16.334 212351 Z= 0.335 Chirality : 0.040 0.338 26580 Planarity : 0.005 0.100 13600 Dihedral : 14.794 178.759 51010 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.94 % Favored : 93.97 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.28 (0.10), residues: 7134 helix: 0.75 (0.10), residues: 2734 sheet: -0.56 (0.17), residues: 904 loop : -0.79 (0.10), residues: 3496 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1175 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1126 time to evaluate : 6.743 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 37 residues processed: 1140 average time/residue: 1.2366 time to fit residues: 2496.3635 Evaluate side-chains 1127 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1090 time to evaluate : 6.904 Switching outliers to nearest non-outliers outliers start: 37 outliers final: 1 residues processed: 37 average time/residue: 1.0842 time to fit residues: 83.7706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 625 optimal weight: 8.9990 chunk 1007 optimal weight: 20.0000 chunk 615 optimal weight: 3.9990 chunk 478 optimal weight: 1.9990 chunk 700 optimal weight: 10.0000 chunk 1057 optimal weight: 2.9990 chunk 972 optimal weight: 20.0000 chunk 841 optimal weight: 10.0000 chunk 87 optimal weight: 9.9990 chunk 650 optimal weight: 10.0000 chunk 516 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LA 132 ASN ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 296 GLN LE 97 ASN LG 59 GLN ** LH 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 50 ASN A ** LR 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 138 GLN LT 49 GLN ** LT 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LW 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.061 144346 Z= 0.222 Angle : 0.573 16.082 212351 Z= 0.300 Chirality : 0.035 0.257 26580 Planarity : 0.004 0.095 13600 Dihedral : 14.730 179.951 51010 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.23 % Favored : 94.69 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.17 (0.10), residues: 7134 helix: 0.85 (0.10), residues: 2730 sheet: -0.50 (0.17), residues: 920 loop : -0.73 (0.11), residues: 3484 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14268 Ramachandran restraints generated. 7134 Oldfield, 0 Emsley, 7134 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1158 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1143 time to evaluate : 6.914 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: 15 outliers final: 9 residues processed: 1149 average time/residue: 1.1876 time to fit residues: 2413.3943 Evaluate side-chains 1137 residues out of total 6125 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1128 time to evaluate : 6.815 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 1 residues processed: 9 average time/residue: 1.0212 time to fit residues: 25.2779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1061 random chunks: chunk 668 optimal weight: 10.0000 chunk 896 optimal weight: 10.0000 chunk 257 optimal weight: 10.0000 chunk 776 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 233 optimal weight: 6.9990 chunk 843 optimal weight: 10.0000 chunk 352 optimal weight: 0.8980 chunk 865 optimal weight: 10.0000 chunk 106 optimal weight: 2.9990 chunk 155 optimal weight: 0.5980 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LB 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 104 GLN LF 225 GLN LG 59 GLN ** LH 163 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 50 ASN A ** LR 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 138 GLN LT 127 GLN ** LV 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LW 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** La 120 ASN Le 35 GLN Lf 77 ASN ** Lf 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lh 59 ASN ** Ll 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 464 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.075627 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.052573 restraints weight = 488230.185| |-----------------------------------------------------------------------------| r_work (start): 0.2883 rms_B_bonded: 2.06 r_work: 0.2777 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.044 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2674 r_free = 0.2674 target_work(ls_wunit_k1) = 0.043 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 144346 Z= 0.240 Angle : 0.572 15.393 212351 Z= 0.300 Chirality : 0.036 0.328 26580 Planarity : 0.004 0.096 13600 Dihedral : 14.703 179.933 51010 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.48 % Favored : 94.44 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.42 % Cis-general : 0.00 % Twisted Proline : 0.38 % 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: -0.16 (0.10), residues: 7134 helix: 0.88 (0.10), residues: 2730 sheet: -0.51 (0.17), residues: 914 loop : -0.73 (0.11), residues: 3490 =============================================================================== Job complete usr+sys time: 40502.93 seconds wall clock time: 705 minutes 41.21 seconds (42341.21 seconds total)