Starting phenix.real_space_refine on Wed Mar 20 02:10:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/03_2024/8bjq_16090.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/03_2024/8bjq_16090.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/03_2024/8bjq_16090.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/03_2024/8bjq_16090.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/03_2024/8bjq_16090.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bjq_16090/03_2024/8bjq_16090.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.011 sd= 0.093 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3580 5.49 5 Mg 206 5.21 5 S 172 5.16 5 C 75216 2.51 5 N 25748 2.21 5 O 36457 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "LE ASP 137": "OD1" <-> "OD2" Residue "D PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 515": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 141384 Number of models: 1 Model: "" Number of chains: 64 Chain: "A" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1612 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 184} Chain: "B" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6536 Classifications: {'peptide': 796} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 776} Chain: "C4" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "C3" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "LA" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 1899 Classifications: {'peptide': 251} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 239} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LB" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 5 Chain: "LC" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "LD" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LE" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1305 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "LF" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "LG" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "LH" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "LI" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "LJ" Number of atoms: 1350 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1350 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "LL" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "LM" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "LN" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "LO" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "LP" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "LQ" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "LR" Number of atoms: 1378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1378 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 168} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "LS" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "LT" Number of atoms: 1276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1276 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 6, 'TRANS': 152} Chain: "LU" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "LV" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "LW" Number of atoms: 538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 538 Classifications: {'peptide': 67} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 64} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "LX" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "LY" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "LZ" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1092 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "La" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1173 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 7, 'TRANS': 140} Chain: "Lb" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "Lc" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Ld" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 880 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Le" Number of atoms: 1017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1017 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Lf" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "Lg" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Lh" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "Li" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Lj" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 670 Classifications: {'peptide': 85} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 82} Chain: "Lk" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Ll" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Lm" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 417 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "Ln" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 229 Classifications: {'peptide': 25} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "Lo" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "Lp" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "1" Number of atoms: 70586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3301, 70586 Classifications: {'RNA': 3301} Modifications used: {'rna2p_pur': 333, 'rna2p_pyr': 219, 'rna3p_pur': 1483, 'rna3p_pyr': 1266} Link IDs: {'rna2p': 552, 'rna3p': 2748} Chain breaks: 3 Chain: "C" Number of atoms: 571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 571 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "D" Number of atoms: 6536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 796, 6536 Classifications: {'peptide': 796} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 776} Chain: "C4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LA" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "LB" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LN" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LP" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LR" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "LV" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "La" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Le" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Lg" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lj" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lm" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lo" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Lp" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 195 Unusual residues: {' MG': 195} Classifications: {'undetermined': 195} Link IDs: {None: 194} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 57351 SG CYSLg 47 89.225 175.502 73.683 1.00117.34 S ATOM 57604 SG CYSLg 81 89.741 178.491 71.910 1.00126.28 S ATOM 57623 SG CYSLg 84 86.214 176.122 72.595 1.00117.22 S ATOM 59734 SG CYSLj 19 92.241 164.192 132.198 1.00104.18 S ATOM 59759 SG CYSLj 22 93.883 162.744 135.248 1.00106.83 S ATOM 59859 SG CYSLj 34 92.791 160.482 132.411 1.00101.40 S ATOM 59877 SG CYSLj 37 90.101 162.158 134.479 1.00100.07 S ATOM 61466 SG CYSLm 96 160.014 70.577 129.691 1.00129.51 S ATOM 61492 SG CYSLm 99 161.593 72.745 130.066 1.00126.38 S ATOM 61579 SG CYSLm 110 162.955 70.888 131.865 1.00128.15 S ATOM 61625 SG CYSLm 115 160.112 71.947 133.874 1.00127.10 S ATOM 62052 SG CYSLo 12 50.210 80.088 149.915 1.00139.72 S ATOM 62087 SG CYSLo 17 46.711 78.622 151.274 1.00145.97 S ATOM 62551 SG CYSLo 74 47.932 78.239 147.404 1.00139.03 S ATOM 62573 SG CYSLo 77 46.960 80.802 149.483 1.00143.74 S ATOM 63096 SG CYSLp 39 88.731 160.303 64.737 1.00116.21 S ATOM 63119 SG CYSLp 42 90.448 161.921 63.329 1.00116.67 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N AVALLO 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 3 " occ=0.50 residue: pdb=" N AGLULO 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLULO 4 " occ=0.50 residue: pdb=" N APROLO 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APROLO 5 " occ=0.50 residue: pdb=" N AVALLO 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 6 " occ=0.50 residue: pdb=" N AVALLO 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 7 " occ=0.50 residue: pdb=" N AVALLO 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVALLO 8 " occ=0.50 residue: pdb=" N AILELO 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILELO 9 " occ=0.50 residue: pdb=" N AASPLO 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASPLO 10 " occ=0.50 residue: pdb=" N AGLYLO 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLYLO 11 " occ=0.50 residue: pdb=" N ALYSLO 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYSLO 12 " occ=0.50 residue: pdb=" N AGLYLO 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLYLO 13 " occ=0.50 residue: pdb=" N AHISLO 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHISLO 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 54.19, per 1000 atoms: 0.38 Number of scatterers: 141384 At special positions: 0 Unit cell: (238.26, 281.105, 246.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 172 16.00 P 3580 15.00 Mg 206 11.99 O 36457 8.00 N 25748 7.00 C 75216 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM A05GP O5' A 12092 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 58.37 Conformation dependent library (CDL) restraints added in 9.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNLg 201 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 47 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 84 " pdb="ZN ZNLg 201 " - pdb=" SG CYSLg 81 " pdb=" ZNLj 101 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 19 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 34 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 37 " pdb="ZN ZNLj 101 " - pdb=" SG CYSLj 22 " pdb=" ZNLm 201 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 96 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 110 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 115 " pdb="ZN ZNLm 201 " - pdb=" SG CYSLm 99 " pdb=" ZNLo 201 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 12 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 17 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 74 " pdb="ZN ZNLo 201 " - pdb=" SG CYSLo 77 " pdb=" ZNLp 501 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 39 " pdb="ZN ZNLp 501 " - pdb=" SG CYSLp 42 " Number of angles added : 18 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15212 Finding SS restraints... Secondary structure from input PDB file: 346 helices and 68 sheets defined 47.4% alpha, 12.4% beta 1149 base pairs and 1743 stacking pairs defined. Time for finding SS restraints: 46.99 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 removed outlier: 3.543A pdb=" N LEU A 12 " --> pdb=" O PRO A 9 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 28 through 39 removed outlier: 3.615A pdb=" N TYR A 35 " --> pdb=" O PHE A 31 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET A 36 " --> pdb=" O TYR A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 70 through 73 Processing helix chain 'A' and resid 85 through 88 Processing helix chain 'A' and resid 91 through 105 Processing helix chain 'A' and resid 122 through 132 removed outlier: 3.600A pdb=" N LEU A 132 " --> pdb=" O LEU A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 Processing helix chain 'A' and resid 182 through 185 Processing helix chain 'A' and resid 189 through 193 Processing helix chain 'B' and resid 2 through 15 removed outlier: 3.625A pdb=" N GLN B 6 " --> pdb=" O SER B 2 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU B 8 " --> pdb=" O LYS B 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 32 removed outlier: 4.170A pdb=" N CYS B 21 " --> pdb=" O ASN B 17 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 22 " --> pdb=" O PHE B 18 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 50 removed outlier: 3.640A pdb=" N LYS B 39 " --> pdb=" O ALA B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 54 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 60 through 65 Processing helix chain 'B' and resid 74 through 88 Processing helix chain 'B' and resid 90 through 105 removed outlier: 3.551A pdb=" N LEU B 95 " --> pdb=" O TYR B 91 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N TYR B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.721A pdb=" N SER B 128 " --> pdb=" O TYR B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 141 Processing helix chain 'B' and resid 144 through 163 removed outlier: 4.017A pdb=" N TYR B 148 " --> pdb=" O PRO B 144 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR B 149 " --> pdb=" O LYS B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 167 Processing helix chain 'B' and resid 168 through 185 removed outlier: 3.594A pdb=" N ILE B 173 " --> pdb=" O ASP B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 206 Processing helix chain 'B' and resid 209 through 224 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'B' and resid 245 through 259 Processing helix chain 'B' and resid 263 through 277 removed outlier: 3.532A pdb=" N LYS B 276 " --> pdb=" O ASP B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 293 Processing helix chain 'B' and resid 295 through 311 removed outlier: 3.799A pdb=" N LEU B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 326 removed outlier: 4.161A pdb=" N LYS B 324 " --> pdb=" O TYR B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 338 removed outlier: 3.728A pdb=" N TYR B 338 " --> pdb=" O ASP B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 342 Processing helix chain 'B' and resid 343 through 354 removed outlier: 3.592A pdb=" N TYR B 354 " --> pdb=" O ILE B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 370 Processing helix chain 'B' and resid 376 through 385 Processing helix chain 'B' and resid 386 through 388 No H-bonds generated for 'chain 'B' and resid 386 through 388' Processing helix chain 'B' and resid 398 through 412 removed outlier: 4.229A pdb=" N PHE B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 435 removed outlier: 3.664A pdb=" N ASN B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 452 removed outlier: 3.618A pdb=" N TRP B 444 " --> pdb=" O ASP B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 463 removed outlier: 3.754A pdb=" N ALA B 458 " --> pdb=" O LEU B 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 466 No H-bonds generated for 'chain 'B' and resid 464 through 466' Processing helix chain 'B' and resid 470 through 476 removed outlier: 3.556A pdb=" N SER B 474 " --> pdb=" O VAL B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 Processing helix chain 'B' and resid 482 through 487 Processing helix chain 'B' and resid 492 through 497 Processing helix chain 'B' and resid 497 through 503 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 508 through 523 Proline residue: B 514 - end of helix removed outlier: 3.647A pdb=" N PHE B 521 " --> pdb=" O ILE B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 542 removed outlier: 3.636A pdb=" N ILE B 529 " --> pdb=" O SER B 525 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU B 530 " --> pdb=" O TYR B 526 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLY B 531 " --> pdb=" O SER B 527 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N MET B 535 " --> pdb=" O GLY B 531 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG B 536 " --> pdb=" O MET B 532 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASP B 537 " --> pdb=" O LEU B 533 " (cutoff:3.500A) Processing helix chain 'B' and resid 542 through 559 removed outlier: 3.568A pdb=" N THR B 549 " --> pdb=" O ARG B 545 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 580 removed outlier: 3.935A pdb=" N THR B 580 " --> pdb=" O SER B 576 " (cutoff:3.500A) Processing helix chain 'B' and resid 590 through 594 removed outlier: 3.829A pdb=" N ILE B 593 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 603 removed outlier: 4.160A pdb=" N ASN B 603 " --> pdb=" O ALA B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 4.903A pdb=" N TYR B 610 " --> pdb=" O ILE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 614 through 631 removed outlier: 3.518A pdb=" N GLU B 629 " --> pdb=" O GLU B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 647 Processing helix chain 'B' and resid 651 through 660 removed outlier: 3.875A pdb=" N LEU B 655 " --> pdb=" O ASN B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 678 removed outlier: 3.549A pdb=" N PHE B 672 " --> pdb=" O PHE B 668 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ILE B 674 " --> pdb=" O ILE B 670 " (cutoff:3.500A) Processing helix chain 'B' and resid 681 through 692 Processing helix chain 'B' and resid 699 through 719 removed outlier: 4.270A pdb=" N SER B 703 " --> pdb=" O ASN B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 724 through 742 Processing helix chain 'B' and resid 743 through 762 removed outlier: 3.560A pdb=" N LEU B 753 " --> pdb=" O TYR B 749 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN B 755 " --> pdb=" O LYS B 751 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 772 Processing helix chain 'B' and resid 778 through 795 removed outlier: 3.966A pdb=" N ILE B 782 " --> pdb=" O ASN B 778 " (cutoff:3.500A) Processing helix chain 'LA' and resid 5 through 10 Processing helix chain 'LA' and resid 33 through 39 Processing helix chain 'LA' and resid 103 through 107 removed outlier: 3.843A pdb=" N VALLA 107 " --> pdb=" O LEULA 104 " (cutoff:3.500A) Processing helix chain 'LA' and resid 173 through 177 removed outlier: 3.702A pdb=" N LYSLA 177 " --> pdb=" O ARGLA 174 " (cutoff:3.500A) Processing helix chain 'LA' and resid 181 through 191 removed outlier: 4.022A pdb=" N LEULA 191 " --> pdb=" O HISLA 187 " (cutoff:3.500A) Processing helix chain 'LA' and resid 200 through 204 Processing helix chain 'LB' and resid 13 through 17 removed outlier: 3.516A pdb=" N PHELB 16 " --> pdb=" O HISLB 13 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEULB 17 " --> pdb=" O LEULB 14 " (cutoff:3.500A) No H-bonds generated for 'chain 'LB' and resid 13 through 17' Processing helix chain 'LB' and resid 111 through 116 removed outlier: 3.521A pdb=" N LYSLB 115 " --> pdb=" O SERLB 111 " (cutoff:3.500A) Processing helix chain 'LB' and resid 117 through 119 No H-bonds generated for 'chain 'LB' and resid 117 through 119' Processing helix chain 'LB' and resid 130 through 135 Processing helix chain 'LB' and resid 141 through 154 removed outlier: 3.873A pdb=" N ARGLB 146 " --> pdb=" O ALALB 142 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLULB 147 " --> pdb=" O GLYLB 143 " (cutoff:3.500A) Processing helix chain 'LB' and resid 165 through 169 Processing helix chain 'LB' and resid 187 through 198 Processing helix chain 'LB' and resid 204 through 208 Processing helix chain 'LB' and resid 228 through 234 Processing helix chain 'LB' and resid 372 through 381 Processing helix chain 'LC' and resid 31 through 43 Processing helix chain 'LC' and resid 114 through 130 removed outlier: 4.271A pdb=" N ALALC 130 " --> pdb=" O ILELC 126 " (cutoff:3.500A) Processing helix chain 'LC' and resid 131 through 138 Processing helix chain 'LC' and resid 154 through 159 Processing helix chain 'LC' and resid 161 through 173 Processing helix chain 'LC' and resid 174 through 184 Processing helix chain 'LC' and resid 190 through 195 removed outlier: 4.183A pdb=" N LYSLC 193 " --> pdb=" O GLYLC 190 " (cutoff:3.500A) Processing helix chain 'LC' and resid 214 through 221 removed outlier: 4.494A pdb=" N ASNLC 221 " --> pdb=" O LYSLC 217 " (cutoff:3.500A) Processing helix chain 'LC' and resid 234 through 239 Processing helix chain 'LC' and resid 240 through 243 Processing helix chain 'LC' and resid 252 through 263 removed outlier: 4.680A pdb=" N ASPLC 259 " --> pdb=" O PHELC 255 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLNLC 260 " --> pdb=" O THRLC 256 " (cutoff:3.500A) Processing helix chain 'LC' and resid 285 through 291 removed outlier: 3.605A pdb=" N ILELC 289 " --> pdb=" O ASPLC 285 " (cutoff:3.500A) Processing helix chain 'LC' and resid 293 through 299 Processing helix chain 'LC' and resid 320 through 328 removed outlier: 3.628A pdb=" N LEULC 324 " --> pdb=" O ASNLC 320 " (cutoff:3.500A) Processing helix chain 'LC' and resid 330 through 338 Processing helix chain 'LC' and resid 339 through 342 removed outlier: 3.686A pdb=" N LYSLC 342 " --> pdb=" O LEULC 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'LC' and resid 339 through 342' Processing helix chain 'LC' and resid 352 through 361 Processing helix chain 'LD' and resid 9 through 16 Processing helix chain 'LD' and resid 29 through 38 removed outlier: 4.312A pdb=" N ARGLD 35 " --> pdb=" O TYRLD 31 " (cutoff:3.500A) Processing helix chain 'LD' and resid 82 through 87 Processing helix chain 'LD' and resid 94 through 113 Processing helix chain 'LD' and resid 158 through 170 Processing helix chain 'LD' and resid 191 through 200 Processing helix chain 'LD' and resid 201 through 215 removed outlier: 4.049A pdb=" N TYRLD 207 " --> pdb=" O HISLD 203 " (cutoff:3.500A) Processing helix chain 'LD' and resid 215 through 222 Processing helix chain 'LD' and resid 223 through 229 removed outlier: 3.525A pdb=" N LEULD 227 " --> pdb=" O PHELD 223 " (cutoff:3.500A) Processing helix chain 'LD' and resid 234 through 250 removed outlier: 4.403A pdb=" N ASPLD 238 " --> pdb=" O ASPLD 234 " (cutoff:3.500A) Processing helix chain 'LD' and resid 261 through 273 removed outlier: 3.774A pdb=" N GLULD 268 " --> pdb=" O GLNLD 264 " (cutoff:3.500A) Processing helix chain 'LD' and resid 278 through 294 Processing helix chain 'LE' and resid 80 through 82 No H-bonds generated for 'chain 'LE' and resid 80 through 82' Processing helix chain 'LE' and resid 131 through 150 removed outlier: 3.736A pdb=" N ALALE 147 " --> pdb=" O LYSLE 143 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLULE 148 " --> pdb=" O ALALE 144 " (cutoff:3.500A) Processing helix chain 'LE' and resid 154 through 161 Processing helix chain 'LF' and resid 27 through 72 Processing helix chain 'LF' and resid 96 through 106 Processing helix chain 'LF' and resid 120 through 130 removed outlier: 4.124A pdb=" N GLULF 125 " --> pdb=" O LYSLF 121 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEULF 126 " --> pdb=" O ALALF 122 " (cutoff:3.500A) Processing helix chain 'LF' and resid 140 through 151 Processing helix chain 'LF' and resid 165 through 174 removed outlier: 4.250A pdb=" N ILELF 169 " --> pdb=" O ASPLF 165 " (cutoff:3.500A) Processing helix chain 'LF' and resid 180 through 190 Processing helix chain 'LF' and resid 194 through 202 Processing helix chain 'LF' and resid 222 through 226 Processing helix chain 'LF' and resid 235 through 244 removed outlier: 3.588A pdb=" N LEULF 239 " --> pdb=" O PHELF 235 " (cutoff:3.500A) Processing helix chain 'LG' and resid 46 through 50 removed outlier: 3.568A pdb=" N VALLG 50 " --> pdb=" O SERLG 47 " (cutoff:3.500A) Processing helix chain 'LG' and resid 53 through 69 removed outlier: 4.107A pdb=" N LYSLG 63 " --> pdb=" O GLNLG 59 " (cutoff:3.500A) Processing helix chain 'LG' and resid 83 through 96 removed outlier: 3.972A pdb=" N LYSLG 96 " --> pdb=" O LYSLG 92 " (cutoff:3.500A) Processing helix chain 'LG' and resid 101 through 119 Processing helix chain 'LG' and resid 135 through 145 Processing helix chain 'LG' and resid 159 through 163 Processing helix chain 'LG' and resid 165 through 174 Processing helix chain 'LG' and resid 182 through 190 Processing helix chain 'LG' and resid 204 through 206 No H-bonds generated for 'chain 'LG' and resid 204 through 206' Processing helix chain 'LG' and resid 207 through 222 removed outlier: 3.907A pdb=" N ALALG 220 " --> pdb=" O SERLG 216 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASNLG 221 " --> pdb=" O THRLG 217 " (cutoff:3.500A) Processing helix chain 'LG' and resid 225 through 230 Processing helix chain 'LG' and resid 239 through 254 removed outlier: 4.219A pdb=" N LYSLG 245 " --> pdb=" O LYSLG 241 " (cutoff:3.500A) Processing helix chain 'LH' and resid 61 through 84 removed outlier: 3.595A pdb=" N LEULH 68 " --> pdb=" O HISLH 64 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ARGLH 69 " --> pdb=" O VALLH 65 " (cutoff:3.500A) Processing helix chain 'LH' and resid 116 through 120 Processing helix chain 'LH' and resid 150 through 164 Processing helix chain 'LI' and resid 5 through 10 removed outlier: 3.926A pdb=" N ARGLI 10 " --> pdb=" O ARGLI 7 " (cutoff:3.500A) Processing helix chain 'LI' and resid 62 through 80 Processing helix chain 'LI' and resid 107 through 111 Processing helix chain 'LI' and resid 144 through 157 removed outlier: 3.595A pdb=" N GLULI 150 " --> pdb=" O ASPLI 146 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TYRLI 157 " --> pdb=" O ARGLI 153 " (cutoff:3.500A) Processing helix chain 'LI' and resid 178 through 187 removed outlier: 3.983A pdb=" N ALALI 187 " --> pdb=" O LYSLI 183 " (cutoff:3.500A) Processing helix chain 'LI' and resid 205 through 212 Processing helix chain 'LI' and resid 213 through 218 removed outlier: 4.107A pdb=" N PHELI 217 " --> pdb=" O PHELI 213 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 27 through 41 Processing helix chain 'LJ' and resid 73 through 87 removed outlier: 3.588A pdb=" N VALLJ 86 " --> pdb=" O ARGLJ 82 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 92 through 96 Processing helix chain 'LJ' and resid 108 through 112 Processing helix chain 'LJ' and resid 135 through 140 removed outlier: 3.720A pdb=" N VALLJ 138 " --> pdb=" O GLYLJ 135 " (cutoff:3.500A) Processing helix chain 'LJ' and resid 149 through 153 Processing helix chain 'LJ' and resid 155 through 166 removed outlier: 3.531A pdb=" N SERLJ 161 " --> pdb=" O GLULJ 157 " (cutoff:3.500A) Processing helix chain 'LL' and resid 17 through 20 Processing helix chain 'LL' and resid 27 through 46 Processing helix chain 'LL' and resid 77 through 84 Processing helix chain 'LL' and resid 86 through 92 removed outlier: 3.502A pdb=" N THRLL 92 " --> pdb=" O ALALL 88 " (cutoff:3.500A) Processing helix chain 'LL' and resid 105 through 122 Processing helix chain 'LL' and resid 140 through 145 removed outlier: 3.556A pdb=" N THRLL 144 " --> pdb=" O SERLL 140 " (cutoff:3.500A) Processing helix chain 'LL' and resid 167 through 179 Processing helix chain 'LL' and resid 179 through 192 removed outlier: 3.801A pdb=" N GLULL 192 " --> pdb=" O ARGLL 188 " (cutoff:3.500A) Processing helix chain 'LM' and resid 77 through 88 Processing helix chain 'LM' and resid 89 through 96 removed outlier: 3.778A pdb=" N LYSLM 93 " --> pdb=" O ALALM 89 " (cutoff:3.500A) Processing helix chain 'LM' and resid 97 through 112 removed outlier: 3.599A pdb=" N LEULM 112 " --> pdb=" O ARGLM 108 " (cutoff:3.500A) Processing helix chain 'LM' and resid 113 through 135 Processing helix chain 'LN' and resid 3 through 12 removed outlier: 3.509A pdb=" N ARGLN 12 " --> pdb=" O GLULN 8 " (cutoff:3.500A) Processing helix chain 'LN' and resid 16 through 33 removed outlier: 3.597A pdb=" N TRPLN 28 " --> pdb=" O ARGLN 24 " (cutoff:3.500A) Processing helix chain 'LN' and resid 44 through 52 Processing helix chain 'LN' and resid 75 through 79 Processing helix chain 'LN' and resid 83 through 87 Processing helix chain 'LN' and resid 97 through 110 Processing helix chain 'LN' and resid 139 through 144 Processing helix chain 'LN' and resid 148 through 157 Proline residue: LN 154 - end of helix removed outlier: 3.561A pdb=" N LYSLN 157 " --> pdb=" O PROLN 154 " (cutoff:3.500A) Processing helix chain 'LN' and resid 158 through 163 Processing helix chain 'LN' and resid 165 through 173 Processing helix chain 'LN' and resid 177 through 181 Processing helix chain 'LN' and resid 186 through 195 Processing helix chain 'LO' and resid 15 through 29 Processing helix chain 'LO' and resid 37 through 40 Processing helix chain 'LO' and resid 46 through 60 removed outlier: 4.013A pdb=" N ALYSLO 60 " --> pdb=" O AASPLO 56 " (cutoff:3.500A) Processing helix chain 'LO' and resid 65 through 69 removed outlier: 3.646A pdb=" N AGLYLO 69 " --> pdb=" O ALYSLO 66 " (cutoff:3.500A) Processing helix chain 'LO' and resid 75 through 86 Processing helix chain 'LO' and resid 92 through 101 Processing helix chain 'LO' and resid 120 through 123 Processing helix chain 'LO' and resid 124 through 129 Processing helix chain 'LO' and resid 138 through 146 Processing helix chain 'LO' and resid 149 through 186 Processing helix chain 'LO' and resid 188 through 197 Processing helix chain 'LP' and resid 10 through 12 No H-bonds generated for 'chain 'LP' and resid 10 through 12' Processing helix chain 'LP' and resid 25 through 35 Processing helix chain 'LP' and resid 40 through 53 Processing helix chain 'LP' and resid 70 through 77 removed outlier: 3.510A pdb=" N GLYLP 73 " --> pdb=" O THRLP 70 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLULP 75 " --> pdb=" O GLNLP 72 " (cutoff:3.500A) Processing helix chain 'LP' and resid 84 through 106 Processing helix chain 'LP' and resid 132 through 134 No H-bonds generated for 'chain 'LP' and resid 132 through 134' Processing helix chain 'LP' and resid 169 through 183 Processing helix chain 'LQ' and resid 23 through 41 removed outlier: 4.393A pdb=" N ASPLQ 41 " --> pdb=" O ALALQ 37 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 42 through 54 removed outlier: 3.760A pdb=" N LYSLQ 46 " --> pdb=" O ALALQ 42 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N PHELQ 53 " --> pdb=" O LEULQ 49 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEULQ 54 " --> pdb=" O LYSLQ 50 " (cutoff:3.500A) Processing helix chain 'LQ' and resid 64 through 72 Processing helix chain 'LQ' and resid 107 through 117 Processing helix chain 'LQ' and resid 123 through 131 Processing helix chain 'LQ' and resid 148 through 153 Processing helix chain 'LR' and resid 4 through 16 Processing helix chain 'LR' and resid 28 through 35 Processing helix chain 'LR' and resid 37 through 47 Processing helix chain 'LR' and resid 60 through 72 Processing helix chain 'LR' and resid 84 through 89 Processing helix chain 'LR' and resid 90 through 112 Processing helix chain 'LR' and resid 116 through 129 removed outlier: 3.529A pdb=" N VALLR 122 " --> pdb=" O HISLR 118 " (cutoff:3.500A) Processing helix chain 'LR' and resid 134 through 172 Processing helix chain 'LS' and resid 33 through 49 Processing helix chain 'LS' and resid 52 through 54 No H-bonds generated for 'chain 'LS' and resid 52 through 54' Processing helix chain 'LS' and resid 98 through 115 Processing helix chain 'LS' and resid 117 through 119 No H-bonds generated for 'chain 'LS' and resid 117 through 119' Processing helix chain 'LS' and resid 137 through 142 Processing helix chain 'LS' and resid 143 through 145 No H-bonds generated for 'chain 'LS' and resid 143 through 145' Processing helix chain 'LT' and resid 27 through 32 Processing helix chain 'LT' and resid 54 through 58 Processing helix chain 'LT' and resid 99 through 121 removed outlier: 3.864A pdb=" N GLNLT 103 " --> pdb=" O SERLT 99 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALALT 121 " --> pdb=" O ALALT 117 " (cutoff:3.500A) Processing helix chain 'LU' and resid 19 through 24 removed outlier: 3.652A pdb=" N THRLU 23 " --> pdb=" O VALLU 19 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLULU 24 " --> pdb=" O SERLU 20 " (cutoff:3.500A) No H-bonds generated for 'chain 'LU' and resid 19 through 24' Processing helix chain 'LU' and resid 29 through 41 Processing helix chain 'LU' and resid 72 through 87 Processing helix chain 'LV' and resid 119 through 126 removed outlier: 3.501A pdb=" N LEULV 125 " --> pdb=" O GLULV 121 " (cutoff:3.500A) Processing helix chain 'LV' and resid 126 through 133 Processing helix chain 'LW' and resid 33 through 42 Processing helix chain 'LW' and resid 45 through 49 Processing helix chain 'LW' and resid 52 through 59 Processing helix chain 'LX' and resid 58 through 62 Processing helix chain 'LX' and resid 69 through 80 removed outlier: 3.915A pdb=" N ASNLX 80 " --> pdb=" O VALLX 76 " (cutoff:3.500A) Processing helix chain 'LX' and resid 91 through 104 Processing helix chain 'LX' and resid 131 through 140 removed outlier: 3.545A pdb=" N ASNLX 137 " --> pdb=" O LEULX 133 " (cutoff:3.500A) Processing helix chain 'LY' and resid 11 through 21 Processing helix chain 'LY' and resid 23 through 31 removed outlier: 3.778A pdb=" N VALLY 29 " --> pdb=" O SERLY 25 " (cutoff:3.500A) Processing helix chain 'LY' and resid 36 through 44 Processing helix chain 'LY' and resid 74 through 78 Processing helix chain 'LY' and resid 100 through 102 No H-bonds generated for 'chain 'LY' and resid 100 through 102' Processing helix chain 'LY' and resid 112 through 122 Processing helix chain 'LZ' and resid 60 through 66 Processing helix chain 'LZ' and resid 103 through 124 removed outlier: 3.895A pdb=" N ARGLZ 107 " --> pdb=" O GLNLZ 103 " (cutoff:3.500A) Processing helix chain 'LZ' and resid 127 through 132 Processing helix chain 'La' and resid 2 through 5 removed outlier: 3.518A pdb=" N PHELa 5 " --> pdb=" O PROLa 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'La' and resid 2 through 5' Processing helix chain 'La' and resid 6 through 12 removed outlier: 3.904A pdb=" N LYSLa 10 " --> pdb=" O THRLa 6 " (cutoff:3.500A) Processing helix chain 'La' and resid 41 through 49 Processing helix chain 'La' and resid 83 through 93 removed outlier: 4.001A pdb=" N ASPLa 88 " --> pdb=" O GLULa 84 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N GLNLa 89 " --> pdb=" O ASPLa 85 " (cutoff:3.500A) Processing helix chain 'La' and resid 104 through 108 Processing helix chain 'La' and resid 131 through 141 Processing helix chain 'Lb' and resid 11 through 19 removed outlier: 4.082A pdb=" N ASNLb 19 " --> pdb=" O LYSLb 15 " (cutoff:3.500A) Processing helix chain 'Lb' and resid 36 through 59 removed outlier: 3.511A pdb=" N ASNLb 42 " --> pdb=" O LYSLb 38 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HISLb 45 " --> pdb=" O ARGLb 41 " (cutoff:3.500A) Processing helix chain 'Lc' and resid 10 through 21 Processing helix chain 'Lc' and resid 26 through 36 Processing helix chain 'Lc' and resid 49 through 64 Processing helix chain 'Lc' and resid 73 through 81 Processing helix chain 'Ld' and resid 16 through 20 Processing helix chain 'Ld' and resid 24 through 26 No H-bonds generated for 'chain 'Ld' and resid 24 through 26' Processing helix chain 'Ld' and resid 27 through 45 Processing helix chain 'Ld' and resid 52 through 61 Processing helix chain 'Le' and resid 54 through 58 Processing helix chain 'Le' and resid 78 through 83 removed outlier: 3.552A pdb=" N LEULe 82 " --> pdb=" O ASNLe 78 " (cutoff:3.500A) Processing helix chain 'Le' and resid 84 through 86 No H-bonds generated for 'chain 'Le' and resid 84 through 86' Processing helix chain 'Le' and resid 101 through 116 Processing helix chain 'Lf' and resid 37 through 42 Processing helix chain 'Lf' and resid 43 through 45 No H-bonds generated for 'chain 'Lf' and resid 43 through 45' Processing helix chain 'Lg' and resid 15 through 18 Processing helix chain 'Lg' and resid 58 through 65 removed outlier: 3.555A pdb=" N VALLg 65 " --> pdb=" O TYRLg 62 " (cutoff:3.500A) Processing helix chain 'Lg' and resid 67 through 71 Processing helix chain 'Lg' and resid 81 through 113 removed outlier: 3.591A pdb=" N LYSLg 113 " --> pdb=" O THRLg 109 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 5 through 10 removed outlier: 3.900A pdb=" N LEULh 9 " --> pdb=" O LYSLh 5 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 13 through 36 removed outlier: 3.722A pdb=" N GLNLh 34 " --> pdb=" O GLULh 30 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEULh 36 " --> pdb=" O LYSLh 32 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 43 through 70 removed outlier: 3.697A pdb=" N VALLh 47 " --> pdb=" O LYSLh 43 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 77 through 81 removed outlier: 3.533A pdb=" N ARGLh 81 " --> pdb=" O LYSLh 78 " (cutoff:3.500A) Processing helix chain 'Lh' and resid 85 through 91 Processing helix chain 'Lh' and resid 93 through 99 Processing helix chain 'Lh' and resid 101 through 111 Processing helix chain 'Li' and resid 34 through 49 Processing helix chain 'Li' and resid 51 through 64 Processing helix chain 'Li' and resid 64 through 77 removed outlier: 4.673A pdb=" N ARGLi 68 " --> pdb=" O SERLi 64 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ALALi 69 " --> pdb=" O GLYLi 65 " (cutoff:3.500A) Processing helix chain 'Li' and resid 79 through 100 Processing helix chain 'Lj' and resid 4 through 9 removed outlier: 3.596A pdb=" N GLYLj 9 " --> pdb=" O THRLj 5 " (cutoff:3.500A) Processing helix chain 'Lj' and resid 50 through 58 Processing helix chain 'Lj' and resid 69 through 76 Processing helix chain 'Lk' and resid 7 through 15 Processing helix chain 'Lk' and resid 58 through 69 Processing helix chain 'Ll' and resid 6 through 20 Processing helix chain 'Ll' and resid 24 through 30 Processing helix chain 'Lm' and resid 80 through 91 removed outlier: 3.880A pdb=" N TYRLm 89 " --> pdb=" O LEULm 85 " (cutoff:3.500A) Processing helix chain 'Ln' and resid 2 through 24 removed outlier: 4.123A pdb=" N SERLn 24 " --> pdb=" O VALLn 20 " (cutoff:3.500A) Processing helix chain 'Lo' and resid 37 through 48 Processing helix chain 'Lp' and resid 8 through 15 removed outlier: 3.848A pdb=" N LYSLp 13 " --> pdb=" O ILELp 10 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 19 through 35 removed outlier: 3.905A pdb=" N GLNLp 32 " --> pdb=" O LYSLp 28 " (cutoff:3.500A) Processing helix chain 'Lp' and resid 73 through 91 Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'D' and resid 2 through 16 removed outlier: 4.227A pdb=" N ARG D 15 " --> pdb=" O GLY D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 32 Processing helix chain 'D' and resid 35 through 50 removed outlier: 3.964A pdb=" N LYS D 39 " --> pdb=" O ALA D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 54 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 60 through 65 Processing helix chain 'D' and resid 74 through 88 Processing helix chain 'D' and resid 90 through 105 removed outlier: 3.811A pdb=" N LEU D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 121 Processing helix chain 'D' and resid 123 through 137 Processing helix chain 'D' and resid 138 through 141 Processing helix chain 'D' and resid 144 through 163 removed outlier: 4.213A pdb=" N TYR D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N TYR D 149 " --> pdb=" O LYS D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 191 through 206 Processing helix chain 'D' and resid 209 through 224 removed outlier: 3.576A pdb=" N ASN D 223 " --> pdb=" O ILE D 219 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 243 Processing helix chain 'D' and resid 245 through 259 Processing helix chain 'D' and resid 263 through 277 Processing helix chain 'D' and resid 280 through 293 Processing helix chain 'D' and resid 295 through 311 removed outlier: 3.919A pdb=" N LEU D 303 " --> pdb=" O ARG D 299 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 326 removed outlier: 4.298A pdb=" N LYS D 324 " --> pdb=" O TYR D 320 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 337 Processing helix chain 'D' and resid 338 through 342 removed outlier: 3.546A pdb=" N ILE D 342 " --> pdb=" O SER D 339 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 353 Processing helix chain 'D' and resid 360 through 370 Processing helix chain 'D' and resid 376 through 385 Processing helix chain 'D' and resid 386 through 388 No H-bonds generated for 'chain 'D' and resid 386 through 388' Processing helix chain 'D' and resid 399 through 412 removed outlier: 3.621A pdb=" N LEU D 403 " --> pdb=" O CYS D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 417 through 433 Processing helix chain 'D' and resid 438 through 452 Processing helix chain 'D' and resid 454 through 463 removed outlier: 3.543A pdb=" N HIS D 461 " --> pdb=" O ASP D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 464 through 466 No H-bonds generated for 'chain 'D' and resid 464 through 466' Processing helix chain 'D' and resid 470 through 476 removed outlier: 3.695A pdb=" N SER D 474 " --> pdb=" O VAL D 470 " (cutoff:3.500A) Processing helix chain 'D' and resid 476 through 481 removed outlier: 3.564A pdb=" N SER D 481 " --> pdb=" O TYR D 477 " (cutoff:3.500A) Processing helix chain 'D' and resid 482 through 487 Processing helix chain 'D' and resid 492 through 497 Processing helix chain 'D' and resid 497 through 503 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 508 through 523 Proline residue: D 514 - end of helix Processing helix chain 'D' and resid 525 through 541 removed outlier: 3.827A pdb=" N ILE D 529 " --> pdb=" O SER D 525 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N LEU D 530 " --> pdb=" O TYR D 526 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLY D 531 " --> pdb=" O SER D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 559 Processing helix chain 'D' and resid 563 through 580 removed outlier: 3.641A pdb=" N THR D 580 " --> pdb=" O SER D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 597 through 603 removed outlier: 3.624A pdb=" N ASN D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 605 through 612 removed outlier: 5.116A pdb=" N TYR D 610 " --> pdb=" O ILE D 607 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 631 Processing helix chain 'D' and resid 637 through 647 removed outlier: 3.550A pdb=" N LEU D 647 " --> pdb=" O LEU D 643 " (cutoff:3.500A) Processing helix chain 'D' and resid 651 through 660 Processing helix chain 'D' and resid 661 through 678 Processing helix chain 'D' and resid 681 through 692 Processing helix chain 'D' and resid 700 through 719 Processing helix chain 'D' and resid 724 through 761 removed outlier: 4.885A pdb=" N ASP D 743 " --> pdb=" O ARG D 739 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ASP D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS D 761 " --> pdb=" O TYR D 757 " (cutoff:3.500A) Processing helix chain 'D' and resid 762 through 772 Processing helix chain 'D' and resid 779 through 795 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 6 removed outlier: 4.045A pdb=" N PHE A 44 " --> pdb=" O MET A 63 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY A 61 " --> pdb=" O SER A 46 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU A 48 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N ILE A 59 " --> pdb=" O GLU A 48 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N SER A 60 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N VAL A 83 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N TYR A 62 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N VAL A 81 " --> pdb=" O TYR A 62 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N MET A 64 " --> pdb=" O THR A 79 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 117 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ALA A 80 " --> pdb=" O PHE A 117 " (cutoff:3.500A) removed outlier: 12.728A pdb=" N LYS A 119 " --> pdb=" O ALA A 80 " (cutoff:3.500A) removed outlier: 14.768A pdb=" N THR A 82 " --> pdb=" O LYS A 119 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ALA A 164 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N ARG A 139 " --> pdb=" O ALA A 164 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP A 166 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N CYS A 188 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ARG A 139 " --> pdb=" O CYS A 188 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'LA' and resid 73 through 77 removed outlier: 3.639A pdb=" N GLNLA 47 " --> pdb=" O LYSLA 60 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VALLA 62 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N VALLA 45 " --> pdb=" O VALLA 62 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'LA' and resid 155 through 158 removed outlier: 6.682A pdb=" N ARGLA 149 " --> pdb=" O ILELA 136 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N ILELA 136 " --> pdb=" O ARGLA 149 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'LA' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'LB' and resid 356 through 359 removed outlier: 6.829A pdb=" N VALLB 57 " --> pdb=" O LYSLB 357 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N ILELB 359 " --> pdb=" O THRLB 55 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N THRLB 55 " --> pdb=" O ILELB 359 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N ILELB 335 " --> pdb=" O VALLB 220 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N VALLB 220 " --> pdb=" O ILELB 335 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILELB 215 " --> pdb=" O ASNLB 279 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASNLB 279 " --> pdb=" O ILELB 215 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYSLB 281 " --> pdb=" O LYSLB 325 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N METLB 323 " --> pdb=" O TYRLB 283 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N VALLB 285 " --> pdb=" O PHELB 321 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N PHELB 321 " --> pdb=" O VALLB 285 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ASPLB 80 " --> pdb=" O LYSLB 50 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N LYSLB 50 " --> pdb=" O ASPLB 80 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'LB' and resid 100 through 105 removed outlier: 7.360A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THRLB 104 " --> pdb=" O VALLB 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VALLB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N VALLB 86 " --> pdb=" O HISLB 163 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N HISLB 163 " --> pdb=" O VALLB 86 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLYLB 88 " --> pdb=" O LEULB 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'LB' and resid 100 through 105 removed outlier: 7.360A pdb=" N GLYLB 91 " --> pdb=" O LEULB 102 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N THRLB 104 " --> pdb=" O VALLB 89 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VALLB 89 " --> pdb=" O THRLB 104 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LYSLB 201 " --> pdb=" O VALLB 86 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'LB' and resid 226 through 227 Processing sheet with id=AA9, first strand: chain 'LC' and resid 19 through 20 removed outlier: 4.594A pdb=" N VALLC 151 " --> pdb=" O THRLC 7 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEULC 150 " --> pdb=" O VALLC 248 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEULC 206 " --> pdb=" O ILELC 249 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THRLC 251 " --> pdb=" O LEULC 206 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N VALLC 208 " --> pdb=" O THRLC 251 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N VALLC 207 " --> pdb=" O ALALC 228 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'LC' and resid 63 through 64 Processing sheet with id=AB2, first strand: chain 'LC' and resid 186 through 187 Processing sheet with id=AB3, first strand: chain 'LD' and resid 71 through 79 removed outlier: 6.567A pdb=" N ILELD 64 " --> pdb=" O LEULD 75 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ALALD 77 " --> pdb=" O CYSLD 62 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N CYSLD 62 " --> pdb=" O ALALD 77 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N TYRLD 79 " --> pdb=" O ILELD 60 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N ILELD 60 " --> pdb=" O TYRLD 79 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'LE' and resid 77 through 79 removed outlier: 3.605A pdb=" N LYSLE 56 " --> pdb=" O LEULE 64 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N THRLE 66 " --> pdb=" O TYRLE 54 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TYRLE 54 " --> pdb=" O THRLE 66 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N THRLE 38 " --> pdb=" O TYRLE 54 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N VALLE 39 " --> pdb=" O THRLE 87 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'LF' and resid 75 through 77 Processing sheet with id=AB6, first strand: chain 'LF' and resid 205 through 206 removed outlier: 4.349A pdb=" N SERLF 113 " --> pdb=" O ARGLF 88 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'LF' and resid 153 through 156 Processing sheet with id=AB8, first strand: chain 'LG' and resid 70 through 71 Processing sheet with id=AB9, first strand: chain 'LG' and resid 133 through 134 removed outlier: 6.685A pdb=" N VALLG 151 " --> pdb=" O ALALG 178 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N VALLG 180 " --> pdb=" O VALLG 151 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ILELG 153 " --> pdb=" O VALLG 180 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'LH' and resid 6 through 11 removed outlier: 3.631A pdb=" N GLNLH 8 " --> pdb=" O VALLH 55 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VALLH 55 " --> pdb=" O GLNLH 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'LH' and resid 32 through 37 removed outlier: 3.612A pdb=" N LYSLH 36 " --> pdb=" O VALLH 25 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N VALLH 18 " --> pdb=" O ILELM 6 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'LH' and resid 132 through 135 removed outlier: 6.925A pdb=" N LYSLH 87 " --> pdb=" O LYSLH 184 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYSLH 184 " --> pdb=" O LYSLH 87 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LYSLH 89 " --> pdb=" O SERLH 182 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'LH' and resid 100 through 104 Processing sheet with id=AC5, first strand: chain 'LI' and resid 35 through 37 removed outlier: 6.393A pdb=" N LEULI 52 " --> pdb=" O ILELI 135 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N SERLI 137 " --> pdb=" O VALLI 50 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VALLI 50 " --> pdb=" O SERLI 137 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ARGLI 139 " --> pdb=" O LEULI 48 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N LEULI 48 " --> pdb=" O ARGLI 139 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'LI' and resid 58 through 61 removed outlier: 3.704A pdb=" N GLULI 58 " --> pdb=" O VALLI 129 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ILELI 99 " --> pdb=" O PROLI 122 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLYLI 124 " --> pdb=" O LEULI 97 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'LI' and resid 170 through 171 removed outlier: 5.737A pdb=" N LEULI 176 " --> pdb=" O TRPLI 171 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'LI' and resid 190 through 192 Processing sheet with id=AC9, first strand: chain 'LJ' and resid 46 through 48 removed outlier: 3.542A pdb=" N ALALJ 66 " --> pdb=" O SERLJ 48 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASNLJ 132 " --> pdb=" O LYSLJ 13 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VALLJ 130 " --> pdb=" O GLULJ 15 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N LEULJ 17 " --> pdb=" O TYRLJ 128 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N TYRLJ 128 " --> pdb=" O LEULJ 17 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEULJ 19 " --> pdb=" O ASPLJ 126 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASPLJ 126 " --> pdb=" O LEULJ 19 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'LJ' and resid 90 through 91 removed outlier: 3.519A pdb=" N LEULJ 91 " --> pdb=" O ASPLJ 170 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'LL' and resid 22 through 24 removed outlier: 6.075A pdb=" N LYSLL 23 " --> pdb=" O LEULN 199 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'LL' and resid 57 through 59 Processing sheet with id=AD4, first strand: chain 'LL' and resid 123 through 125 Processing sheet with id=AD5, first strand: chain 'LM' and resid 53 through 59 removed outlier: 4.621A pdb=" N GLYLM 48 " --> pdb=" O PROLM 54 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LYSLM 43 " --> pdb=" O ILELM 38 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ILELM 38 " --> pdb=" O LYSLM 43 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEULM 45 " --> pdb=" O VALLM 36 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ARGLM 19 " --> pdb=" O ILELM 35 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N VALLM 20 " --> pdb=" O THRLM 66 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'LN' and resid 36 through 39 removed outlier: 4.433A pdb=" N ILELN 61 " --> pdb=" O ALALN 39 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N TYRLN 127 " --> pdb=" O GLNLN 123 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLNLN 123 " --> pdb=" O TYRLN 127 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N TYRLN 129 " --> pdb=" O VALLN 121 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASNLN 117 " --> pdb=" O ILELN 133 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VALLN 135 " --> pdb=" O VALLN 115 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VALLN 115 " --> pdb=" O VALLN 135 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'LO' and resid 6 through 10 removed outlier: 5.915A pdb=" N AVALLO 7 " --> pdb=" O AVALLO 34 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N AVALLO 36 " --> pdb=" O AVALLO 7 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N AILELO 9 " --> pdb=" O AVALLO 36 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'LO' and resid 42 through 44 Processing sheet with id=AD9, first strand: chain 'LP' and resid 14 through 22 removed outlier: 3.648A pdb=" N TYRLP 21 " --> pdb=" O SERLP 144 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N SERLP 144 " --> pdb=" O TYRLP 21 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N THRLP 151 " --> pdb=" O VALLP 114 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N VALLP 114 " --> pdb=" O THRLP 151 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'LP' and resid 58 through 59 Processing sheet with id=AE2, first strand: chain 'LP' and resid 125 through 131 removed outlier: 3.760A pdb=" N GLNLP 125 " --> pdb=" O SERLP 141 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARGLP 135 " --> pdb=" O ARGLP 131 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'LQ' and resid 62 through 63 removed outlier: 3.667A pdb=" N LEULQ 104 " --> pdb=" O VALLQ 83 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N GLYLQ 85 " --> pdb=" O LEULQ 104 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N PHELQ 106 " --> pdb=" O GLYLQ 85 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VALLQ 87 " --> pdb=" O PHELQ 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VALLQ 101 " --> pdb=" O ILELQ 122 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'LQ' and resid 62 through 63 Processing sheet with id=AE5, first strand: chain 'LR' and resid 23 through 24 removed outlier: 3.585A pdb=" N VALLR 51 " --> pdb=" O TRPLR 23 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'LS' and resid 56 through 63 removed outlier: 5.211A pdb=" N ILELS 58 " --> pdb=" O ARGLS 12 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ARGLS 12 " --> pdb=" O ILELS 58 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SERLS 60 " --> pdb=" O ILELS 10 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LS' and resid 87 through 96 removed outlier: 3.516A pdb=" N LYSLS 125 " --> pdb=" O TRPLS 78 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N ARGLS 80 " --> pdb=" O ILELS 123 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ILELS 123 " --> pdb=" O ARGLS 80 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ASPLS 82 " --> pdb=" O ILELS 121 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ILELS 121 " --> pdb=" O ASPLS 82 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LT' and resid 83 through 92 removed outlier: 5.987A pdb=" N ILELT 75 " --> pdb=" O VALLT 64 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N VALLT 64 " --> pdb=" O ILELT 75 " (cutoff:3.500A) removed outlier: 8.402A pdb=" N ASNLT 77 " --> pdb=" O GLYLT 62 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLYLT 62 " --> pdb=" O ASNLT 77 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYSLT 97 " --> pdb=" O ASPLT 41 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LU' and resid 54 through 58 Processing sheet with id=AF1, first strand: chain 'LU' and resid 42 through 43 Processing sheet with id=AF2, first strand: chain 'LV' and resid 17 through 18 Processing sheet with id=AF3, first strand: chain 'LV' and resid 22 through 25 removed outlier: 6.498A pdb=" N METLV 59 " --> pdb=" O ILELV 37 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N VALLV 39 " --> pdb=" O METLV 57 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N METLV 57 " --> pdb=" O VALLV 39 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ALALV 99 " --> pdb=" O VALLV 79 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N GLYLV 100 " --> pdb=" O ILELV 22 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N ASNLV 24 " --> pdb=" O GLYLV 100 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ILELV 102 " --> pdb=" O ASNLV 24 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'LV' and resid 85 through 86 removed outlier: 6.465A pdb=" N PHELV 92 " --> pdb=" O LEULW 20 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N VALLW 22 " --> pdb=" O PHELV 92 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TYRLV 94 " --> pdb=" O VALLW 22 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'LW' and resid 4 through 5 Processing sheet with id=AF6, first strand: chain 'LX' and resid 63 through 66 removed outlier: 4.060A pdb=" N GLNLX 65 " --> pdb=" O GLNLX 85 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYSLX 120 " --> pdb=" O VALLX 86 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'LY' and resid 32 through 34 Processing sheet with id=AF8, first strand: chain 'LY' and resid 94 through 99 removed outlier: 10.061A pdb=" N VALLY 95 " --> pdb=" O LYSLY 84 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYSLY 84 " --> pdb=" O VALLY 95 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N ILELY 97 " --> pdb=" O VALLY 82 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N VALLY 82 " --> pdb=" O ILELY 97 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLNLY 81 " --> pdb=" O SERLY 71 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYSLY 69 " --> pdb=" O ASPLY 83 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N VALLY 85 " --> pdb=" O GLULY 67 " (cutoff:3.500A) removed outlier: 9.939A pdb=" N GLULY 67 " --> pdb=" O VALLY 85 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLULY 55 " --> pdb=" O THRLY 107 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'LZ' and resid 69 through 72 removed outlier: 6.555A pdb=" N LYSLZ 69 " --> pdb=" O GLULZ 47 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILELZ 46 " --> pdb=" O LYSLZ 22 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N LYSLZ 22 " --> pdb=" O ILELZ 46 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N VALLZ 10 " --> pdb=" O THRLZ 83 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'LZ' and resid 28 through 29 Processing sheet with id=AG2, first strand: chain 'La' and resid 72 through 74 removed outlier: 5.963A pdb=" N LEULa 73 " --> pdb=" O LEULa 113 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'La' and resid 101 through 103 removed outlier: 6.479A pdb=" N VALLa 125 " --> pdb=" O GLULa 146 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Lc' and resid 22 through 25 removed outlier: 7.086A pdb=" N THRLc 24 " --> pdb=" O ILELc 92 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N ILELc 92 " --> pdb=" O THRLc 24 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEULc 41 " --> pdb=" O ILELc 92 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ILELc 42 " --> pdb=" O TYRLc 68 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Ld' and resid 49 through 51 Processing sheet with id=AG6, first strand: chain 'Le' and resid 72 through 76 Processing sheet with id=AG7, first strand: chain 'Lf' and resid 8 through 18 removed outlier: 9.867A pdb=" N VALLf 9 " --> pdb=" O ILELf 32 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N ILELf 32 " --> pdb=" O VALLf 9 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N GLYLf 11 " --> pdb=" O ILELf 30 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N ILELf 30 " --> pdb=" O GLYLf 11 " (cutoff:3.500A) removed outlier: 8.778A pdb=" N HISLf 13 " --> pdb=" O SERLf 28 " (cutoff:3.500A) removed outlier: 9.930A pdb=" N SERLf 28 " --> pdb=" O HISLf 13 " (cutoff:3.500A) removed outlier: 11.481A pdb=" N SERLf 15 " --> pdb=" O ASNLf 26 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ASNLf 26 " --> pdb=" O SERLf 15 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLNLf 17 " --> pdb=" O ASNLf 24 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASNLf 26 " --> pdb=" O PHELf 85 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N PHELf 85 " --> pdb=" O ASNLf 26 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARGLf 73 " --> pdb=" O ARGLf 82 " (cutoff:3.500A) removed outlier: 6.101A pdb=" N THRLf 84 " --> pdb=" O VALLf 71 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N VALLf 71 " --> pdb=" O THRLf 84 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ARGLf 48 " --> pdb=" O PHELf 101 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N VALLf 52 " --> pdb=" O SERLf 97 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N SERLf 97 " --> pdb=" O VALLf 52 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'Lg' and resid 20 through 24 Processing sheet with id=AG9, first strand: chain 'Lj' and resid 16 through 17 removed outlier: 3.606A pdb=" N THRLj 33 " --> pdb=" O HISLj 28 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Lk' and resid 3 through 5 removed outlier: 4.425A pdb=" N VALLk 55 " --> pdb=" O ILELk 5 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N THRLk 22 " --> pdb=" O ARGLk 46 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Lm' and resid 102 through 103 Processing sheet with id=AH3, first strand: chain 'Lo' and resid 7 through 12 removed outlier: 4.415A pdb=" N VALLo 68 " --> pdb=" O LEULo 85 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'Lp' and resid 37 through 38 removed outlier: 6.849A pdb=" N ILELp 54 " --> pdb=" O GLYLp 50 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'C' and resid 2 through 6 removed outlier: 3.627A pdb=" N GLY C 61 " --> pdb=" O SER C 46 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU C 48 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N ILE C 59 " --> pdb=" O GLU C 48 " (cutoff:3.500A) 2887 hydrogen bonds defined for protein. 8130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2814 hydrogen bonds 4468 hydrogen bond angles 0 basepair planarities 1149 basepair parallelities 1743 stacking parallelities Total time for adding SS restraints: 259.98 Time building geometry restraints manager: 63.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 27001 1.33 - 1.45: 55999 1.45 - 1.58: 61063 1.58 - 1.70: 7151 1.70 - 1.82: 272 Bond restraints: 151486 Sorted by residual: bond pdb=" O3' C 12094 " pdb=" P G 12095 " ideal model delta sigma weight residual 1.607 1.404 0.203 1.50e-02 4.44e+03 1.83e+02 bond pdb=" O3' U 11950 " pdb=" P C 11951 " ideal model delta sigma weight residual 1.607 1.429 0.178 1.50e-02 4.44e+03 1.41e+02 bond pdb=" N SER D 16 " pdb=" CA SER D 16 " ideal model delta sigma weight residual 1.457 1.500 -0.043 1.29e-02 6.01e+03 1.09e+01 bond pdb=" CZ ARG D 161 " pdb=" NH2 ARG D 161 " ideal model delta sigma weight residual 1.330 1.289 0.041 1.30e-02 5.92e+03 9.84e+00 bond pdb=" CD2 HIS D 364 " pdb=" NE2 HIS D 364 " ideal model delta sigma weight residual 1.374 1.408 -0.034 1.10e-02 8.26e+03 9.35e+00 ... (remaining 151481 not shown) Histogram of bond angle deviations from ideal: 77.02 - 92.88: 2 92.88 - 108.73: 46678 108.73 - 124.59: 159713 124.59 - 140.45: 15580 140.45 - 156.31: 1 Bond angle restraints: 221974 Sorted by residual: angle pdb=" O3' U 11950 " pdb=" P C 11951 " pdb=" O5' C 11951 " ideal model delta sigma weight residual 104.00 156.31 -52.31 1.50e+00 4.44e-01 1.22e+03 angle pdb=" O3' U 11950 " pdb=" P C 11951 " pdb=" OP2 C 11951 " ideal model delta sigma weight residual 108.00 77.02 30.98 3.00e+00 1.11e-01 1.07e+02 angle pdb=" C3' U 11950 " pdb=" O3' U 11950 " pdb=" P C 11951 " ideal model delta sigma weight residual 120.20 106.03 14.17 1.50e+00 4.44e-01 8.92e+01 angle pdb=" C ARG D 15 " pdb=" N SER D 16 " pdb=" CA SER D 16 " ideal model delta sigma weight residual 121.54 135.67 -14.13 1.91e+00 2.74e-01 5.47e+01 angle pdb=" O3' U 11950 " pdb=" P C 11951 " pdb=" OP1 C 11951 " ideal model delta sigma weight residual 108.00 87.69 20.31 3.00e+00 1.11e-01 4.58e+01 ... (remaining 221969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 86704 35.98 - 71.96: 8317 71.96 - 107.95: 886 107.95 - 143.93: 23 143.93 - 179.91: 53 Dihedral angle restraints: 95983 sinusoidal: 72427 harmonic: 23556 Sorted by residual: dihedral pdb=" CA APROLO 110 " pdb=" C APROLO 110 " pdb=" N APROLO 111 " pdb=" CA APROLO 111 " ideal model delta harmonic sigma weight residual -180.00 -118.24 -61.76 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" C4' U 12501 " pdb=" C3' U 12501 " pdb=" C2' U 12501 " pdb=" C1' U 12501 " ideal model delta sinusoidal sigma weight residual -35.00 31.85 -66.85 1 8.00e+00 1.56e-02 9.10e+01 dihedral pdb=" O4' U 12846 " pdb=" C1' U 12846 " pdb=" N1 U 12846 " pdb=" C2 U 12846 " ideal model delta sinusoidal sigma weight residual 200.00 31.65 168.35 1 1.50e+01 4.44e-03 8.45e+01 ... (remaining 95980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 25795 0.076 - 0.153: 1666 0.153 - 0.229: 162 0.229 - 0.305: 15 0.305 - 0.381: 5 Chirality restraints: 27643 Sorted by residual: chirality pdb=" CA SER D 16 " pdb=" N SER D 16 " pdb=" C SER D 16 " pdb=" CB SER D 16 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.64e+00 chirality pdb=" CB ILELh 118 " pdb=" CA ILELh 118 " pdb=" CG1 ILELh 118 " pdb=" CG2 ILELh 118 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" CA ASPLG 158 " pdb=" N ASPLG 158 " pdb=" C ASPLG 158 " pdb=" CB ASPLG 158 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 27640 not shown) Planarity restraints: 14813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 574 " -0.127 2.00e-02 2.50e+03 6.41e-02 1.03e+02 pdb=" CG TRP D 574 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP D 574 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 574 " 0.084 2.00e-02 2.50e+03 pdb=" NE1 TRP D 574 " 0.024 2.00e-02 2.50e+03 pdb=" CE2 TRP D 574 " 0.029 2.00e-02 2.50e+03 pdb=" CE3 TRP D 574 " 0.067 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 574 " -0.078 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 574 " 0.008 2.00e-02 2.50e+03 pdb=" CH2 TRP D 574 " -0.059 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 502 " -0.093 2.00e-02 2.50e+03 7.13e-02 7.63e+01 pdb=" CG HIS D 502 " 0.088 2.00e-02 2.50e+03 pdb=" ND1 HIS D 502 " 0.069 2.00e-02 2.50e+03 pdb=" CD2 HIS D 502 " 0.050 2.00e-02 2.50e+03 pdb=" CE1 HIS D 502 " -0.070 2.00e-02 2.50e+03 pdb=" NE2 HIS D 502 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 56 " -0.103 2.00e-02 2.50e+03 5.74e-02 6.60e+01 pdb=" CG TYR D 56 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR D 56 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR D 56 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR D 56 " 0.035 2.00e-02 2.50e+03 pdb=" CE2 TYR D 56 " 0.035 2.00e-02 2.50e+03 pdb=" CZ TYR D 56 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 56 " -0.090 2.00e-02 2.50e+03 ... (remaining 14810 not shown) Histogram of nonbonded interaction distances: 1.02 - 1.79: 14 1.79 - 2.57: 1816 2.57 - 3.35: 176882 3.35 - 4.12: 440853 4.12 - 4.90: 656867 Nonbonded interactions: 1276432 Sorted by model distance: nonbonded pdb=" CE MET C 1 " pdb=" O ILE D 333 " model vdw 1.017 3.460 nonbonded pdb=" CB ILELR 143 " pdb=" OP2 A 12093 " model vdw 1.236 3.470 nonbonded pdb=" O2' U 11763 " pdb=" CE1 PHE D 105 " model vdw 1.359 3.340 nonbonded pdb=" O MET C 49 " pdb=" CD1 ILE D 333 " model vdw 1.400 3.460 nonbonded pdb=" CZ PHE D 18 " pdb=" CB GLN D 49 " model vdw 1.431 3.740 ... (remaining 1276427 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.150 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: 0.130 Extract box with map and model: 18.090 Check model and map are aligned: 1.540 Set scattering table: 0.960 Process input model: 546.590 Find NCS groups from input model: 3.280 Set up NCS constraints: 0.400 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:2.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 577.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.203 151486 Z= 0.285 Angle : 0.687 52.305 221974 Z= 0.401 Chirality : 0.039 0.381 27643 Planarity : 0.006 0.098 14813 Dihedral : 22.023 179.910 80771 Min Nonbonded Distance : 1.017 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.42 % Favored : 95.43 % Rotamer: Outliers : 0.16 % Allowed : 0.49 % Favored : 99.35 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 7994 helix: 0.66 (0.09), residues: 3202 sheet: -0.34 (0.17), residues: 888 loop : -0.63 (0.10), residues: 3904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.127 0.004 TRP D 574 HIS 0.025 0.002 HIS D 337 PHE 0.043 0.003 PHE D 80 TYR 0.103 0.004 TYR D 56 ARG 0.014 0.001 ARG D 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2460 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2449 time to evaluate : 7.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 3 THR cc_start: 0.5379 (t) cc_final: 0.5113 (p) REVERT: A 33 PHE cc_start: 0.3663 (m-10) cc_final: 0.2770 (m-10) REVERT: A 43 PHE cc_start: 0.4811 (t80) cc_final: 0.2938 (t80) REVERT: A 64 MET cc_start: 0.1770 (mpp) cc_final: 0.0845 (mmt) REVERT: B 108 TYR cc_start: 0.4724 (p90) cc_final: 0.4387 (t80) REVERT: B 127 MET cc_start: 0.2231 (mpp) cc_final: 0.0790 (mpp) REVERT: B 148 TYR cc_start: 0.4083 (m-80) cc_final: 0.3486 (m-80) REVERT: B 202 LEU cc_start: 0.1328 (mt) cc_final: 0.0299 (mt) REVERT: B 223 ASN cc_start: 0.5233 (m110) cc_final: 0.4941 (t0) REVERT: B 384 PHE cc_start: 0.5770 (m-80) cc_final: 0.5502 (m-80) REVERT: B 427 ILE cc_start: 0.8903 (mt) cc_final: 0.8627 (pt) REVERT: B 428 LEU cc_start: 0.8362 (mt) cc_final: 0.7712 (mt) REVERT: B 447 VAL cc_start: 0.8637 (t) cc_final: 0.8215 (p) REVERT: B 452 LEU cc_start: 0.8987 (mt) cc_final: 0.8668 (mm) REVERT: B 503 ASN cc_start: 0.6114 (m-40) cc_final: 0.5896 (m110) REVERT: B 532 MET cc_start: 0.4271 (tmm) cc_final: 0.3748 (mmm) REVERT: B 577 LEU cc_start: 0.6868 (tp) cc_final: 0.6481 (tp) REVERT: B 598 PHE cc_start: 0.8128 (t80) cc_final: 0.7889 (t80) REVERT: B 607 ILE cc_start: 0.8248 (tp) cc_final: 0.6741 (tp) REVERT: B 613 LEU cc_start: 0.6986 (tp) cc_final: 0.6397 (tp) REVERT: B 619 PHE cc_start: 0.7874 (t80) cc_final: 0.7612 (t80) REVERT: B 623 ILE cc_start: 0.8582 (mm) cc_final: 0.8279 (mm) REVERT: B 631 LEU cc_start: 0.8296 (mt) cc_final: 0.7135 (mt) REVERT: B 644 LEU cc_start: 0.8342 (tp) cc_final: 0.7933 (mt) REVERT: B 714 LYS cc_start: 0.8705 (mtpt) cc_final: 0.8456 (ttpp) REVERT: B 724 ASP cc_start: 0.8440 (m-30) cc_final: 0.8036 (t70) REVERT: LA 20 THR cc_start: 0.8189 (p) cc_final: 0.7889 (p) REVERT: LA 71 LEU cc_start: 0.8930 (tp) cc_final: 0.8711 (tt) REVERT: LA 115 ASN cc_start: 0.8390 (t0) cc_final: 0.7861 (t0) REVERT: LA 133 TYR cc_start: 0.8666 (p90) cc_final: 0.8079 (p90) REVERT: LA 227 ARG cc_start: 0.8140 (ttm-80) cc_final: 0.7831 (ttm-80) REVERT: LB 53 MET cc_start: 0.7699 (mtp) cc_final: 0.7498 (mtt) REVERT: LB 139 GLN cc_start: 0.7468 (pm20) cc_final: 0.6975 (pp30) REVERT: LB 194 TRP cc_start: 0.9212 (t60) cc_final: 0.8919 (t60) REVERT: LB 345 ASN cc_start: 0.8295 (t0) cc_final: 0.7593 (t0) REVERT: LC 41 SER cc_start: 0.9732 (m) cc_final: 0.9465 (t) REVERT: LC 50 TYR cc_start: 0.8183 (p90) cc_final: 0.7830 (p90) REVERT: LC 99 MET cc_start: 0.7823 (ppp) cc_final: 0.7431 (ptt) REVERT: LC 156 LEU cc_start: 0.8956 (tp) cc_final: 0.8627 (tp) REVERT: LC 290 ILE cc_start: 0.9125 (mt) cc_final: 0.8881 (tt) REVERT: LD 31 TYR cc_start: 0.8608 (t80) cc_final: 0.7983 (t80) REVERT: LD 111 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8879 (tm-30) REVERT: LD 227 LEU cc_start: 0.8136 (mp) cc_final: 0.7731 (pp) REVERT: LD 242 SER cc_start: 0.9210 (m) cc_final: 0.8962 (p) REVERT: LE 10 TYR cc_start: 0.8053 (m-80) cc_final: 0.7631 (m-10) REVERT: LE 13 GLU cc_start: 0.6771 (mm-30) cc_final: 0.5824 (mm-30) REVERT: LE 39 VAL cc_start: 0.9079 (t) cc_final: 0.8876 (t) REVERT: LE 101 PHE cc_start: 0.8419 (m-80) cc_final: 0.8039 (m-80) REVERT: LE 105 TYR cc_start: 0.8210 (t80) cc_final: 0.7800 (t80) REVERT: LE 106 PHE cc_start: 0.8779 (m-80) cc_final: 0.7749 (m-80) REVERT: LF 68 ASP cc_start: 0.8978 (m-30) cc_final: 0.8489 (m-30) REVERT: LF 109 THR cc_start: 0.8833 (p) cc_final: 0.8116 (t) REVERT: LF 112 ASN cc_start: 0.8371 (m-40) cc_final: 0.7994 (t0) REVERT: LG 91 PHE cc_start: 0.8443 (m-80) cc_final: 0.8195 (m-10) REVERT: LG 194 THR cc_start: 0.6673 (p) cc_final: 0.5856 (p) REVERT: LH 12 VAL cc_start: 0.8357 (t) cc_final: 0.8065 (t) REVERT: LH 135 GLU cc_start: 0.8002 (mm-30) cc_final: 0.7588 (mp0) REVERT: LI 66 GLU cc_start: 0.8791 (tp30) cc_final: 0.8490 (tp30) REVERT: LI 70 ILE cc_start: 0.9290 (mm) cc_final: 0.9047 (pt) REVERT: LI 76 MET cc_start: 0.8559 (mmt) cc_final: 0.8338 (mmt) REVERT: LI 146 ASP cc_start: 0.7913 (p0) cc_final: 0.7616 (m-30) REVERT: LI 150 GLU cc_start: 0.8193 (mm-30) cc_final: 0.7924 (tp30) REVERT: LJ 14 ILE cc_start: 0.9261 (mm) cc_final: 0.9045 (mm) REVERT: LJ 19 LEU cc_start: 0.8119 (mt) cc_final: 0.7743 (mt) REVERT: LJ 62 ASN cc_start: 0.8273 (m-40) cc_final: 0.7964 (m-40) REVERT: LJ 80 LEU cc_start: 0.9467 (tt) cc_final: 0.9169 (tt) REVERT: LJ 106 ILE cc_start: 0.6696 (mm) cc_final: 0.6474 (mm) REVERT: LL 24 VAL cc_start: 0.9073 (t) cc_final: 0.8471 (t) REVERT: LL 119 TYR cc_start: 0.8409 (t80) cc_final: 0.8094 (t80) REVERT: LL 123 ILE cc_start: 0.9440 (pt) cc_final: 0.9198 (pt) REVERT: LM 14 LEU cc_start: 0.8946 (mm) cc_final: 0.8365 (mm) REVERT: LM 16 GLU cc_start: 0.8390 (pt0) cc_final: 0.7976 (pm20) REVERT: LM 24 LYS cc_start: 0.8694 (ttmt) cc_final: 0.8429 (ptpp) REVERT: LM 56 GLN cc_start: 0.8481 (pt0) cc_final: 0.8001 (pm20) REVERT: LM 94 TRP cc_start: 0.9113 (t-100) cc_final: 0.8672 (t-100) REVERT: LN 153 ASP cc_start: 0.8865 (t70) cc_final: 0.8661 (t0) REVERT: LN 155 VAL cc_start: 0.8819 (m) cc_final: 0.8358 (p) REVERT: LN 165 THR cc_start: 0.8158 (p) cc_final: 0.7819 (p) REVERT: LN 202 TYR cc_start: 0.8571 (m-80) cc_final: 0.7966 (m-80) REVERT: LO 14 HIS cc_start: 0.7628 (m90) cc_final: 0.6962 (m90) REVERT: LO 33 ILE cc_start: 0.9232 (mm) cc_final: 0.8973 (mm) REVERT: LO 50 ASN cc_start: 0.8144 (m110) cc_final: 0.7882 (m110) REVERT: LO 51 LYS cc_start: 0.9306 (tttm) cc_final: 0.8959 (tttt) REVERT: LO 102 LEU cc_start: 0.9117 (tp) cc_final: 0.8905 (tt) REVERT: LP 29 THR cc_start: 0.9528 (p) cc_final: 0.9206 (p) REVERT: LP 42 THR cc_start: 0.9407 (p) cc_final: 0.9169 (p) REVERT: LP 64 ASN cc_start: 0.7339 (p0) cc_final: 0.7114 (p0) REVERT: LR 25 ASP cc_start: 0.8092 (p0) cc_final: 0.7879 (p0) REVERT: LR 27 ASN cc_start: 0.9286 (m110) cc_final: 0.8899 (t0) REVERT: LR 75 HIS cc_start: 0.7807 (m-70) cc_final: 0.7547 (m-70) REVERT: LR 76 SER cc_start: 0.9262 (m) cc_final: 0.8981 (p) REVERT: LS 7 TYR cc_start: 0.6803 (m-10) cc_final: 0.6220 (m-10) REVERT: LS 62 ASN cc_start: 0.8539 (m110) cc_final: 0.8270 (m110) REVERT: LS 104 GLU cc_start: 0.9286 (tt0) cc_final: 0.9075 (mt-10) REVERT: LS 165 TYR cc_start: 0.8910 (m-80) cc_final: 0.8685 (m-80) REVERT: LU 90 ARG cc_start: 0.8509 (mmm-85) cc_final: 0.8172 (tpp80) REVERT: LV 27 ASP cc_start: 0.6878 (p0) cc_final: 0.6574 (p0) REVERT: LV 36 ILE cc_start: 0.8695 (mm) cc_final: 0.8480 (mm) REVERT: LV 92 PHE cc_start: 0.8055 (m-80) cc_final: 0.7847 (m-10) REVERT: LV 120 LYS cc_start: 0.9469 (ttpt) cc_final: 0.9265 (mtpp) REVERT: LV 132 ASN cc_start: 0.9245 (m110) cc_final: 0.8635 (m-40) REVERT: LW 28 ILE cc_start: 0.9042 (pt) cc_final: 0.8366 (pt) REVERT: LW 58 HIS cc_start: 0.8913 (t-90) cc_final: 0.8194 (t-90) REVERT: LY 28 ARG cc_start: 0.8152 (ttt-90) cc_final: 0.7901 (ttp-170) REVERT: LY 98 ASN cc_start: 0.8703 (m-40) cc_final: 0.8476 (m-40) REVERT: La 69 TRP cc_start: 0.7582 (t60) cc_final: 0.7226 (t60) REVERT: La 91 LEU cc_start: 0.9150 (mt) cc_final: 0.8913 (mt) REVERT: Lc 29 SER cc_start: 0.9010 (m) cc_final: 0.8718 (p) REVERT: Ld 80 ASN cc_start: 0.8159 (t0) cc_final: 0.7753 (t0) REVERT: Ld 84 ASP cc_start: 0.5662 (p0) cc_final: 0.5078 (p0) REVERT: Le 22 SER cc_start: 0.8307 (p) cc_final: 0.7867 (t) REVERT: Le 63 THR cc_start: 0.9322 (m) cc_final: 0.9108 (p) REVERT: Le 75 LEU cc_start: 0.9177 (tp) cc_final: 0.8966 (tp) REVERT: Le 120 THR cc_start: 0.9153 (p) cc_final: 0.7751 (p) REVERT: Lf 8 TYR cc_start: 0.8518 (p90) cc_final: 0.8316 (p90) REVERT: Lf 39 GLN cc_start: 0.8726 (mp10) cc_final: 0.8356 (mp10) REVERT: Lf 97 SER cc_start: 0.9067 (t) cc_final: 0.8592 (p) REVERT: Lg 11 ASN cc_start: 0.8785 (t0) cc_final: 0.8415 (t0) REVERT: Lh 41 LEU cc_start: 0.7505 (tp) cc_final: 0.7068 (tt) REVERT: Lh 75 TYR cc_start: 0.7690 (m-80) cc_final: 0.7448 (m-80) REVERT: Lh 76 GLN cc_start: 0.8595 (pt0) cc_final: 0.8034 (pm20) REVERT: Lh 107 LYS cc_start: 0.8226 (mtmt) cc_final: 0.7568 (mttt) REVERT: Li 58 ILE cc_start: 0.8744 (mm) cc_final: 0.8513 (mm) REVERT: Li 80 PHE cc_start: 0.7952 (t80) cc_final: 0.6844 (t80) REVERT: Lj 12 HIS cc_start: 0.8022 (p90) cc_final: 0.7656 (p-80) REVERT: Lj 64 MET cc_start: 0.8355 (mpp) cc_final: 0.8089 (mpp) REVERT: Lj 76 ASN cc_start: 0.6958 (m110) cc_final: 0.6275 (m110) REVERT: Lk 54 LEU cc_start: 0.8781 (tp) cc_final: 0.8486 (tp) REVERT: Ll 27 ILE cc_start: 0.8266 (mm) cc_final: 0.7993 (mm) REVERT: Lm 98 LYS cc_start: 0.9096 (mmmt) cc_final: 0.8888 (mtmt) REVERT: Lm 113 ARG cc_start: 0.8391 (mtp-110) cc_final: 0.8032 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8774 (mt0) cc_final: 0.8526 (mp10) REVERT: Ln 4 LYS cc_start: 0.3308 (mptt) cc_final: 0.3061 (ttpt) REVERT: Ln 5 TRP cc_start: 0.7319 (m100) cc_final: 0.6358 (m-10) REVERT: Ln 9 ARG cc_start: 0.8018 (ttm170) cc_final: 0.7590 (ttp-110) REVERT: Lo 57 VAL cc_start: 0.8757 (t) cc_final: 0.8259 (p) REVERT: Lp 48 LYS cc_start: 0.8992 (mtpp) cc_final: 0.8756 (mttm) REVERT: Lp 61 LYS cc_start: 0.9059 (mmmt) cc_final: 0.8053 (pptt) REVERT: Lp 79 VAL cc_start: 0.9691 (t) cc_final: 0.9418 (p) REVERT: Lp 81 SER cc_start: 0.9500 (t) cc_final: 0.9243 (p) REVERT: C 1 MET cc_start: 0.1640 (mtm) cc_final: -0.0292 (mmt) REVERT: D 2 SER cc_start: -0.0821 (OUTLIER) cc_final: -0.1186 (t) REVERT: D 127 MET cc_start: 0.0917 (mtp) cc_final: 0.0555 (mtp) REVERT: D 690 MET cc_start: 0.1003 (mmm) cc_final: 0.0187 (ptt) outliers start: 11 outliers final: 2 residues processed: 2456 average time/residue: 1.4529 time to fit residues: 6112.6677 Evaluate side-chains 1432 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1429 time to evaluate : 7.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 2 SER Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 782 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 966 optimal weight: 20.0000 chunk 867 optimal weight: 20.0000 chunk 481 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 584 optimal weight: 30.0000 chunk 463 optimal weight: 8.9990 chunk 896 optimal weight: 20.0000 chunk 346 optimal weight: 7.9990 chunk 545 optimal weight: 7.9990 chunk 667 optimal weight: 0.8980 chunk 1038 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 341 HIS ** B 364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 382 ASN B 469 ASN B 554 GLN B 681 ASN LA 218 HIS LB 165 GLN LB 243 HIS LC 58 HIS LC 296 GLN ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LD 274 GLN LE 57 HIS LF 80 GLN ** LF 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN ** LG 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LG 221 ASN ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 100 ASN LI 59 GLN LI 73 ASN LI 95 HIS LI 113 GLN LI 209 ASN LL 6 ASN LL 66 ASN LM 27 GLN LM 119 GLN LN 70 ASN LN 86 ASN LN 175 ASN LO 55 HIS A ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 78 ASN ** LR 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 8 GLN ** LS 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LU 101 ASN LV 24 ASN LV 81 GLN LX 65 GLN LY 4 GLN LY 120 GLN La 25 HIS La 28 HIS Ld 21 HIS Le 26 HIS ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 17 GLN Lf 87 ASN Lf 106 ASN Lh 59 ASN ** Lh 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 76 ASN Ll 32 ASN D 17 ASN ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 96 HIS ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 337 HIS D 681 ASN D 699 ASN ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.2245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 151486 Z= 0.275 Angle : 0.670 14.428 221974 Z= 0.347 Chirality : 0.039 0.360 27643 Planarity : 0.006 0.092 14813 Dihedral : 22.961 179.431 64440 Min Nonbonded Distance : 1.759 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.73 % Favored : 95.15 % Rotamer: Outliers : 3.56 % Allowed : 12.83 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -0.18 (0.09), residues: 7994 helix: 0.67 (0.09), residues: 3324 sheet: -0.32 (0.17), residues: 896 loop : -0.70 (0.10), residues: 3774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRPLe 32 HIS 0.011 0.002 HISLA 218 PHE 0.044 0.003 PHE C 44 TYR 0.031 0.003 TYRLH 92 ARG 0.016 0.001 ARG D 545 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1764 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1519 time to evaluate : 7.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.1591 (mpp) cc_final: 0.0838 (tpp) REVERT: A 102 THR cc_start: 0.4117 (t) cc_final: 0.3614 (p) REVERT: A 103 MET cc_start: 0.1029 (OUTLIER) cc_final: 0.0735 (mmt) REVERT: B 57 ASN cc_start: 0.6526 (m-40) cc_final: 0.6282 (t0) REVERT: B 108 TYR cc_start: 0.4666 (p90) cc_final: 0.4385 (t80) REVERT: B 148 TYR cc_start: 0.4384 (m-80) cc_final: 0.3961 (m-80) REVERT: B 223 ASN cc_start: 0.5353 (m110) cc_final: 0.5055 (t0) REVERT: B 351 MET cc_start: 0.5448 (OUTLIER) cc_final: 0.2863 (tmm) REVERT: B 462 PHE cc_start: 0.7664 (m-80) cc_final: 0.6629 (m-80) REVERT: B 532 MET cc_start: 0.4977 (tmm) cc_final: 0.4360 (mmt) REVERT: B 535 MET cc_start: 0.2358 (OUTLIER) cc_final: 0.2106 (ptm) REVERT: B 619 PHE cc_start: 0.7710 (t80) cc_final: 0.7414 (t80) REVERT: B 623 ILE cc_start: 0.8300 (mm) cc_final: 0.7743 (mm) REVERT: B 631 LEU cc_start: 0.7555 (mt) cc_final: 0.6787 (mt) REVERT: B 724 ASP cc_start: 0.8179 (m-30) cc_final: 0.7836 (t70) REVERT: LA 20 THR cc_start: 0.8277 (p) cc_final: 0.8032 (p) REVERT: LA 133 TYR cc_start: 0.8809 (p90) cc_final: 0.8143 (p90) REVERT: LA 227 ARG cc_start: 0.8263 (ttm-80) cc_final: 0.8056 (ttm-80) REVERT: LB 53 MET cc_start: 0.7829 (mtp) cc_final: 0.7489 (mtt) REVERT: LB 167 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8534 (ptm-80) REVERT: LB 214 MET cc_start: 0.7993 (tpp) cc_final: 0.7764 (tpp) REVERT: LB 323 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.8272 (ppp) REVERT: LB 345 ASN cc_start: 0.8420 (t0) cc_final: 0.7626 (t0) REVERT: LB 349 LYS cc_start: 0.9509 (OUTLIER) cc_final: 0.9160 (ttmt) REVERT: LC 41 SER cc_start: 0.9723 (m) cc_final: 0.9348 (t) REVERT: LC 108 LYS cc_start: 0.8674 (mttt) cc_final: 0.8437 (mttp) REVERT: LC 177 ASP cc_start: 0.8853 (p0) cc_final: 0.8608 (p0) REVERT: LC 229 ASN cc_start: 0.8629 (t0) cc_final: 0.8414 (t0) REVERT: LD 31 TYR cc_start: 0.8636 (t80) cc_final: 0.8091 (t80) REVERT: LD 32 GLN cc_start: 0.7965 (mm-40) cc_final: 0.7391 (tp40) REVERT: LD 36 LEU cc_start: 0.8956 (mt) cc_final: 0.8380 (mt) REVERT: LD 43 LYS cc_start: 0.8692 (OUTLIER) cc_final: 0.8462 (mmtp) REVERT: LD 111 GLN cc_start: 0.9307 (tm-30) cc_final: 0.9011 (tm-30) REVERT: LD 180 PHE cc_start: 0.8692 (m-80) cc_final: 0.8279 (m-80) REVERT: LD 227 LEU cc_start: 0.8159 (mp) cc_final: 0.7775 (pp) REVERT: LD 242 SER cc_start: 0.9168 (m) cc_final: 0.8959 (p) REVERT: LE 9 TRP cc_start: 0.7812 (t60) cc_final: 0.7504 (t60) REVERT: LE 10 TYR cc_start: 0.8441 (m-80) cc_final: 0.7868 (m-10) REVERT: LE 13 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6107 (mm-30) REVERT: LF 52 GLN cc_start: 0.9114 (tm-30) cc_final: 0.8048 (tm-30) REVERT: LF 68 ASP cc_start: 0.8672 (m-30) cc_final: 0.8460 (m-30) REVERT: LF 112 ASN cc_start: 0.8524 (m-40) cc_final: 0.8128 (t0) REVERT: LF 125 GLU cc_start: 0.7045 (mp0) cc_final: 0.6703 (mp0) REVERT: LF 146 GLN cc_start: 0.8901 (tp40) cc_final: 0.8451 (tp40) REVERT: LF 173 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8569 (mm) REVERT: LG 221 ASN cc_start: 0.8313 (m-40) cc_final: 0.7995 (m-40) REVERT: LH 12 VAL cc_start: 0.8334 (t) cc_final: 0.7664 (t) REVERT: LH 23 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.6898 (mtp85) REVERT: LH 72 LYS cc_start: 0.9558 (OUTLIER) cc_final: 0.8816 (tttp) REVERT: LH 177 ASP cc_start: 0.8193 (OUTLIER) cc_final: 0.7436 (m-30) REVERT: LI 73 ASN cc_start: 0.8442 (m-40) cc_final: 0.7920 (m110) REVERT: LI 146 ASP cc_start: 0.7956 (p0) cc_final: 0.7715 (m-30) REVERT: LJ 17 LEU cc_start: 0.8889 (tp) cc_final: 0.8617 (tp) REVERT: LJ 38 GLU cc_start: 0.7719 (tp30) cc_final: 0.7515 (tp30) REVERT: LJ 88 GLU cc_start: 0.9129 (tm-30) cc_final: 0.8821 (tm-30) REVERT: LJ 101 ASN cc_start: 0.7235 (m-40) cc_final: 0.6800 (t0) REVERT: LL 92 THR cc_start: 0.8646 (p) cc_final: 0.8353 (t) REVERT: LM 24 LYS cc_start: 0.8528 (ttmt) cc_final: 0.8297 (ptpt) REVERT: LM 56 GLN cc_start: 0.8635 (pt0) cc_final: 0.8062 (pm20) REVERT: LM 94 TRP cc_start: 0.9073 (t-100) cc_final: 0.8655 (t-100) REVERT: LN 87 GLN cc_start: 0.8860 (mt0) cc_final: 0.8470 (mt0) REVERT: LN 104 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8112 (mp0) REVERT: LN 153 ASP cc_start: 0.8903 (t70) cc_final: 0.8691 (t0) REVERT: LO 42 ASN cc_start: 0.8507 (m110) cc_final: 0.8284 (m-40) REVERT: LP 64 ASN cc_start: 0.7644 (p0) cc_final: 0.7320 (p0) REVERT: LR 25 ASP cc_start: 0.8401 (p0) cc_final: 0.8189 (p0) REVERT: LR 27 ASN cc_start: 0.9333 (m110) cc_final: 0.8810 (t0) REVERT: LR 68 GLN cc_start: 0.9063 (tp40) cc_final: 0.8688 (tm-30) REVERT: LR 76 SER cc_start: 0.9386 (m) cc_final: 0.9125 (p) REVERT: LR 95 TRP cc_start: 0.9348 (t-100) cc_final: 0.9091 (t-100) REVERT: LS 71 LYS cc_start: 0.8788 (tttt) cc_final: 0.8460 (ttmt) REVERT: LS 104 GLU cc_start: 0.9232 (tt0) cc_final: 0.8787 (mt-10) REVERT: LS 165 TYR cc_start: 0.9116 (m-80) cc_final: 0.8845 (m-80) REVERT: LV 15 LEU cc_start: 0.9255 (mm) cc_final: 0.8797 (mm) REVERT: LV 40 LYS cc_start: 0.9154 (mmmm) cc_final: 0.8926 (mmmt) REVERT: LV 70 ARG cc_start: 0.8433 (ttm-80) cc_final: 0.7647 (ttm-80) REVERT: LV 74 MET cc_start: 0.8205 (ptp) cc_final: 0.7502 (ptp) REVERT: LV 92 PHE cc_start: 0.8448 (m-80) cc_final: 0.8070 (m-10) REVERT: LV 120 LYS cc_start: 0.9499 (ttpt) cc_final: 0.9257 (ttmm) REVERT: LV 125 LEU cc_start: 0.9516 (mp) cc_final: 0.9286 (mp) REVERT: LV 132 ASN cc_start: 0.9039 (m110) cc_final: 0.8746 (t0) REVERT: LW 12 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8699 (mtmm) REVERT: LW 27 LYS cc_start: 0.8772 (tmtt) cc_final: 0.8398 (tptp) REVERT: LX 27 ARG cc_start: 0.7781 (mmt90) cc_final: 0.7481 (mtt180) REVERT: LY 28 ARG cc_start: 0.8268 (ttt-90) cc_final: 0.7977 (ttp80) REVERT: LY 53 ASP cc_start: 0.8220 (m-30) cc_final: 0.7961 (m-30) REVERT: LY 54 ASP cc_start: 0.6071 (m-30) cc_final: 0.5627 (m-30) REVERT: LZ 48 ARG cc_start: 0.7967 (ttm170) cc_final: 0.7672 (mtm180) REVERT: LZ 77 TYR cc_start: 0.8413 (m-10) cc_final: 0.8169 (m-80) REVERT: LZ 90 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7689 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8436 (tt0) cc_final: 0.8174 (mm-30) REVERT: La 7 LYS cc_start: 0.8913 (mmtt) cc_final: 0.8650 (mmtt) REVERT: La 69 TRP cc_start: 0.7893 (t60) cc_final: 0.7588 (t60) REVERT: La 120 ASN cc_start: 0.8146 (m-40) cc_final: 0.7908 (p0) REVERT: Lc 29 SER cc_start: 0.9096 (m) cc_final: 0.8722 (p) REVERT: Lc 70 PHE cc_start: 0.7737 (t80) cc_final: 0.7522 (t80) REVERT: Ld 6 ASP cc_start: 0.7574 (p0) cc_final: 0.7342 (p0) REVERT: Ld 80 ASN cc_start: 0.8126 (t0) cc_final: 0.7882 (t0) REVERT: Ld 84 ASP cc_start: 0.5798 (p0) cc_final: 0.5106 (p0) REVERT: Le 63 THR cc_start: 0.9426 (m) cc_final: 0.9172 (p) REVERT: Lf 92 LYS cc_start: 0.9364 (tttm) cc_final: 0.8849 (tptm) REVERT: Lf 97 SER cc_start: 0.8924 (t) cc_final: 0.8370 (p) REVERT: Lg 11 ASN cc_start: 0.8963 (t0) cc_final: 0.8580 (t0) REVERT: Lg 29 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8865 (tp) REVERT: Lg 96 GLU cc_start: 0.8016 (pp20) cc_final: 0.7748 (pp20) REVERT: Lh 60 GLU cc_start: 0.9033 (pt0) cc_final: 0.8782 (pt0) REVERT: Lh 76 GLN cc_start: 0.8625 (pt0) cc_final: 0.8004 (pm20) REVERT: Li 80 PHE cc_start: 0.8304 (t80) cc_final: 0.7886 (t80) REVERT: Lj 64 MET cc_start: 0.8438 (mpp) cc_final: 0.8197 (mpp) REVERT: Lm 103 LEU cc_start: 0.9245 (mm) cc_final: 0.8928 (mp) REVERT: Lm 113 ARG cc_start: 0.8373 (mtp-110) cc_final: 0.7980 (ttp80) REVERT: Lm 119 ASN cc_start: 0.9017 (t0) cc_final: 0.8616 (t0) REVERT: Lm 120 GLN cc_start: 0.8765 (mt0) cc_final: 0.8562 (mp10) REVERT: Ln 4 LYS cc_start: 0.3203 (mptt) cc_final: 0.2885 (ttpt) REVERT: Ln 5 TRP cc_start: 0.7358 (m100) cc_final: 0.6278 (m-10) REVERT: Ln 9 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7607 (ttp-110) REVERT: Lo 41 ARG cc_start: 0.8102 (mtm180) cc_final: 0.7691 (mtp180) REVERT: Lo 92 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7464 (tm-30) REVERT: Lp 48 LYS cc_start: 0.8976 (mtpp) cc_final: 0.8757 (mttp) REVERT: Lp 81 SER cc_start: 0.9540 (t) cc_final: 0.9318 (p) REVERT: C 49 MET cc_start: 0.3261 (mpp) cc_final: 0.2631 (mmt) REVERT: D 690 MET cc_start: 0.1790 (mmm) cc_final: 0.1099 (ptt) outliers start: 245 outliers final: 139 residues processed: 1642 average time/residue: 1.2958 time to fit residues: 3721.5845 Evaluate side-chains 1425 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 1273 time to evaluate : 7.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 103 MET Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 351 MET Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 754 VAL Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 116 VAL Chi-restraints excluded: chain LA residue 168 VAL Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 322 ILE Chi-restraints excluded: chain LB residue 323 MET Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LD residue 43 LYS Chi-restraints excluded: chain LD residue 53 VAL Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LF residue 62 ILE Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LG residue 71 VAL Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 72 LYS Chi-restraints excluded: chain LH residue 92 TYR Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LL residue 10 LEU Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 147 ILE Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 27 GLN Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LM residue 107 GLU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 43 THR Chi-restraints excluded: chain LN residue 64 VAL Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 171 SER Chi-restraints excluded: chain LO residue 43 ILE Chi-restraints excluded: chain LO residue 99 LEU Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LO residue 184 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 49 GLU Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 127 SER Chi-restraints excluded: chain LR residue 139 VAL Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 39 LEU Chi-restraints excluded: chain LX residue 38 LEU Chi-restraints excluded: chain LX residue 71 THR Chi-restraints excluded: chain LX residue 81 ILE Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 80 VAL Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 13 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 11 ASN Chi-restraints excluded: chain Lc residue 48 THR Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 90 VAL Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Lc residue 102 THR Chi-restraints excluded: chain Lc residue 103 THR Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 107 VAL Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lf residue 78 SER Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 23 VAL Chi-restraints excluded: chain Lg residue 29 ILE Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 30 GLU Chi-restraints excluded: chain Lh residue 58 ILE Chi-restraints excluded: chain Li residue 26 ILE Chi-restraints excluded: chain Li residue 50 LEU Chi-restraints excluded: chain Li residue 77 LEU Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lk residue 25 VAL Chi-restraints excluded: chain Lk residue 76 ASN Chi-restraints excluded: chain Lm residue 78 ILE Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 64 THR Chi-restraints excluded: chain Lo residue 68 VAL Chi-restraints excluded: chain Lo residue 72 LEU Chi-restraints excluded: chain Lp residue 56 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 9 ILE Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 744 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 577 optimal weight: 6.9990 chunk 322 optimal weight: 5.9990 chunk 864 optimal weight: 20.0000 chunk 707 optimal weight: 6.9990 chunk 286 optimal weight: 7.9990 chunk 1040 optimal weight: 20.0000 chunk 1124 optimal weight: 8.9990 chunk 926 optimal weight: 40.0000 chunk 1032 optimal weight: 20.0000 chunk 354 optimal weight: 5.9990 chunk 834 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 364 HIS B 379 ASN B 438 ASN B 503 ASN B 512 ASN B 560 ASN ** B 600 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 205 ASN ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 159 GLN LF 194 HIS ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN ** LG 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 162 GLN LL 19 GLN LM 27 GLN LM 126 GLN ** LN 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 50 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 137 ASN ** LQ 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LR 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 8 GLN ** LS 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 77 ASN LV 24 ASN ** LW 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LY 42 GLN ** LZ 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** La 67 HIS Le 26 HIS ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lg 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 704 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 151486 Z= 0.266 Angle : 0.617 10.408 221974 Z= 0.323 Chirality : 0.037 0.301 27643 Planarity : 0.005 0.093 14813 Dihedral : 22.967 178.909 64437 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.68 % Favored : 95.20 % Rotamer: Outliers : 3.89 % Allowed : 15.50 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.09), residues: 7994 helix: 0.75 (0.09), residues: 3329 sheet: -0.48 (0.17), residues: 895 loop : -0.73 (0.10), residues: 3770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 700 HIS 0.019 0.002 HIS D 500 PHE 0.045 0.002 PHE D 18 TYR 0.036 0.002 TYR D 459 ARG 0.017 0.001 ARGLN 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1340 time to evaluate : 7.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.1789 (mpp) cc_final: 0.1094 (tpp) REVERT: B 57 ASN cc_start: 0.6451 (m-40) cc_final: 0.6250 (t0) REVERT: B 223 ASN cc_start: 0.5276 (m110) cc_final: 0.4887 (t0) REVERT: B 346 MET cc_start: 0.5952 (tpt) cc_final: 0.5319 (mtt) REVERT: B 384 PHE cc_start: 0.6499 (m-80) cc_final: 0.6085 (m-80) REVERT: B 428 LEU cc_start: 0.7980 (mt) cc_final: 0.7765 (mt) REVERT: B 450 MET cc_start: 0.8295 (mmt) cc_final: 0.7827 (mmt) REVERT: B 462 PHE cc_start: 0.7677 (m-80) cc_final: 0.7034 (m-80) REVERT: B 479 ILE cc_start: 0.7424 (tt) cc_final: 0.6961 (tp) REVERT: B 532 MET cc_start: 0.4968 (OUTLIER) cc_final: 0.4409 (mmt) REVERT: B 619 PHE cc_start: 0.7635 (t80) cc_final: 0.7420 (t80) REVERT: B 623 ILE cc_start: 0.8050 (mm) cc_final: 0.7770 (mm) REVERT: B 631 LEU cc_start: 0.7847 (mt) cc_final: 0.7403 (mt) REVERT: B 644 LEU cc_start: 0.8120 (OUTLIER) cc_final: 0.7750 (mt) REVERT: B 724 ASP cc_start: 0.8098 (m-30) cc_final: 0.7828 (t70) REVERT: LA 69 TYR cc_start: 0.7064 (t80) cc_final: 0.6774 (t80) REVERT: LA 133 TYR cc_start: 0.8852 (p90) cc_final: 0.8388 (p90) REVERT: LA 149 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7905 (mmt-90) REVERT: LA 186 PHE cc_start: 0.9216 (t80) cc_final: 0.8989 (t80) REVERT: LB 167 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8386 (ptm-80) REVERT: LB 214 MET cc_start: 0.8358 (tpp) cc_final: 0.8036 (tpp) REVERT: LB 345 ASN cc_start: 0.8459 (t0) cc_final: 0.7755 (t0) REVERT: LB 349 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9214 (ttmt) REVERT: LC 41 SER cc_start: 0.9669 (m) cc_final: 0.9274 (p) REVERT: LC 93 MET cc_start: 0.8998 (pmm) cc_final: 0.8761 (pmm) REVERT: LC 118 LYS cc_start: 0.8467 (mttt) cc_final: 0.8154 (mtmm) REVERT: LC 166 VAL cc_start: 0.9400 (m) cc_final: 0.9197 (p) REVERT: LC 177 ASP cc_start: 0.8669 (p0) cc_final: 0.8290 (p0) REVERT: LC 274 TYR cc_start: 0.8821 (t80) cc_final: 0.8561 (t80) REVERT: LC 345 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7625 (tp30) REVERT: LD 31 TYR cc_start: 0.8768 (t80) cc_final: 0.8351 (t80) REVERT: LD 36 LEU cc_start: 0.9024 (mt) cc_final: 0.8796 (mt) REVERT: LD 111 GLN cc_start: 0.9319 (tm-30) cc_final: 0.9058 (tm-30) REVERT: LD 180 PHE cc_start: 0.8671 (m-80) cc_final: 0.8320 (m-80) REVERT: LD 227 LEU cc_start: 0.8272 (mp) cc_final: 0.7877 (pp) REVERT: LD 242 SER cc_start: 0.9202 (m) cc_final: 0.8964 (p) REVERT: LE 10 TYR cc_start: 0.8500 (m-80) cc_final: 0.7875 (m-10) REVERT: LE 13 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6372 (mm-30) REVERT: LF 173 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8811 (mm) REVERT: LH 23 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.6815 (mtp85) REVERT: LH 177 ASP cc_start: 0.8393 (OUTLIER) cc_final: 0.7564 (m-30) REVERT: LI 181 TYR cc_start: 0.8087 (t80) cc_final: 0.7887 (t80) REVERT: LI 183 LYS cc_start: 0.9424 (ptmm) cc_final: 0.9126 (mmmt) REVERT: LJ 35 LYS cc_start: 0.9336 (mtmt) cc_final: 0.8591 (tppt) REVERT: LJ 38 GLU cc_start: 0.7967 (tp30) cc_final: 0.7736 (tp30) REVERT: LJ 88 GLU cc_start: 0.8941 (tm-30) cc_final: 0.8708 (tm-30) REVERT: LJ 101 ASN cc_start: 0.7748 (m-40) cc_final: 0.7120 (t0) REVERT: LJ 123 PHE cc_start: 0.6259 (m-10) cc_final: 0.5630 (m-10) REVERT: LM 14 LEU cc_start: 0.9121 (mm) cc_final: 0.8465 (mm) REVERT: LM 16 GLU cc_start: 0.8481 (pt0) cc_final: 0.8047 (pm20) REVERT: LM 24 LYS cc_start: 0.8499 (ttmt) cc_final: 0.8279 (ptpt) REVERT: LM 47 ASP cc_start: 0.7015 (OUTLIER) cc_final: 0.6725 (m-30) REVERT: LM 94 TRP cc_start: 0.9134 (t-100) cc_final: 0.8718 (t-100) REVERT: LO 189 ASP cc_start: 0.8464 (OUTLIER) cc_final: 0.8180 (t70) REVERT: LP 28 ASN cc_start: 0.9230 (m-40) cc_final: 0.8970 (m110) REVERT: LR 7 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8807 (mm-40) REVERT: LR 25 ASP cc_start: 0.8542 (p0) cc_final: 0.8219 (p0) REVERT: LR 27 ASN cc_start: 0.9359 (m110) cc_final: 0.8801 (t0) REVERT: LR 68 GLN cc_start: 0.9065 (tp40) cc_final: 0.8577 (tm-30) REVERT: LS 25 PHE cc_start: 0.7991 (m-10) cc_final: 0.7762 (m-80) REVERT: LS 104 GLU cc_start: 0.9227 (tt0) cc_final: 0.8751 (mt-10) REVERT: LT 79 MET cc_start: 0.9139 (tpp) cc_final: 0.8918 (tpp) REVERT: LV 40 LYS cc_start: 0.9205 (mmmm) cc_final: 0.8891 (mmmt) REVERT: LV 74 MET cc_start: 0.8109 (ptp) cc_final: 0.7855 (ptp) REVERT: LV 92 PHE cc_start: 0.8579 (m-80) cc_final: 0.8180 (m-10) REVERT: LV 120 LYS cc_start: 0.9440 (ttpt) cc_final: 0.9234 (ttmm) REVERT: LV 125 LEU cc_start: 0.9516 (mp) cc_final: 0.9205 (mp) REVERT: LW 12 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8827 (mtmm) REVERT: LW 27 LYS cc_start: 0.8723 (tmtt) cc_final: 0.8353 (tptp) REVERT: LW 58 HIS cc_start: 0.8589 (t-90) cc_final: 0.8229 (t-90) REVERT: LX 27 ARG cc_start: 0.7825 (mmt90) cc_final: 0.7486 (mtt180) REVERT: LX 65 GLN cc_start: 0.9163 (pm20) cc_final: 0.8773 (pm20) REVERT: LX 137 ASN cc_start: 0.9126 (p0) cc_final: 0.8891 (m-40) REVERT: LY 28 ARG cc_start: 0.8387 (ttt-90) cc_final: 0.8014 (ttp-110) REVERT: LZ 42 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.8005 (mm) REVERT: LZ 47 GLU cc_start: 0.8726 (tm-30) cc_final: 0.7826 (pp20) REVERT: LZ 48 ARG cc_start: 0.8126 (ttm170) cc_final: 0.7421 (mtm180) REVERT: LZ 90 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7804 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8539 (tt0) cc_final: 0.8126 (mm-30) REVERT: La 7 LYS cc_start: 0.8975 (mmtt) cc_final: 0.8749 (mmtt) REVERT: La 69 TRP cc_start: 0.8138 (t60) cc_final: 0.7530 (t60) REVERT: Lc 29 SER cc_start: 0.9116 (m) cc_final: 0.8741 (p) REVERT: Ld 11 GLU cc_start: 0.8301 (mm-30) cc_final: 0.7909 (mm-30) REVERT: Ld 84 ASP cc_start: 0.5656 (p0) cc_final: 0.4850 (p0) REVERT: Le 63 THR cc_start: 0.9410 (m) cc_final: 0.9098 (p) REVERT: Le 75 LEU cc_start: 0.9181 (tp) cc_final: 0.8966 (tp) REVERT: Le 87 MET cc_start: 0.9009 (pmm) cc_final: 0.8751 (pmm) REVERT: Le 92 TYR cc_start: 0.8819 (m-10) cc_final: 0.8556 (m-10) REVERT: Le 95 GLU cc_start: 0.7489 (tt0) cc_final: 0.7182 (mm-30) REVERT: Lf 92 LYS cc_start: 0.9381 (tttm) cc_final: 0.8849 (tptp) REVERT: Lf 93 THR cc_start: 0.8986 (p) cc_final: 0.8661 (p) REVERT: Lf 97 SER cc_start: 0.9041 (t) cc_final: 0.8532 (p) REVERT: Lg 11 ASN cc_start: 0.8968 (t0) cc_final: 0.8596 (t0) REVERT: Lg 96 GLU cc_start: 0.7990 (pp20) cc_final: 0.7732 (pp20) REVERT: Lh 60 GLU cc_start: 0.8974 (pt0) cc_final: 0.8619 (pt0) REVERT: Lh 75 TYR cc_start: 0.7754 (m-80) cc_final: 0.6981 (m-80) REVERT: Lh 76 GLN cc_start: 0.8719 (pt0) cc_final: 0.8014 (pm20) REVERT: Li 80 PHE cc_start: 0.8466 (t80) cc_final: 0.8112 (t80) REVERT: Lj 64 MET cc_start: 0.8407 (mpp) cc_final: 0.8189 (mpp) REVERT: Lk 76 ASN cc_start: 0.9056 (OUTLIER) cc_final: 0.8712 (p0) REVERT: Lm 113 ARG cc_start: 0.8406 (mtp-110) cc_final: 0.7976 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8784 (mt0) cc_final: 0.8546 (mp10) REVERT: Ln 4 LYS cc_start: 0.3420 (mptt) cc_final: 0.2966 (ttpt) REVERT: Ln 9 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7771 (ttp-110) REVERT: Lo 92 GLU cc_start: 0.7696 (tm-30) cc_final: 0.7425 (tm-30) REVERT: Lp 25 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8400 (mp10) REVERT: Lp 45 LYS cc_start: 0.8948 (tppp) cc_final: 0.8700 (tppp) REVERT: Lp 48 LYS cc_start: 0.9005 (mtpp) cc_final: 0.8642 (mttm) REVERT: Lp 58 SER cc_start: 0.9272 (p) cc_final: 0.9055 (p) REVERT: Lp 61 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.7842 (pttt) REVERT: Lp 81 SER cc_start: 0.9548 (t) cc_final: 0.9305 (p) REVERT: C 49 MET cc_start: 0.3630 (mpp) cc_final: 0.2949 (mmt) REVERT: D 261 LEU cc_start: 0.7059 (tp) cc_final: 0.6227 (mm) REVERT: D 478 MET cc_start: 0.2456 (ttt) cc_final: 0.2133 (ttt) REVERT: D 690 MET cc_start: 0.1965 (mmm) cc_final: 0.1250 (ptt) outliers start: 268 outliers final: 177 residues processed: 1473 average time/residue: 1.2240 time to fit residues: 3190.2762 Evaluate side-chains 1376 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1183 time to evaluate : 6.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 438 ASN Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain LA residue 31 THR Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 75 ILE Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 116 VAL Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 2 SER Chi-restraints excluded: chain LC residue 11 LEU Chi-restraints excluded: chain LC residue 154 THR Chi-restraints excluded: chain LC residue 306 THR Chi-restraints excluded: chain LC residue 345 GLU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LG residue 71 VAL Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 3 TYR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 74 LEU Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LH residue 181 VAL Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 32 GLN Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 43 ILE Chi-restraints excluded: chain LO residue 166 GLU Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LO residue 182 ASN Chi-restraints excluded: chain LO residue 189 ASP Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 36 ILE Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 61 THR Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 57 THR Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 88 GLN Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 61 THR Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 52 THR Chi-restraints excluded: chain LX residue 38 LEU Chi-restraints excluded: chain LX residue 71 THR Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 26 VAL Chi-restraints excluded: chain LZ residue 42 LEU Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 11 ASN Chi-restraints excluded: chain Lc residue 42 ILE Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Lc residue 102 THR Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Ld residue 46 THR Chi-restraints excluded: chain Ld residue 51 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 97 LEU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 41 VAL Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 55 ILE Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 107 VAL Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lf residue 78 SER Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 29 ILE Chi-restraints excluded: chain Lg residue 35 VAL Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 58 ILE Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Li residue 26 ILE Chi-restraints excluded: chain Li residue 77 LEU Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 25 VAL Chi-restraints excluded: chain Lk residue 76 ASN Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 118 THR Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 68 VAL Chi-restraints excluded: chain Lo residue 72 LEU Chi-restraints excluded: chain Lp residue 25 GLN Chi-restraints excluded: chain Lp residue 31 ILE Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain Lp residue 61 LYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 334 ASP Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 744 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 1028 optimal weight: 20.0000 chunk 782 optimal weight: 20.0000 chunk 540 optimal weight: 9.9990 chunk 115 optimal weight: 20.0000 chunk 496 optimal weight: 9.9990 chunk 698 optimal weight: 2.9990 chunk 1044 optimal weight: 20.0000 chunk 1105 optimal weight: 8.9990 chunk 545 optimal weight: 5.9990 chunk 989 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 343 ASN ** B 380 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 437 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN LC 229 ASN ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN LG 138 HIS ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LJ 43 GLN ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 11 GLN ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 50 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 49 GLN ** LT 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LT 77 ASN LV 24 ASN ** LZ 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lc 71 GLN ** Ld 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Le 26 HIS ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 88 ASN ** Lg 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lg 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ll 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 699 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 151486 Z= 0.293 Angle : 0.639 12.653 221974 Z= 0.333 Chirality : 0.038 0.273 27643 Planarity : 0.005 0.093 14813 Dihedral : 22.995 179.935 64437 Min Nonbonded Distance : 1.548 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.13 % Favored : 94.76 % Rotamer: Outliers : 4.49 % Allowed : 17.45 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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 (0.09), residues: 7994 helix: 0.73 (0.09), residues: 3324 sheet: -0.64 (0.16), residues: 930 loop : -0.75 (0.10), residues: 3740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP D 114 HIS 0.010 0.001 HIS D 500 PHE 0.034 0.002 PHELP 63 TYR 0.031 0.002 TYRLH 92 ARG 0.010 0.001 ARGLE 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1577 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 309 poor density : 1268 time to evaluate : 7.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 MET cc_start: 0.0997 (mpp) cc_final: -0.0109 (tpt) REVERT: B 57 ASN cc_start: 0.6578 (m-40) cc_final: 0.6377 (t0) REVERT: B 223 ASN cc_start: 0.5360 (m110) cc_final: 0.4951 (t0) REVERT: B 346 MET cc_start: 0.6005 (tpt) cc_final: 0.5411 (mtt) REVERT: B 351 MET cc_start: 0.5036 (ttt) cc_final: 0.2152 (tmm) REVERT: B 428 LEU cc_start: 0.7735 (mt) cc_final: 0.7534 (mt) REVERT: B 450 MET cc_start: 0.8195 (mmt) cc_final: 0.7956 (mmt) REVERT: B 462 PHE cc_start: 0.7807 (m-80) cc_final: 0.7363 (m-80) REVERT: B 532 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.4488 (mmm) REVERT: B 579 MET cc_start: 0.5771 (mtm) cc_final: 0.5396 (mtm) REVERT: B 631 LEU cc_start: 0.7842 (mt) cc_final: 0.7535 (mt) REVERT: B 724 ASP cc_start: 0.8127 (m-30) cc_final: 0.7882 (t70) REVERT: LA 8 GLN cc_start: 0.9117 (mt0) cc_final: 0.8762 (mt0) REVERT: LA 69 TYR cc_start: 0.7138 (t80) cc_final: 0.6860 (t80) REVERT: LA 133 TYR cc_start: 0.8852 (p90) cc_final: 0.8410 (p90) REVERT: LB 167 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8516 (ptm-80) REVERT: LB 345 ASN cc_start: 0.8488 (t0) cc_final: 0.7817 (t0) REVERT: LB 349 LYS cc_start: 0.9559 (OUTLIER) cc_final: 0.9234 (ttmt) REVERT: LC 41 SER cc_start: 0.9703 (m) cc_final: 0.9378 (p) REVERT: LC 93 MET cc_start: 0.9028 (pmm) cc_final: 0.8799 (pmm) REVERT: LC 99 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7613 (ppp) REVERT: LC 108 LYS cc_start: 0.8462 (mttp) cc_final: 0.8259 (pttm) REVERT: LC 118 LYS cc_start: 0.8554 (mttt) cc_final: 0.8233 (mtmm) REVERT: LC 177 ASP cc_start: 0.8776 (p0) cc_final: 0.8403 (p0) REVERT: LC 274 TYR cc_start: 0.8887 (t80) cc_final: 0.8684 (t80) REVERT: LD 31 TYR cc_start: 0.8917 (t80) cc_final: 0.8339 (t80) REVERT: LD 43 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8312 (mmtp) REVERT: LD 93 THR cc_start: 0.8398 (OUTLIER) cc_final: 0.8158 (m) REVERT: LD 111 GLN cc_start: 0.9287 (tm-30) cc_final: 0.9021 (tm-30) REVERT: LD 180 PHE cc_start: 0.8714 (m-80) cc_final: 0.8401 (m-80) REVERT: LD 227 LEU cc_start: 0.8426 (mp) cc_final: 0.8012 (pp) REVERT: LE 10 TYR cc_start: 0.8507 (m-80) cc_final: 0.7964 (m-10) REVERT: LE 13 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6988 (mm-30) REVERT: LF 102 VAL cc_start: 0.9646 (t) cc_final: 0.9407 (m) REVERT: LF 173 LEU cc_start: 0.9192 (OUTLIER) cc_final: 0.8888 (mm) REVERT: LH 23 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7002 (mtp85) REVERT: LH 177 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.7671 (m-30) REVERT: LI 181 TYR cc_start: 0.8044 (t80) cc_final: 0.7792 (t80) REVERT: LJ 60 ARG cc_start: 0.7203 (OUTLIER) cc_final: 0.6819 (ptp-170) REVERT: LJ 88 GLU cc_start: 0.9021 (tm-30) cc_final: 0.8769 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8202 (m-40) cc_final: 0.7520 (t0) REVERT: LJ 123 PHE cc_start: 0.6119 (m-80) cc_final: 0.5532 (m-10) REVERT: LM 14 LEU cc_start: 0.9207 (mm) cc_final: 0.8614 (mm) REVERT: LM 16 GLU cc_start: 0.8526 (pt0) cc_final: 0.8022 (pm20) REVERT: LM 42 LYS cc_start: 0.8043 (mttt) cc_final: 0.7608 (mttt) REVERT: LM 47 ASP cc_start: 0.6996 (OUTLIER) cc_final: 0.6702 (m-30) REVERT: LM 94 TRP cc_start: 0.9171 (t-100) cc_final: 0.8768 (t-100) REVERT: LN 6 TYR cc_start: 0.8442 (m-80) cc_final: 0.8232 (m-80) REVERT: LN 160 GLU cc_start: 0.8017 (pm20) cc_final: 0.7531 (pm20) REVERT: LN 175 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8047 (m110) REVERT: LP 28 ASN cc_start: 0.9267 (m-40) cc_final: 0.9022 (m110) REVERT: LR 25 ASP cc_start: 0.8723 (p0) cc_final: 0.8367 (p0) REVERT: LR 27 ASN cc_start: 0.9304 (m110) cc_final: 0.8736 (t0) REVERT: LR 68 GLN cc_start: 0.9177 (tp40) cc_final: 0.8699 (tm-30) REVERT: LR 95 TRP cc_start: 0.9356 (t-100) cc_final: 0.9035 (t-100) REVERT: LS 25 PHE cc_start: 0.8136 (m-10) cc_final: 0.7769 (m-80) REVERT: LS 104 GLU cc_start: 0.9200 (tt0) cc_final: 0.8765 (mt-10) REVERT: LV 15 LEU cc_start: 0.9172 (mm) cc_final: 0.8836 (mm) REVERT: LV 92 PHE cc_start: 0.8619 (m-80) cc_final: 0.8294 (m-10) REVERT: LV 120 LYS cc_start: 0.9471 (ttpt) cc_final: 0.9204 (ttmm) REVERT: LV 125 LEU cc_start: 0.9571 (mp) cc_final: 0.9249 (mp) REVERT: LW 12 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8965 (mtmm) REVERT: LW 27 LYS cc_start: 0.8833 (tmtt) cc_final: 0.8449 (tptp) REVERT: LW 31 PHE cc_start: 0.8588 (m-10) cc_final: 0.8352 (m-10) REVERT: LW 58 HIS cc_start: 0.8602 (t-90) cc_final: 0.8226 (t-90) REVERT: LX 27 ARG cc_start: 0.7863 (mmt90) cc_final: 0.7649 (mmt180) REVERT: LY 6 LEU cc_start: 0.9049 (tt) cc_final: 0.8821 (mp) REVERT: LY 26 GLN cc_start: 0.9315 (pm20) cc_final: 0.9042 (pm20) REVERT: LY 53 ASP cc_start: 0.8277 (m-30) cc_final: 0.7625 (t0) REVERT: LZ 47 GLU cc_start: 0.8702 (tm-30) cc_final: 0.7680 (pp20) REVERT: LZ 48 ARG cc_start: 0.8220 (ttm170) cc_final: 0.7425 (mtm180) REVERT: LZ 90 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7732 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8551 (tt0) cc_final: 0.8091 (mm-30) REVERT: La 64 GLN cc_start: 0.8658 (pt0) cc_final: 0.8235 (pt0) REVERT: Lc 25 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7786 (mm) REVERT: Lc 29 SER cc_start: 0.9142 (m) cc_final: 0.8763 (p) REVERT: Ld 11 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7858 (mm-30) REVERT: Ld 82 GLU cc_start: 0.7409 (pp20) cc_final: 0.7199 (pp20) REVERT: Ld 84 ASP cc_start: 0.6216 (p0) cc_final: 0.5961 (p0) REVERT: Lf 92 LYS cc_start: 0.9438 (tttm) cc_final: 0.8856 (tptp) REVERT: Lf 97 SER cc_start: 0.9111 (t) cc_final: 0.8594 (p) REVERT: Lg 11 ASN cc_start: 0.9097 (t0) cc_final: 0.8846 (t0) REVERT: Lh 60 GLU cc_start: 0.9040 (pt0) cc_final: 0.8635 (pt0) REVERT: Li 53 TYR cc_start: 0.8421 (p90) cc_final: 0.8024 (p90) REVERT: Li 80 PHE cc_start: 0.8520 (t80) cc_final: 0.8150 (t80) REVERT: Li 91 ASN cc_start: 0.8810 (m-40) cc_final: 0.8546 (m110) REVERT: Lj 64 MET cc_start: 0.8433 (mpp) cc_final: 0.8199 (mpp) REVERT: Ll 28 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8309 (mtt-85) REVERT: Lm 113 ARG cc_start: 0.8426 (mtp-110) cc_final: 0.7880 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8803 (mt0) cc_final: 0.8560 (mp10) REVERT: Ln 4 LYS cc_start: 0.3526 (mptt) cc_final: 0.2919 (ttpt) REVERT: Ln 9 ARG cc_start: 0.8259 (ttm170) cc_final: 0.7773 (ttp-110) REVERT: Lo 29 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7263 (ptpp) REVERT: Lo 92 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7242 (tm-30) REVERT: Lp 32 GLN cc_start: 0.8994 (mt0) cc_final: 0.8734 (mt0) REVERT: Lp 45 LYS cc_start: 0.9040 (tppp) cc_final: 0.8706 (tppp) REVERT: Lp 48 LYS cc_start: 0.9025 (mtpp) cc_final: 0.8712 (mttp) REVERT: Lp 81 SER cc_start: 0.9537 (t) cc_final: 0.9290 (p) REVERT: D 126 GLN cc_start: 0.5871 (OUTLIER) cc_final: 0.5079 (mm-40) REVERT: D 198 TYR cc_start: 0.4943 (t80) cc_final: 0.4501 (t80) REVERT: D 261 LEU cc_start: 0.7011 (tp) cc_final: 0.6566 (mm) REVERT: D 532 MET cc_start: 0.5989 (mmt) cc_final: 0.4029 (tpt) REVERT: D 535 MET cc_start: 0.4030 (tpp) cc_final: 0.3770 (mtm) REVERT: D 690 MET cc_start: 0.2009 (mmm) cc_final: 0.1236 (ptt) outliers start: 309 outliers final: 212 residues processed: 1435 average time/residue: 1.1994 time to fit residues: 3037.3066 Evaluate side-chains 1385 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1157 time to evaluate : 7.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 655 LEU Chi-restraints excluded: chain B residue 686 ILE Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain LA residue 24 GLN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LA residue 204 MET Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 2 SER Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 327 LEU Chi-restraints excluded: chain LC residue 345 GLU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LD residue 43 LYS Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 97 ASN Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LG residue 36 ILE Chi-restraints excluded: chain LG residue 71 VAL Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 74 LEU Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 131 ILE Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LJ residue 60 ARG Chi-restraints excluded: chain LJ residue 62 ASN Chi-restraints excluded: chain LL residue 10 LEU Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 141 LEU Chi-restraints excluded: chain LO residue 166 GLU Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 47 ASN Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 94 VAL Chi-restraints excluded: chain LR residue 139 VAL Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 11 THR Chi-restraints excluded: chain LT residue 61 THR Chi-restraints excluded: chain LT residue 70 SER Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 34 LEU Chi-restraints excluded: chain LV residue 53 SER Chi-restraints excluded: chain LV residue 61 THR Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 109 MET Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LW residue 5 ILE Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 39 LEU Chi-restraints excluded: chain LW residue 52 THR Chi-restraints excluded: chain LX residue 81 ILE Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LX residue 126 LEU Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 13 THR Chi-restraints excluded: chain Lb residue 19 ASN Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 11 ASN Chi-restraints excluded: chain Lc residue 25 LEU Chi-restraints excluded: chain Lc residue 42 ILE Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Lc residue 102 THR Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Ld residue 46 THR Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 41 VAL Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Le residue 107 VAL Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 58 ILE Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Lh residue 98 SER Chi-restraints excluded: chain Li residue 26 ILE Chi-restraints excluded: chain Li residue 77 LEU Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 15 SER Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 25 VAL Chi-restraints excluded: chain Lk residue 41 THR Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 78 ILE Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lm residue 118 THR Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 29 LYS Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 64 THR Chi-restraints excluded: chain Lo residue 68 VAL Chi-restraints excluded: chain Lo residue 72 LEU Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 126 GLN Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 744 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 920 optimal weight: 20.0000 chunk 627 optimal weight: 9.9990 chunk 16 optimal weight: 40.0000 chunk 823 optimal weight: 20.0000 chunk 456 optimal weight: 6.9990 chunk 943 optimal weight: 20.0000 chunk 764 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 564 optimal weight: 5.9990 chunk 992 optimal weight: 20.0000 chunk 279 optimal weight: 6.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 297 ASN B 382 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 211 HIS LB 121 ASN ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 167 ASN ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LH 58 HIS ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 156 HIS ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 50 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LS 138 GLN ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN LZ 57 HIS Lb 43 HIS Lc 47 ASN ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 88 ASN ** Lg 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Li 63 ASN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 76 ASN ** Ll 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lp 34 HIS D 82 HIS D 113 HIS D 126 GLN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 571 HIS D 581 GLN D 699 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 151486 Z= 0.296 Angle : 0.647 14.352 221974 Z= 0.336 Chirality : 0.038 0.313 27643 Planarity : 0.005 0.094 14813 Dihedral : 23.039 179.721 64437 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 19.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.09 % Favored : 94.80 % Rotamer: Outliers : 4.72 % Allowed : 19.03 % Favored : 76.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % Twisted General : 0.03 % 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: -0.29 (0.09), residues: 7994 helix: 0.69 (0.09), residues: 3318 sheet: -0.59 (0.17), residues: 870 loop : -0.83 (0.10), residues: 3806 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP B 700 HIS 0.012 0.002 HIS D 337 PHE 0.030 0.002 PHELc 70 TYR 0.039 0.002 TYR B 610 ARG 0.011 0.001 ARGLb 14 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1558 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 325 poor density : 1233 time to evaluate : 7.496 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.4615 (tm-30) cc_final: 0.4147 (mm-30) REVERT: A 64 MET cc_start: -0.0049 (mpp) cc_final: -0.1267 (tpp) REVERT: B 57 ASN cc_start: 0.6591 (m-40) cc_final: 0.6374 (t0) REVERT: B 223 ASN cc_start: 0.5416 (m110) cc_final: 0.5048 (t0) REVERT: B 346 MET cc_start: 0.5962 (tpt) cc_final: 0.5460 (mtt) REVERT: B 351 MET cc_start: 0.4862 (ttt) cc_final: 0.2235 (tmm) REVERT: B 447 VAL cc_start: 0.7591 (OUTLIER) cc_final: 0.6761 (p) REVERT: B 462 PHE cc_start: 0.7930 (OUTLIER) cc_final: 0.7348 (m-80) REVERT: B 532 MET cc_start: 0.5335 (OUTLIER) cc_final: 0.4798 (mmm) REVERT: B 724 ASP cc_start: 0.8051 (m-30) cc_final: 0.7813 (t70) REVERT: B 736 LYS cc_start: 0.7948 (OUTLIER) cc_final: 0.7538 (mmtt) REVERT: LA 8 GLN cc_start: 0.9130 (mt0) cc_final: 0.8849 (mt0) REVERT: LA 69 TYR cc_start: 0.7202 (t80) cc_final: 0.6884 (t80) REVERT: LA 133 TYR cc_start: 0.8953 (p90) cc_final: 0.8523 (p90) REVERT: LA 149 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7828 (mmt-90) REVERT: LA 246 LEU cc_start: 0.8960 (tt) cc_final: 0.8639 (tt) REVERT: LB 167 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8602 (ptm-80) REVERT: LB 298 PHE cc_start: 0.8813 (m-80) cc_final: 0.8456 (m-10) REVERT: LB 345 ASN cc_start: 0.8505 (t0) cc_final: 0.7804 (t0) REVERT: LB 349 LYS cc_start: 0.9551 (OUTLIER) cc_final: 0.9230 (ttmt) REVERT: LC 41 SER cc_start: 0.9691 (m) cc_final: 0.9319 (p) REVERT: LC 93 MET cc_start: 0.9081 (pmm) cc_final: 0.8833 (pmm) REVERT: LC 99 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.7585 (ppp) REVERT: LC 118 LYS cc_start: 0.8548 (mttt) cc_final: 0.8236 (mtmm) REVERT: LC 166 VAL cc_start: 0.9368 (m) cc_final: 0.9160 (p) REVERT: LC 177 ASP cc_start: 0.8678 (p0) cc_final: 0.8294 (p0) REVERT: LC 274 TYR cc_start: 0.8915 (t80) cc_final: 0.8713 (t80) REVERT: LD 31 TYR cc_start: 0.8962 (t80) cc_final: 0.8284 (t80) REVERT: LD 43 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8343 (mmtp) REVERT: LD 111 GLN cc_start: 0.9289 (tm-30) cc_final: 0.9017 (tm-30) REVERT: LD 180 PHE cc_start: 0.8782 (m-80) cc_final: 0.8486 (m-80) REVERT: LD 227 LEU cc_start: 0.8391 (mp) cc_final: 0.8064 (pp) REVERT: LE 10 TYR cc_start: 0.8455 (m-80) cc_final: 0.7952 (m-10) REVERT: LE 77 ARG cc_start: 0.7113 (OUTLIER) cc_final: 0.6215 (tpt-90) REVERT: LF 173 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9062 (mm) REVERT: LG 152 LEU cc_start: 0.9063 (mt) cc_final: 0.8831 (mm) REVERT: LH 23 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7058 (mtp85) REVERT: LH 177 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.7717 (m-30) REVERT: LI 181 TYR cc_start: 0.8115 (t80) cc_final: 0.7848 (t80) REVERT: LJ 32 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.8093 (ptt-90) REVERT: LJ 38 GLU cc_start: 0.8191 (pt0) cc_final: 0.7613 (tp30) REVERT: LJ 88 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8762 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8204 (m-40) cc_final: 0.7641 (t0) REVERT: LJ 123 PHE cc_start: 0.6290 (m-80) cc_final: 0.5986 (m-10) REVERT: LM 14 LEU cc_start: 0.9193 (mm) cc_final: 0.8619 (mm) REVERT: LM 16 GLU cc_start: 0.8593 (pt0) cc_final: 0.8353 (pm20) REVERT: LM 41 GLN cc_start: 0.8315 (OUTLIER) cc_final: 0.6749 (tm-30) REVERT: LM 42 LYS cc_start: 0.8073 (mttt) cc_final: 0.7715 (mttt) REVERT: LM 47 ASP cc_start: 0.6997 (OUTLIER) cc_final: 0.6696 (m-30) REVERT: LM 94 TRP cc_start: 0.9195 (t-100) cc_final: 0.8802 (t-100) REVERT: LM 107 GLU cc_start: 0.9115 (pm20) cc_final: 0.8852 (pm20) REVERT: LN 6 TYR cc_start: 0.8422 (m-80) cc_final: 0.8212 (m-80) REVERT: LN 175 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8142 (m110) REVERT: LO 40 GLU cc_start: 0.7589 (mp0) cc_final: 0.7354 (mp0) REVERT: LP 147 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7056 (pt0) REVERT: LR 25 ASP cc_start: 0.8750 (p0) cc_final: 0.8376 (p0) REVERT: LR 27 ASN cc_start: 0.9307 (m110) cc_final: 0.8715 (t0) REVERT: LR 68 GLN cc_start: 0.9120 (tp40) cc_final: 0.8672 (tm-30) REVERT: LR 95 TRP cc_start: 0.9376 (t-100) cc_final: 0.9145 (t-100) REVERT: LS 25 PHE cc_start: 0.8169 (m-10) cc_final: 0.7630 (m-80) REVERT: LS 104 GLU cc_start: 0.9191 (tt0) cc_final: 0.8656 (mt-10) REVERT: LV 11 PHE cc_start: 0.8237 (m-80) cc_final: 0.7708 (m-80) REVERT: LV 40 LYS cc_start: 0.9346 (mmmt) cc_final: 0.9039 (mmmt) REVERT: LV 74 MET cc_start: 0.8033 (ptm) cc_final: 0.7773 (ptp) REVERT: LV 92 PHE cc_start: 0.8789 (m-80) cc_final: 0.8436 (m-10) REVERT: LV 108 GLU cc_start: 0.8302 (tp30) cc_final: 0.7799 (tp30) REVERT: LV 120 LYS cc_start: 0.9498 (ttpt) cc_final: 0.9198 (ttmm) REVERT: LV 125 LEU cc_start: 0.9591 (OUTLIER) cc_final: 0.9272 (mp) REVERT: LW 12 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8985 (mtmm) REVERT: LW 58 HIS cc_start: 0.8589 (t-90) cc_final: 0.8210 (t-90) REVERT: LX 65 GLN cc_start: 0.9164 (pm20) cc_final: 0.8908 (pm20) REVERT: LY 6 LEU cc_start: 0.9061 (tt) cc_final: 0.8860 (mp) REVERT: LY 53 ASP cc_start: 0.8306 (m-30) cc_final: 0.7653 (t0) REVERT: LZ 47 GLU cc_start: 0.8729 (tm-30) cc_final: 0.7625 (pp20) REVERT: LZ 48 ARG cc_start: 0.8226 (ttm170) cc_final: 0.7392 (mtm180) REVERT: LZ 90 GLU cc_start: 0.8016 (tm-30) cc_final: 0.7744 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8616 (tt0) cc_final: 0.8144 (mm-30) REVERT: La 64 GLN cc_start: 0.8571 (pt0) cc_final: 0.8194 (pt0) REVERT: La 69 TRP cc_start: 0.8385 (t60) cc_final: 0.7636 (t60) REVERT: Lb 27 TYR cc_start: 0.8255 (m-10) cc_final: 0.8015 (m-10) REVERT: Lc 25 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7601 (mm) REVERT: Lc 29 SER cc_start: 0.9170 (m) cc_final: 0.8418 (p) REVERT: Ld 6 ASP cc_start: 0.7891 (p0) cc_final: 0.7670 (p0) REVERT: Ld 11 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7957 (mm-30) REVERT: Lf 92 LYS cc_start: 0.9435 (tttm) cc_final: 0.8843 (tptp) REVERT: Lf 97 SER cc_start: 0.9102 (t) cc_final: 0.8605 (p) REVERT: Lg 11 ASN cc_start: 0.9084 (t0) cc_final: 0.8812 (t0) REVERT: Lh 14 LYS cc_start: 0.8227 (mmtt) cc_final: 0.7751 (mtpt) REVERT: Lh 60 GLU cc_start: 0.9057 (pt0) cc_final: 0.8650 (pt0) REVERT: Lh 75 TYR cc_start: 0.8068 (m-80) cc_final: 0.7441 (m-80) REVERT: Li 53 TYR cc_start: 0.8446 (p90) cc_final: 0.8051 (p90) REVERT: Li 80 PHE cc_start: 0.8521 (t80) cc_final: 0.8148 (t80) REVERT: Lj 64 MET cc_start: 0.8429 (mpp) cc_final: 0.8221 (mpp) REVERT: Lm 113 ARG cc_start: 0.8382 (mtp-110) cc_final: 0.7697 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8820 (mt0) cc_final: 0.8544 (mp10) REVERT: Ln 4 LYS cc_start: 0.3586 (mptt) cc_final: 0.2950 (ttmt) REVERT: Ln 9 ARG cc_start: 0.8231 (ttm170) cc_final: 0.7640 (ttp-110) REVERT: Lo 29 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7371 (ptpp) REVERT: Lo 79 THR cc_start: 0.8034 (m) cc_final: 0.7531 (p) REVERT: Lo 92 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7239 (tm-30) REVERT: Lo 102 GLN cc_start: 0.8509 (pm20) cc_final: 0.8103 (pm20) REVERT: Lp 25 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8402 (mp10) REVERT: Lp 32 GLN cc_start: 0.9059 (mt0) cc_final: 0.8825 (mt0) REVERT: Lp 48 LYS cc_start: 0.9059 (mtpp) cc_final: 0.8704 (mttp) REVERT: Lp 81 SER cc_start: 0.9549 (t) cc_final: 0.9302 (p) REVERT: D 127 MET cc_start: -0.2015 (mtt) cc_final: -0.2238 (mtm) REVERT: D 261 LEU cc_start: 0.7347 (tp) cc_final: 0.6925 (mm) REVERT: D 430 ASN cc_start: 0.6578 (m-40) cc_final: 0.6368 (m110) REVERT: D 495 TYR cc_start: 0.5410 (t80) cc_final: 0.5086 (t80) REVERT: D 532 MET cc_start: 0.6132 (mmt) cc_final: 0.4110 (tpt) REVERT: D 535 MET cc_start: 0.4232 (tpp) cc_final: 0.3995 (mtm) REVERT: D 579 MET cc_start: 0.5954 (ppp) cc_final: 0.5614 (ttp) REVERT: D 690 MET cc_start: 0.2335 (mmm) cc_final: 0.1588 (ptt) outliers start: 325 outliers final: 235 residues processed: 1410 average time/residue: 1.2052 time to fit residues: 3008.1372 Evaluate side-chains 1414 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1156 time to evaluate : 7.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 447 VAL Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain LA residue 20 THR Chi-restraints excluded: chain LA residue 24 GLN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 116 VAL Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 56 ILE Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 2 SER Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 154 THR Chi-restraints excluded: chain LC residue 345 GLU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LD residue 43 LYS Chi-restraints excluded: chain LD residue 153 THR Chi-restraints excluded: chain LE residue 2 THR Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 77 ARG Chi-restraints excluded: chain LE residue 84 VAL Chi-restraints excluded: chain LE residue 97 ASN Chi-restraints excluded: chain LF residue 62 ILE Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LG residue 36 ILE Chi-restraints excluded: chain LG residue 71 VAL Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 131 ILE Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LJ residue 32 ARG Chi-restraints excluded: chain LJ residue 53 THR Chi-restraints excluded: chain LL residue 10 LEU Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 46 ILE Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 41 GLN Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 49 ARG Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 142 SER Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LO residue 182 ASN Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 67 ILE Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LP residue 117 ILE Chi-restraints excluded: chain LP residue 147 GLU Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 86 THR Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 94 VAL Chi-restraints excluded: chain LR residue 122 VAL Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 24 LEU Chi-restraints excluded: chain LS residue 36 ILE Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 80 ARG Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LS residue 129 ILE Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 101 CYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 62 VAL Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 71 PHE Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 34 LEU Chi-restraints excluded: chain LV residue 61 THR Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 109 MET Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LV residue 125 LEU Chi-restraints excluded: chain LW residue 5 ILE Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 52 THR Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LX residue 119 THR Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 81 GLN Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 26 VAL Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 11 ASN Chi-restraints excluded: chain Lc residue 25 LEU Chi-restraints excluded: chain Lc residue 42 ILE Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 51 LEU Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Lc residue 102 THR Chi-restraints excluded: chain Lc residue 103 THR Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Ld residue 46 THR Chi-restraints excluded: chain Ld residue 51 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 97 LEU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 41 VAL Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Le residue 107 VAL Chi-restraints excluded: chain Le residue 119 VAL Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 29 ILE Chi-restraints excluded: chain Lg residue 30 LEU Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 58 ILE Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Lh residue 98 SER Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 15 SER Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 25 VAL Chi-restraints excluded: chain Lk residue 41 THR Chi-restraints excluded: chain Lk residue 76 ASN Chi-restraints excluded: chain Ll residue 29 LEU Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lm residue 118 THR Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 29 LYS Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 57 VAL Chi-restraints excluded: chain Lo residue 64 THR Chi-restraints excluded: chain Lo residue 68 VAL Chi-restraints excluded: chain Lo residue 88 CYS Chi-restraints excluded: chain Lp residue 25 GLN Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 372 optimal weight: 6.9990 chunk 995 optimal weight: 20.0000 chunk 218 optimal weight: 7.9990 chunk 649 optimal weight: 1.9990 chunk 272 optimal weight: 7.9990 chunk 1106 optimal weight: 40.0000 chunk 918 optimal weight: 20.0000 chunk 512 optimal weight: 9.9990 chunk 92 optimal weight: 10.0000 chunk 366 optimal weight: 20.0000 chunk 581 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN B 382 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LB 121 ASN LC 213 ASN ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LE 57 HIS ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LL 162 ASN LM 27 GLN ** LN 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LO 26 GLN A ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 50 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** LO 90 HIS A ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN ** LZ 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lg 52 GLN ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 500 HIS D 683 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 151486 Z= 0.254 Angle : 0.622 12.668 221974 Z= 0.323 Chirality : 0.037 0.304 27643 Planarity : 0.005 0.093 14813 Dihedral : 23.043 179.726 64437 Min Nonbonded Distance : 1.276 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.15 % Favored : 94.75 % Rotamer: Outliers : 4.44 % Allowed : 20.32 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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: -0.26 (0.09), residues: 7994 helix: 0.73 (0.09), residues: 3319 sheet: -0.62 (0.17), residues: 868 loop : -0.81 (0.10), residues: 3807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 700 HIS 0.009 0.001 HIS D 500 PHE 0.030 0.002 PHE C 44 TYR 0.026 0.002 TYRLH 92 ARG 0.009 0.001 ARGLG 57 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1536 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1230 time to evaluate : 7.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.4258 (tm-30) cc_final: 0.3725 (mm-30) REVERT: A 64 MET cc_start: -0.0209 (mpp) cc_final: -0.1525 (tpt) REVERT: B 223 ASN cc_start: 0.5417 (m110) cc_final: 0.5041 (t0) REVERT: B 346 MET cc_start: 0.5993 (tpt) cc_final: 0.5584 (mtt) REVERT: B 351 MET cc_start: 0.4986 (ttt) cc_final: 0.2414 (tmm) REVERT: B 462 PHE cc_start: 0.7935 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: B 532 MET cc_start: 0.5469 (OUTLIER) cc_final: 0.4950 (mmm) REVERT: B 619 PHE cc_start: 0.7343 (t80) cc_final: 0.7103 (t80) REVERT: B 717 ASP cc_start: 0.8029 (t70) cc_final: 0.7567 (m-30) REVERT: B 724 ASP cc_start: 0.8071 (m-30) cc_final: 0.7799 (t70) REVERT: B 736 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7545 (mmtt) REVERT: LA 8 GLN cc_start: 0.9016 (mt0) cc_final: 0.8725 (mt0) REVERT: LA 69 TYR cc_start: 0.7213 (t80) cc_final: 0.6776 (t80) REVERT: LA 80 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7734 (tp30) REVERT: LA 133 TYR cc_start: 0.8954 (p90) cc_final: 0.8540 (p90) REVERT: LA 149 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7772 (mmt-90) REVERT: LB 167 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8636 (ptm-80) REVERT: LB 298 PHE cc_start: 0.8830 (m-80) cc_final: 0.8469 (m-10) REVERT: LB 345 ASN cc_start: 0.8478 (t0) cc_final: 0.7743 (t0) REVERT: LB 349 LYS cc_start: 0.9547 (OUTLIER) cc_final: 0.9226 (ttmt) REVERT: LC 41 SER cc_start: 0.9687 (m) cc_final: 0.9341 (p) REVERT: LC 93 MET cc_start: 0.9076 (pmm) cc_final: 0.8835 (pmm) REVERT: LC 99 MET cc_start: 0.8723 (OUTLIER) cc_final: 0.7576 (ppp) REVERT: LC 118 LYS cc_start: 0.8566 (mttt) cc_final: 0.8298 (mtmm) REVERT: LC 177 ASP cc_start: 0.8611 (p0) cc_final: 0.8250 (p0) REVERT: LC 212 ASP cc_start: 0.7992 (OUTLIER) cc_final: 0.7769 (t0) REVERT: LC 274 TYR cc_start: 0.8916 (t80) cc_final: 0.8704 (t80) REVERT: LD 31 TYR cc_start: 0.8959 (t80) cc_final: 0.8293 (t80) REVERT: LD 43 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8347 (mmtp) REVERT: LD 88 ILE cc_start: 0.7560 (mm) cc_final: 0.7330 (mm) REVERT: LD 93 THR cc_start: 0.8567 (OUTLIER) cc_final: 0.8255 (m) REVERT: LD 95 TRP cc_start: 0.8799 (OUTLIER) cc_final: 0.7723 (t60) REVERT: LD 111 GLN cc_start: 0.9255 (tm-30) cc_final: 0.9011 (tm-30) REVERT: LD 180 PHE cc_start: 0.8849 (m-80) cc_final: 0.8547 (m-80) REVERT: LD 227 LEU cc_start: 0.8421 (mp) cc_final: 0.8105 (pp) REVERT: LE 9 TRP cc_start: 0.7617 (t60) cc_final: 0.7071 (t60) REVERT: LE 13 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6355 (tp30) REVERT: LE 77 ARG cc_start: 0.7019 (OUTLIER) cc_final: 0.6158 (tpt-90) REVERT: LF 102 VAL cc_start: 0.9633 (t) cc_final: 0.9387 (m) REVERT: LF 173 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9124 (mm) REVERT: LG 152 LEU cc_start: 0.9044 (mt) cc_final: 0.8810 (mm) REVERT: LH 23 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7132 (mtp85) REVERT: LH 111 PHE cc_start: 0.8448 (m-80) cc_final: 0.7815 (t80) REVERT: LH 177 ASP cc_start: 0.8545 (OUTLIER) cc_final: 0.7993 (m-30) REVERT: LI 181 TYR cc_start: 0.8156 (t80) cc_final: 0.7886 (t80) REVERT: LJ 38 GLU cc_start: 0.8157 (pt0) cc_final: 0.7590 (tp30) REVERT: LJ 88 GLU cc_start: 0.9068 (tm-30) cc_final: 0.8801 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8314 (m-40) cc_final: 0.7505 (m-40) REVERT: LJ 123 PHE cc_start: 0.6236 (m-80) cc_final: 0.6025 (m-80) REVERT: LJ 128 TYR cc_start: 0.6670 (t80) cc_final: 0.6154 (t80) REVERT: LL 172 LEU cc_start: 0.9390 (pp) cc_final: 0.9117 (mt) REVERT: LM 14 LEU cc_start: 0.9176 (mm) cc_final: 0.8617 (mm) REVERT: LM 16 GLU cc_start: 0.8631 (pt0) cc_final: 0.8014 (pm20) REVERT: LM 41 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.6778 (tm-30) REVERT: LM 42 LYS cc_start: 0.7996 (mttt) cc_final: 0.7598 (mttt) REVERT: LM 47 ASP cc_start: 0.6948 (OUTLIER) cc_final: 0.6672 (m-30) REVERT: LM 94 TRP cc_start: 0.9201 (t-100) cc_final: 0.8814 (t-100) REVERT: LN 160 GLU cc_start: 0.8215 (pm20) cc_final: 0.7718 (pm20) REVERT: LN 175 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8226 (m110) REVERT: LO 40 GLU cc_start: 0.7505 (mp0) cc_final: 0.7267 (mp0) REVERT: LO 65 ASN cc_start: 0.8172 (t0) cc_final: 0.7910 (t0) REVERT: LR 25 ASP cc_start: 0.8728 (p0) cc_final: 0.8387 (p0) REVERT: LR 27 ASN cc_start: 0.9295 (m110) cc_final: 0.8709 (t0) REVERT: LR 68 GLN cc_start: 0.9117 (tp40) cc_final: 0.8679 (tm-30) REVERT: LR 95 TRP cc_start: 0.9360 (t-100) cc_final: 0.9011 (t-100) REVERT: LS 25 PHE cc_start: 0.7953 (m-10) cc_final: 0.7543 (m-80) REVERT: LS 104 GLU cc_start: 0.9143 (tt0) cc_final: 0.8688 (mt-10) REVERT: LV 11 PHE cc_start: 0.8236 (m-80) cc_final: 0.7662 (m-80) REVERT: LV 40 LYS cc_start: 0.9318 (mmmt) cc_final: 0.8956 (mmmt) REVERT: LV 74 MET cc_start: 0.7974 (ptm) cc_final: 0.7685 (ptp) REVERT: LV 92 PHE cc_start: 0.8844 (m-80) cc_final: 0.8449 (m-10) REVERT: LV 108 GLU cc_start: 0.8173 (tp30) cc_final: 0.7946 (tp30) REVERT: LV 120 LYS cc_start: 0.9511 (ttpt) cc_final: 0.9190 (ttmm) REVERT: LV 125 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9276 (mp) REVERT: LW 12 LYS cc_start: 0.9270 (OUTLIER) cc_final: 0.8951 (mtmm) REVERT: LW 23 ARG cc_start: 0.9145 (ttp-110) cc_final: 0.8941 (ttp-110) REVERT: LW 58 HIS cc_start: 0.8564 (t-90) cc_final: 0.8179 (t-90) REVERT: LX 65 GLN cc_start: 0.9150 (pm20) cc_final: 0.8821 (pm20) REVERT: LY 53 ASP cc_start: 0.8312 (m-30) cc_final: 0.7616 (t0) REVERT: LZ 47 GLU cc_start: 0.8718 (tm-30) cc_final: 0.7626 (pp20) REVERT: LZ 48 ARG cc_start: 0.8216 (ttm170) cc_final: 0.7400 (mtm180) REVERT: LZ 90 GLU cc_start: 0.8041 (tm-30) cc_final: 0.7733 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8634 (tt0) cc_final: 0.8157 (mm-30) REVERT: La 38 GLN cc_start: 0.8753 (mt0) cc_final: 0.8509 (mt0) REVERT: La 58 MET cc_start: 0.8133 (tpp) cc_final: 0.7801 (tpt) REVERT: La 64 GLN cc_start: 0.8516 (pt0) cc_final: 0.8170 (pt0) REVERT: La 69 TRP cc_start: 0.8509 (t60) cc_final: 0.7685 (t60) REVERT: Lb 18 ARG cc_start: 0.7894 (tpp80) cc_final: 0.7272 (ttm170) REVERT: Lb 27 TYR cc_start: 0.8185 (m-10) cc_final: 0.7820 (m-10) REVERT: Ld 11 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7965 (mm-30) REVERT: Lf 39 GLN cc_start: 0.8752 (mp10) cc_final: 0.8322 (mp10) REVERT: Lf 51 TYR cc_start: 0.8994 (t80) cc_final: 0.8679 (t80) REVERT: Lf 86 ARG cc_start: 0.6672 (mtt180) cc_final: 0.5819 (mtt180) REVERT: Lf 92 LYS cc_start: 0.9407 (tttm) cc_final: 0.8676 (tptp) REVERT: Lf 97 SER cc_start: 0.9161 (t) cc_final: 0.8743 (p) REVERT: Lg 11 ASN cc_start: 0.9139 (t0) cc_final: 0.8880 (t0) REVERT: Lg 107 GLU cc_start: 0.8919 (pp20) cc_final: 0.8294 (tm-30) REVERT: Lh 14 LYS cc_start: 0.8177 (mmtt) cc_final: 0.7731 (mtpt) REVERT: Lh 60 GLU cc_start: 0.9055 (pt0) cc_final: 0.8641 (pt0) REVERT: Lh 74 LYS cc_start: 0.7939 (ptmt) cc_final: 0.7564 (ptmm) REVERT: Lh 75 TYR cc_start: 0.8023 (m-80) cc_final: 0.7734 (m-80) REVERT: Li 66 GLU cc_start: 0.8309 (mp0) cc_final: 0.7989 (mp0) REVERT: Li 80 PHE cc_start: 0.8528 (t80) cc_final: 0.8027 (t80) REVERT: Lk 76 ASN cc_start: 0.9059 (OUTLIER) cc_final: 0.8813 (p0) REVERT: Lm 79 GLU cc_start: 0.8792 (pp20) cc_final: 0.8560 (pt0) REVERT: Lm 113 ARG cc_start: 0.8328 (mtp-110) cc_final: 0.7626 (ttp80) REVERT: Lm 119 ASN cc_start: 0.8853 (t0) cc_final: 0.8523 (t0) REVERT: Lm 120 GLN cc_start: 0.8831 (mt0) cc_final: 0.8554 (mp10) REVERT: Ln 4 LYS cc_start: 0.3538 (mptt) cc_final: 0.2887 (ttmt) REVERT: Ln 9 ARG cc_start: 0.8252 (ttm170) cc_final: 0.7625 (ttp-110) REVERT: Lo 29 LYS cc_start: 0.7942 (OUTLIER) cc_final: 0.7403 (ptpp) REVERT: Lo 79 THR cc_start: 0.8170 (m) cc_final: 0.7709 (p) REVERT: Lo 102 GLN cc_start: 0.8504 (pm20) cc_final: 0.8008 (pm20) REVERT: Lp 32 GLN cc_start: 0.9064 (mt0) cc_final: 0.8813 (mt0) REVERT: Lp 48 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8686 (mttp) REVERT: Lp 81 SER cc_start: 0.9550 (t) cc_final: 0.9301 (p) REVERT: D 224 PHE cc_start: 0.5141 (m-10) cc_final: 0.4871 (m-10) REVERT: D 261 LEU cc_start: 0.7426 (tp) cc_final: 0.7019 (mm) REVERT: D 532 MET cc_start: 0.6158 (mmt) cc_final: 0.4073 (tpp) REVERT: D 535 MET cc_start: 0.4172 (tpp) cc_final: 0.3962 (mtm) REVERT: D 579 MET cc_start: 0.6422 (OUTLIER) cc_final: 0.6035 (ttp) REVERT: D 613 LEU cc_start: 0.6480 (tp) cc_final: 0.5822 (mt) REVERT: D 690 MET cc_start: 0.2119 (mmm) cc_final: 0.1372 (ptt) outliers start: 306 outliers final: 225 residues processed: 1395 average time/residue: 1.2060 time to fit residues: 2977.2229 Evaluate side-chains 1401 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1152 time to evaluate : 7.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain B residue 785 SER Chi-restraints excluded: chain LA residue 20 THR Chi-restraints excluded: chain LA residue 24 GLN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 322 ILE Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 2 SER Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 182 LEU Chi-restraints excluded: chain LC residue 212 ASP Chi-restraints excluded: chain LC residue 244 LEU Chi-restraints excluded: chain LC residue 327 LEU Chi-restraints excluded: chain LC residue 345 GLU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LD residue 43 LYS Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 153 THR Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 40 LEU Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 77 ARG Chi-restraints excluded: chain LE residue 84 VAL Chi-restraints excluded: chain LF residue 62 ILE Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LF residue 190 THR Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 71 VAL Chi-restraints excluded: chain LH residue 74 LEU Chi-restraints excluded: chain LH residue 130 ASP Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 149 ASN Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 131 ILE Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LL residue 92 THR Chi-restraints excluded: chain LL residue 129 ASN Chi-restraints excluded: chain LL residue 147 ILE Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 27 GLN Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 41 GLN Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 49 ARG Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 142 SER Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 86 THR Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 122 VAL Chi-restraints excluded: chain LS residue 19 VAL Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 101 CYS Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 71 PHE Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 61 THR Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LV residue 125 LEU Chi-restraints excluded: chain LW residue 5 ILE Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 81 GLN Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 13 VAL Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 11 ASN Chi-restraints excluded: chain Lc residue 42 ILE Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Lc residue 102 THR Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Ld residue 51 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 84 ASP Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 23 ASP Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Le residue 107 VAL Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lf residue 72 THR Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 27 GLU Chi-restraints excluded: chain Lh residue 58 ILE Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Lh residue 98 SER Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 25 VAL Chi-restraints excluded: chain Lk residue 41 THR Chi-restraints excluded: chain Lk residue 75 VAL Chi-restraints excluded: chain Lk residue 76 ASN Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lm residue 118 THR Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 29 LYS Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 64 THR Chi-restraints excluded: chain Lo residue 68 VAL Chi-restraints excluded: chain Lo residue 82 GLN Chi-restraints excluded: chain Lo residue 83 LEU Chi-restraints excluded: chain Lo residue 88 CYS Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 597 ASN Chi-restraints excluded: chain D residue 598 PHE Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 1067 optimal weight: 10.0000 chunk 124 optimal weight: 20.0000 chunk 630 optimal weight: 9.9990 chunk 808 optimal weight: 10.0000 chunk 626 optimal weight: 8.9990 chunk 931 optimal weight: 50.0000 chunk 618 optimal weight: 10.0000 chunk 1102 optimal weight: 20.0000 chunk 690 optimal weight: 0.0980 chunk 672 optimal weight: 0.9990 chunk 509 optimal weight: 20.0000 overall best weight: 6.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 ASN B 382 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 699 ASN ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LC 229 ASN ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 90 ASN ** LN 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 26 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LP 121 GLN LP 137 ASN ** LQ 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LS 8 GLN ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN LV 132 ASN LY 4 GLN Lb 43 HIS ** Ld 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lk 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN D 82 HIS ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 151486 Z= 0.239 Angle : 0.618 12.768 221974 Z= 0.320 Chirality : 0.037 0.292 27643 Planarity : 0.005 0.096 14813 Dihedral : 23.028 179.263 64437 Min Nonbonded Distance : 1.236 Molprobity Statistics. All-atom Clashscore : 18.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.25 % Favored : 94.66 % Rotamer: Outliers : 4.41 % Allowed : 21.14 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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 (0.09), residues: 7994 helix: 0.77 (0.09), residues: 3332 sheet: -0.60 (0.17), residues: 863 loop : -0.84 (0.10), residues: 3799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 700 HIS 0.009 0.001 HISLe 88 PHE 0.041 0.002 PHELP 26 TYR 0.040 0.002 TYRLj 39 ARG 0.021 0.001 ARGLl 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1523 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 1219 time to evaluate : 9.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.4260 (tm-30) cc_final: 0.3779 (mm-30) REVERT: A 64 MET cc_start: 0.0050 (mpp) cc_final: -0.1354 (tpp) REVERT: B 223 ASN cc_start: 0.5593 (m110) cc_final: 0.5202 (t0) REVERT: B 346 MET cc_start: 0.6006 (tpt) cc_final: 0.5710 (mtt) REVERT: B 351 MET cc_start: 0.5127 (ttt) cc_final: 0.2851 (tmm) REVERT: B 462 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7078 (m-80) REVERT: B 532 MET cc_start: 0.5404 (OUTLIER) cc_final: 0.4941 (mmm) REVERT: B 724 ASP cc_start: 0.8070 (m-30) cc_final: 0.7821 (t70) REVERT: B 736 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7456 (mmtt) REVERT: B 775 LYS cc_start: 0.7114 (OUTLIER) cc_final: 0.6299 (mmmt) REVERT: LA 69 TYR cc_start: 0.7187 (t80) cc_final: 0.6742 (t80) REVERT: LA 133 TYR cc_start: 0.8962 (p90) cc_final: 0.8501 (p90) REVERT: LA 149 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7745 (mmt-90) REVERT: LB 167 ARG cc_start: 0.9023 (OUTLIER) cc_final: 0.8691 (ptm-80) REVERT: LB 214 MET cc_start: 0.8375 (tpp) cc_final: 0.7967 (tpp) REVERT: LB 298 PHE cc_start: 0.8858 (m-80) cc_final: 0.8495 (m-10) REVERT: LB 319 ASN cc_start: 0.8439 (t0) cc_final: 0.8134 (p0) REVERT: LB 345 ASN cc_start: 0.8478 (t0) cc_final: 0.7742 (t0) REVERT: LB 349 LYS cc_start: 0.9544 (OUTLIER) cc_final: 0.9227 (ttmt) REVERT: LC 41 SER cc_start: 0.9681 (m) cc_final: 0.9332 (p) REVERT: LC 93 MET cc_start: 0.9133 (pmm) cc_final: 0.8895 (pmm) REVERT: LC 99 MET cc_start: 0.8717 (OUTLIER) cc_final: 0.7607 (ppp) REVERT: LC 118 LYS cc_start: 0.8560 (mttt) cc_final: 0.8300 (mtmm) REVERT: LC 177 ASP cc_start: 0.8631 (p0) cc_final: 0.8280 (p0) REVERT: LC 274 TYR cc_start: 0.8933 (t80) cc_final: 0.8704 (t80) REVERT: LD 17 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8065 (tp40) REVERT: LD 31 TYR cc_start: 0.8973 (t80) cc_final: 0.8281 (t80) REVERT: LD 43 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8324 (mmtp) REVERT: LD 88 ILE cc_start: 0.7830 (mm) cc_final: 0.7586 (mm) REVERT: LD 93 THR cc_start: 0.8569 (OUTLIER) cc_final: 0.8254 (m) REVERT: LD 95 TRP cc_start: 0.8871 (OUTLIER) cc_final: 0.7745 (t60) REVERT: LD 111 GLN cc_start: 0.9295 (tm-30) cc_final: 0.9044 (tm-30) REVERT: LD 180 PHE cc_start: 0.8892 (m-80) cc_final: 0.8573 (m-80) REVERT: LD 227 LEU cc_start: 0.8533 (mp) cc_final: 0.8205 (pp) REVERT: LE 4 GLN cc_start: 0.8239 (tt0) cc_final: 0.7688 (tm-30) REVERT: LE 13 GLU cc_start: 0.7114 (mm-30) cc_final: 0.6771 (tp30) REVERT: LE 77 ARG cc_start: 0.6978 (OUTLIER) cc_final: 0.6120 (tpt-90) REVERT: LF 102 VAL cc_start: 0.9655 (t) cc_final: 0.9404 (m) REVERT: LF 173 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9095 (mm) REVERT: LG 130 TYR cc_start: 0.7624 (m-80) cc_final: 0.7318 (m-80) REVERT: LG 152 LEU cc_start: 0.9042 (mt) cc_final: 0.8807 (mm) REVERT: LH 23 ARG cc_start: 0.8340 (OUTLIER) cc_final: 0.7167 (mtp85) REVERT: LH 177 ASP cc_start: 0.8500 (OUTLIER) cc_final: 0.7660 (m-30) REVERT: LI 146 ASP cc_start: 0.8249 (p0) cc_final: 0.7972 (m-30) REVERT: LI 181 TYR cc_start: 0.8172 (t80) cc_final: 0.7898 (t80) REVERT: LJ 38 GLU cc_start: 0.8202 (pt0) cc_final: 0.7613 (tp30) REVERT: LJ 88 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8798 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8339 (m-40) cc_final: 0.7830 (m-40) REVERT: LJ 123 PHE cc_start: 0.6205 (m-80) cc_final: 0.5972 (m-80) REVERT: LL 70 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7179 (ptp90) REVERT: LL 172 LEU cc_start: 0.9386 (pp) cc_final: 0.9105 (mt) REVERT: LM 14 LEU cc_start: 0.9152 (mm) cc_final: 0.8591 (mm) REVERT: LM 16 GLU cc_start: 0.8623 (pt0) cc_final: 0.8009 (pm20) REVERT: LM 41 GLN cc_start: 0.8286 (OUTLIER) cc_final: 0.6800 (tm-30) REVERT: LM 42 LYS cc_start: 0.8001 (mttt) cc_final: 0.7621 (mttt) REVERT: LM 47 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6272 (m-30) REVERT: LM 94 TRP cc_start: 0.9210 (t-100) cc_final: 0.8823 (t-100) REVERT: LN 59 PHE cc_start: 0.8618 (m-10) cc_final: 0.8292 (m-10) REVERT: LN 160 GLU cc_start: 0.8154 (pm20) cc_final: 0.7624 (pm20) REVERT: LN 175 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8293 (m110) REVERT: LO 65 ASN cc_start: 0.8141 (t0) cc_final: 0.7882 (t0) REVERT: LQ 155 MET cc_start: 0.8110 (tpt) cc_final: 0.7865 (tpp) REVERT: LR 25 ASP cc_start: 0.8754 (p0) cc_final: 0.8413 (p0) REVERT: LR 27 ASN cc_start: 0.9283 (m110) cc_final: 0.8715 (t0) REVERT: LR 68 GLN cc_start: 0.9100 (tp40) cc_final: 0.8679 (tm-30) REVERT: LR 95 TRP cc_start: 0.9342 (t-100) cc_final: 0.8946 (t-100) REVERT: LS 25 PHE cc_start: 0.7964 (m-10) cc_final: 0.7551 (m-80) REVERT: LS 104 GLU cc_start: 0.9180 (tt0) cc_final: 0.8547 (mt-10) REVERT: LT 19 PHE cc_start: 0.8711 (t80) cc_final: 0.8413 (t80) REVERT: LV 11 PHE cc_start: 0.8214 (m-80) cc_final: 0.7790 (m-80) REVERT: LV 40 LYS cc_start: 0.9315 (mmmt) cc_final: 0.8956 (mmmt) REVERT: LV 74 MET cc_start: 0.7963 (ptm) cc_final: 0.7760 (ptp) REVERT: LV 92 PHE cc_start: 0.8845 (m-80) cc_final: 0.8478 (m-10) REVERT: LV 120 LYS cc_start: 0.9510 (ttpt) cc_final: 0.9302 (ttmm) REVERT: LV 125 LEU cc_start: 0.9595 (OUTLIER) cc_final: 0.9279 (mp) REVERT: LW 12 LYS cc_start: 0.9269 (OUTLIER) cc_final: 0.8930 (mtmm) REVERT: LW 23 ARG cc_start: 0.9112 (ttp-110) cc_final: 0.8886 (ttp-110) REVERT: LW 58 HIS cc_start: 0.8529 (t-90) cc_final: 0.8159 (t-90) REVERT: LX 64 GLU cc_start: 0.9081 (pm20) cc_final: 0.8515 (pm20) REVERT: LX 115 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8588 (mtp85) REVERT: LX 123 TYR cc_start: 0.7452 (m-10) cc_final: 0.7199 (m-10) REVERT: LY 53 ASP cc_start: 0.8264 (m-30) cc_final: 0.7588 (t0) REVERT: LY 91 ASN cc_start: 0.9204 (p0) cc_final: 0.8966 (p0) REVERT: LZ 47 GLU cc_start: 0.8700 (tm-30) cc_final: 0.7597 (pp20) REVERT: LZ 48 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7355 (mtm180) REVERT: LZ 90 GLU cc_start: 0.8040 (tm-30) cc_final: 0.7658 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8660 (tt0) cc_final: 0.8176 (mm-30) REVERT: La 38 GLN cc_start: 0.8742 (mt0) cc_final: 0.8512 (mt0) REVERT: La 58 MET cc_start: 0.8029 (tpp) cc_final: 0.7680 (tpt) REVERT: La 64 GLN cc_start: 0.8629 (OUTLIER) cc_final: 0.8269 (pt0) REVERT: La 69 TRP cc_start: 0.8571 (t60) cc_final: 0.7790 (t60) REVERT: Lb 18 ARG cc_start: 0.7853 (tpp80) cc_final: 0.7245 (ttm170) REVERT: Lb 27 TYR cc_start: 0.8197 (m-10) cc_final: 0.7863 (m-10) REVERT: Ld 11 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8034 (mm-30) REVERT: Ld 35 GLU cc_start: 0.8165 (tm-30) cc_final: 0.7887 (tm-30) REVERT: Lf 39 GLN cc_start: 0.8786 (mp10) cc_final: 0.8358 (mp10) REVERT: Lf 51 TYR cc_start: 0.9038 (t80) cc_final: 0.8813 (t80) REVERT: Lf 86 ARG cc_start: 0.6700 (mtt180) cc_final: 0.5853 (mtt180) REVERT: Lf 92 LYS cc_start: 0.9406 (tttm) cc_final: 0.8722 (tptp) REVERT: Lf 97 SER cc_start: 0.9153 (t) cc_final: 0.8730 (p) REVERT: Lg 11 ASN cc_start: 0.9162 (t0) cc_final: 0.8883 (t0) REVERT: Lg 107 GLU cc_start: 0.8947 (pp20) cc_final: 0.8419 (tm-30) REVERT: Lh 60 GLU cc_start: 0.9070 (pt0) cc_final: 0.8634 (pt0) REVERT: Lh 107 LYS cc_start: 0.7929 (mttt) cc_final: 0.7650 (mttt) REVERT: Li 66 GLU cc_start: 0.8464 (mp0) cc_final: 0.8149 (mp0) REVERT: Li 68 ARG cc_start: 0.8280 (mmt180) cc_final: 0.7969 (mmt180) REVERT: Li 80 PHE cc_start: 0.8416 (t80) cc_final: 0.8204 (t80) REVERT: Lm 79 GLU cc_start: 0.8819 (pp20) cc_final: 0.8521 (pt0) REVERT: Lm 113 ARG cc_start: 0.8288 (mtp-110) cc_final: 0.7565 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8868 (mt0) cc_final: 0.8568 (mp10) REVERT: Ln 4 LYS cc_start: 0.3532 (mptt) cc_final: 0.2874 (ttmt) REVERT: Ln 9 ARG cc_start: 0.8271 (ttm170) cc_final: 0.7630 (ttp-110) REVERT: Lo 29 LYS cc_start: 0.8070 (OUTLIER) cc_final: 0.7551 (ptpp) REVERT: Lo 79 THR cc_start: 0.8267 (m) cc_final: 0.7798 (p) REVERT: Lo 102 GLN cc_start: 0.8419 (pm20) cc_final: 0.7906 (pm20) REVERT: Lp 32 GLN cc_start: 0.9070 (mt0) cc_final: 0.8824 (mt0) REVERT: Lp 48 LYS cc_start: 0.9037 (mtpp) cc_final: 0.8678 (mttm) REVERT: Lp 81 SER cc_start: 0.9531 (t) cc_final: 0.9286 (p) REVERT: D 532 MET cc_start: 0.6163 (mmt) cc_final: 0.4092 (tpp) REVERT: D 579 MET cc_start: 0.6270 (OUTLIER) cc_final: 0.5897 (ttp) REVERT: D 613 LEU cc_start: 0.6489 (tp) cc_final: 0.5848 (mt) REVERT: D 690 MET cc_start: 0.2032 (mmm) cc_final: 0.1217 (ptt) outliers start: 304 outliers final: 237 residues processed: 1390 average time/residue: 1.1921 time to fit residues: 2935.2603 Evaluate side-chains 1416 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1154 time to evaluate : 7.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 535 MET Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain LA residue 20 THR Chi-restraints excluded: chain LA residue 24 GLN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 2 SER Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 182 LEU Chi-restraints excluded: chain LC residue 196 ASN Chi-restraints excluded: chain LC residue 229 ASN Chi-restraints excluded: chain LC residue 244 LEU Chi-restraints excluded: chain LC residue 327 LEU Chi-restraints excluded: chain LC residue 345 GLU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LD residue 43 LYS Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 153 THR Chi-restraints excluded: chain LD residue 286 VAL Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 40 LEU Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 77 ARG Chi-restraints excluded: chain LE residue 84 VAL Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LF residue 190 THR Chi-restraints excluded: chain LG residue 36 ILE Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 71 VAL Chi-restraints excluded: chain LH residue 74 LEU Chi-restraints excluded: chain LH residue 130 ASP Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 149 ASN Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LJ residue 30 LEU Chi-restraints excluded: chain LJ residue 80 LEU Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 70 ARG Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 80 VAL Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LL residue 129 ASN Chi-restraints excluded: chain LL residue 147 ILE Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 21 VAL Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 41 GLN Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 29 GLU Chi-restraints excluded: chain LN residue 49 ARG Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 142 SER Chi-restraints excluded: chain LO residue 152 VAL Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 49 GLU Chi-restraints excluded: chain LP residue 51 VAL Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 86 THR Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 122 VAL Chi-restraints excluded: chain LR residue 127 SER Chi-restraints excluded: chain LR residue 139 VAL Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 19 VAL Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 96 ILE Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 17 VAL Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 62 VAL Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 71 PHE Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LV residue 125 LEU Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LX residue 38 LEU Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 81 GLN Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 26 VAL Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain La residue 64 GLN Chi-restraints excluded: chain La residue 82 ILE Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Ld residue 8 VAL Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 84 ASP Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 97 LEU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 23 ASP Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 63 THR Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Le residue 107 VAL Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lg residue 6 THR Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 22 VAL Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Lh residue 98 SER Chi-restraints excluded: chain Li residue 20 MET Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 15 SER Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 25 VAL Chi-restraints excluded: chain Lk residue 41 THR Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 29 LEU Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lm residue 118 THR Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 29 LYS Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 57 VAL Chi-restraints excluded: chain Lo residue 82 GLN Chi-restraints excluded: chain Lo residue 83 LEU Chi-restraints excluded: chain Lo residue 88 CYS Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 704 HIS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 682 optimal weight: 5.9990 chunk 440 optimal weight: 6.9990 chunk 658 optimal weight: 5.9990 chunk 332 optimal weight: 5.9990 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 1.9990 chunk 701 optimal weight: 9.9990 chunk 751 optimal weight: 20.0000 chunk 545 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 chunk 866 optimal weight: 20.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 27 GLN ** LN 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 26 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 50 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN LY 4 GLN ** Ld 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Lf 106 ASN ** Lg 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Lk 76 ASN ** Lo 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.4503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 151486 Z= 0.205 Angle : 0.602 13.211 221974 Z= 0.312 Chirality : 0.036 0.351 27643 Planarity : 0.005 0.091 14813 Dihedral : 22.997 179.490 64437 Min Nonbonded Distance : 1.219 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.22 % Favored : 94.70 % Rotamer: Outliers : 4.09 % Allowed : 22.21 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.70 % 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 (0.09), residues: 7994 helix: 0.80 (0.09), residues: 3327 sheet: -0.57 (0.17), residues: 873 loop : -0.79 (0.10), residues: 3794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP B 700 HIS 0.007 0.001 HISLD 244 PHE 0.038 0.002 PHELP 26 TYR 0.031 0.002 TYRLU 36 ARG 0.017 0.000 ARGLV 32 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 282 poor density : 1217 time to evaluate : 7.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 GLU cc_start: 0.4405 (tm-30) cc_final: 0.3946 (mm-30) REVERT: B 223 ASN cc_start: 0.5660 (m110) cc_final: 0.5345 (t0) REVERT: B 346 MET cc_start: 0.6156 (tpt) cc_final: 0.5900 (mtt) REVERT: B 351 MET cc_start: 0.4919 (ttt) cc_final: 0.2859 (tmm) REVERT: B 462 PHE cc_start: 0.8040 (OUTLIER) cc_final: 0.7370 (m-80) REVERT: B 532 MET cc_start: 0.5406 (OUTLIER) cc_final: 0.4931 (mmm) REVERT: B 724 ASP cc_start: 0.8040 (m-30) cc_final: 0.7778 (t70) REVERT: B 736 LYS cc_start: 0.7886 (OUTLIER) cc_final: 0.7457 (mmtt) REVERT: LA 69 TYR cc_start: 0.7188 (t80) cc_final: 0.6675 (t80) REVERT: LA 133 TYR cc_start: 0.8935 (p90) cc_final: 0.8492 (p90) REVERT: LA 149 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7733 (mmt-90) REVERT: LB 167 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8707 (ptm-80) REVERT: LB 298 PHE cc_start: 0.8872 (m-80) cc_final: 0.8515 (m-10) REVERT: LB 319 ASN cc_start: 0.8378 (t0) cc_final: 0.8116 (p0) REVERT: LB 345 ASN cc_start: 0.8471 (t0) cc_final: 0.7660 (t0) REVERT: LB 349 LYS cc_start: 0.9533 (OUTLIER) cc_final: 0.9216 (ttmt) REVERT: LC 41 SER cc_start: 0.9678 (m) cc_final: 0.9319 (p) REVERT: LC 93 MET cc_start: 0.9124 (pmm) cc_final: 0.8891 (pmm) REVERT: LC 99 MET cc_start: 0.8711 (OUTLIER) cc_final: 0.7492 (ppp) REVERT: LC 118 LYS cc_start: 0.8542 (mttt) cc_final: 0.8305 (mtmm) REVERT: LC 177 ASP cc_start: 0.8577 (p0) cc_final: 0.8230 (p0) REVERT: LD 17 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.7969 (tp40) REVERT: LD 31 TYR cc_start: 0.8954 (t80) cc_final: 0.8305 (t80) REVERT: LD 88 ILE cc_start: 0.7801 (mm) cc_final: 0.7553 (mm) REVERT: LD 93 THR cc_start: 0.8527 (OUTLIER) cc_final: 0.8247 (m) REVERT: LD 95 TRP cc_start: 0.8893 (OUTLIER) cc_final: 0.7715 (t60) REVERT: LD 111 GLN cc_start: 0.9259 (tm-30) cc_final: 0.9005 (tm-30) REVERT: LD 180 PHE cc_start: 0.8904 (m-80) cc_final: 0.8580 (m-80) REVERT: LD 227 LEU cc_start: 0.8545 (mp) cc_final: 0.8176 (pp) REVERT: LE 4 GLN cc_start: 0.8196 (tt0) cc_final: 0.7708 (tm-30) REVERT: LE 9 TRP cc_start: 0.7474 (t60) cc_final: 0.7038 (t60) REVERT: LE 13 GLU cc_start: 0.7209 (mm-30) cc_final: 0.6592 (tp30) REVERT: LE 77 ARG cc_start: 0.6977 (OUTLIER) cc_final: 0.6067 (tpt-90) REVERT: LE 148 GLU cc_start: 0.8127 (tm-30) cc_final: 0.7849 (pm20) REVERT: LF 102 VAL cc_start: 0.9628 (t) cc_final: 0.9391 (m) REVERT: LG 130 TYR cc_start: 0.7648 (m-80) cc_final: 0.7334 (m-80) REVERT: LG 152 LEU cc_start: 0.9062 (mt) cc_final: 0.8836 (mm) REVERT: LH 23 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7172 (mtp85) REVERT: LH 111 PHE cc_start: 0.8450 (m-80) cc_final: 0.7837 (t80) REVERT: LH 177 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.7604 (m-30) REVERT: LI 181 TYR cc_start: 0.8192 (t80) cc_final: 0.7970 (t80) REVERT: LI 192 ASP cc_start: 0.7358 (OUTLIER) cc_final: 0.6940 (t70) REVERT: LJ 32 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.8325 (ptp90) REVERT: LJ 38 GLU cc_start: 0.8170 (pt0) cc_final: 0.7564 (tp30) REVERT: LJ 88 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8797 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8324 (m-40) cc_final: 0.7669 (m-40) REVERT: LJ 116 TYR cc_start: 0.6343 (t80) cc_final: 0.4429 (m-80) REVERT: LJ 123 PHE cc_start: 0.6286 (m-80) cc_final: 0.5865 (m-10) REVERT: LJ 128 TYR cc_start: 0.7028 (t80) cc_final: 0.6448 (t80) REVERT: LM 14 LEU cc_start: 0.9154 (mm) cc_final: 0.8576 (mm) REVERT: LM 16 GLU cc_start: 0.8636 (pt0) cc_final: 0.8316 (pm20) REVERT: LM 41 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.6825 (tm-30) REVERT: LM 42 LYS cc_start: 0.7978 (mttt) cc_final: 0.7596 (mttt) REVERT: LM 47 ASP cc_start: 0.6992 (OUTLIER) cc_final: 0.6397 (m-30) REVERT: LM 94 TRP cc_start: 0.9201 (t-100) cc_final: 0.8801 (t-100) REVERT: LN 59 PHE cc_start: 0.8651 (m-10) cc_final: 0.8354 (m-10) REVERT: LN 91 GLU cc_start: 0.8214 (tt0) cc_final: 0.7478 (tm-30) REVERT: LN 160 GLU cc_start: 0.8198 (pm20) cc_final: 0.7708 (pm20) REVERT: LN 175 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8320 (m-40) REVERT: LO 65 ASN cc_start: 0.8063 (t0) cc_final: 0.7804 (t0) REVERT: LR 25 ASP cc_start: 0.8729 (p0) cc_final: 0.8359 (p0) REVERT: LR 27 ASN cc_start: 0.9289 (m110) cc_final: 0.8755 (t0) REVERT: LR 68 GLN cc_start: 0.9063 (tp40) cc_final: 0.8652 (tm-30) REVERT: LR 95 TRP cc_start: 0.9322 (t-100) cc_final: 0.8822 (t-100) REVERT: LS 25 PHE cc_start: 0.7987 (m-10) cc_final: 0.7579 (m-80) REVERT: LS 104 GLU cc_start: 0.9119 (tt0) cc_final: 0.8674 (mt-10) REVERT: LT 13 TYR cc_start: 0.7606 (m-10) cc_final: 0.7315 (m-10) REVERT: LT 19 PHE cc_start: 0.8682 (t80) cc_final: 0.8360 (t80) REVERT: LV 11 PHE cc_start: 0.8182 (m-80) cc_final: 0.7618 (m-80) REVERT: LV 15 LEU cc_start: 0.9189 (mm) cc_final: 0.8735 (mm) REVERT: LV 32 ARG cc_start: 0.7717 (mtm-85) cc_final: 0.7483 (mtm-85) REVERT: LV 40 LYS cc_start: 0.9291 (mmmt) cc_final: 0.8918 (mmmt) REVERT: LV 92 PHE cc_start: 0.8827 (m-80) cc_final: 0.8494 (m-10) REVERT: LV 120 LYS cc_start: 0.9507 (ttpt) cc_final: 0.9296 (ttmm) REVERT: LV 125 LEU cc_start: 0.9590 (OUTLIER) cc_final: 0.9276 (mp) REVERT: LW 12 LYS cc_start: 0.9280 (OUTLIER) cc_final: 0.8952 (mtmm) REVERT: LW 29 PHE cc_start: 0.8954 (m-80) cc_final: 0.8295 (m-80) REVERT: LW 58 HIS cc_start: 0.8519 (t-90) cc_final: 0.8151 (t-90) REVERT: LX 115 ARG cc_start: 0.8862 (mtp85) cc_final: 0.8566 (mtp85) REVERT: LX 123 TYR cc_start: 0.7524 (m-10) cc_final: 0.7246 (m-10) REVERT: LY 53 ASP cc_start: 0.8344 (m-30) cc_final: 0.7649 (t0) REVERT: LY 91 ASN cc_start: 0.9204 (p0) cc_final: 0.8990 (p0) REVERT: LZ 47 GLU cc_start: 0.8708 (tm-30) cc_final: 0.7717 (pp20) REVERT: LZ 48 ARG cc_start: 0.8149 (ttm170) cc_final: 0.7333 (mtm180) REVERT: LZ 90 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7624 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8677 (tt0) cc_final: 0.8181 (mm-30) REVERT: La 38 GLN cc_start: 0.8704 (mt0) cc_final: 0.8472 (mt0) REVERT: La 58 MET cc_start: 0.8045 (tpp) cc_final: 0.7805 (tpt) REVERT: La 64 GLN cc_start: 0.8570 (pt0) cc_final: 0.8200 (pt0) REVERT: La 69 TRP cc_start: 0.8624 (t60) cc_final: 0.7789 (t60) REVERT: Lb 18 ARG cc_start: 0.7807 (tpp80) cc_final: 0.7228 (ttm170) REVERT: Ld 11 GLU cc_start: 0.8326 (mm-30) cc_final: 0.8037 (mm-30) REVERT: Lf 92 LYS cc_start: 0.9394 (tttm) cc_final: 0.8686 (tptp) REVERT: Lf 97 SER cc_start: 0.9166 (t) cc_final: 0.8760 (p) REVERT: Lg 11 ASN cc_start: 0.9178 (t0) cc_final: 0.8917 (t0) REVERT: Lh 60 GLU cc_start: 0.9030 (pt0) cc_final: 0.8622 (pt0) REVERT: Lh 107 LYS cc_start: 0.7955 (mttt) cc_final: 0.7659 (mttt) REVERT: Li 54 GLU cc_start: 0.8313 (pt0) cc_final: 0.8021 (pm20) REVERT: Li 66 GLU cc_start: 0.8344 (mp0) cc_final: 0.8104 (mp0) REVERT: Li 68 ARG cc_start: 0.8377 (mmt180) cc_final: 0.8081 (mmt180) REVERT: Li 98 ARG cc_start: 0.8295 (mmp-170) cc_final: 0.7944 (mmm160) REVERT: Lm 113 ARG cc_start: 0.8113 (mtp-110) cc_final: 0.7352 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8863 (mt0) cc_final: 0.8552 (mp10) REVERT: Ln 4 LYS cc_start: 0.3759 (mptt) cc_final: 0.3326 (ttmt) REVERT: Ln 9 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7588 (ttp-110) REVERT: Lo 79 THR cc_start: 0.8367 (m) cc_final: 0.7888 (p) REVERT: Lo 102 GLN cc_start: 0.8423 (pm20) cc_final: 0.7972 (pm20) REVERT: Lp 32 GLN cc_start: 0.9060 (mt0) cc_final: 0.8812 (mt0) REVERT: Lp 81 SER cc_start: 0.9520 (t) cc_final: 0.9263 (p) REVERT: D 532 MET cc_start: 0.6200 (mmt) cc_final: 0.4078 (tpp) REVERT: D 613 LEU cc_start: 0.6333 (tp) cc_final: 0.5761 (mt) REVERT: D 690 MET cc_start: 0.1896 (mmm) cc_final: 0.1079 (ptt) outliers start: 282 outliers final: 228 residues processed: 1376 average time/residue: 1.2077 time to fit residues: 2945.4784 Evaluate side-chains 1399 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1151 time to evaluate : 6.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 115 PHE Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain B residue 640 ILE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain LA residue 20 THR Chi-restraints excluded: chain LA residue 24 GLN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 80 GLU Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 322 ILE Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 2 SER Chi-restraints excluded: chain LC residue 5 GLN Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 182 LEU Chi-restraints excluded: chain LC residue 196 ASN Chi-restraints excluded: chain LC residue 222 VAL Chi-restraints excluded: chain LC residue 244 LEU Chi-restraints excluded: chain LC residue 327 LEU Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 153 THR Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 40 LEU Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 77 ARG Chi-restraints excluded: chain LE residue 84 VAL Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 190 THR Chi-restraints excluded: chain LG residue 36 ILE Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 71 VAL Chi-restraints excluded: chain LH residue 74 LEU Chi-restraints excluded: chain LH residue 92 TYR Chi-restraints excluded: chain LH residue 130 ASP Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 149 ASN Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LI residue 190 VAL Chi-restraints excluded: chain LI residue 192 ASP Chi-restraints excluded: chain LJ residue 32 ARG Chi-restraints excluded: chain LJ residue 80 LEU Chi-restraints excluded: chain LL residue 10 LEU Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 80 VAL Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LL residue 129 ASN Chi-restraints excluded: chain LL residue 162 ASN Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 21 VAL Chi-restraints excluded: chain LM residue 27 GLN Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 41 GLN Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 29 GLU Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 86 THR Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 6 THR Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 139 VAL Chi-restraints excluded: chain LR residue 142 ILE Chi-restraints excluded: chain LS residue 19 VAL Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 96 ILE Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 62 VAL Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 61 THR Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LV residue 125 LEU Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 81 GLN Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 26 VAL Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain LZ residue 98 THR Chi-restraints excluded: chain La residue 82 ILE Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 29 SER Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Ld residue 42 LEU Chi-restraints excluded: chain Ld residue 51 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 84 ASP Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Ld residue 97 LEU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 23 ASP Chi-restraints excluded: chain Le residue 32 TRP Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 63 THR Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lg residue 6 THR Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 22 VAL Chi-restraints excluded: chain Lg residue 40 THR Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lh residue 28 LEU Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Li residue 20 MET Chi-restraints excluded: chain Li residue 26 ILE Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 15 SER Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 41 THR Chi-restraints excluded: chain Lk residue 72 THR Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lm residue 118 THR Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 57 VAL Chi-restraints excluded: chain Lo residue 88 CYS Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 162 PHE Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 467 ILE Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 579 MET Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 704 HIS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 1003 optimal weight: 20.0000 chunk 1056 optimal weight: 20.0000 chunk 963 optimal weight: 20.0000 chunk 1027 optimal weight: 20.0000 chunk 618 optimal weight: 6.9990 chunk 447 optimal weight: 7.9990 chunk 806 optimal weight: 20.0000 chunk 315 optimal weight: 6.9990 chunk 928 optimal weight: 50.0000 chunk 971 optimal weight: 20.0000 chunk 1023 optimal weight: 20.0000 overall best weight: 12.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 GLN A 186 HIS B 96 HIS ** B 382 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 588 ASN ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 677 ASN ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** LD 63 GLN ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LF 225 GLN ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LN 90 ASN ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN ** LY 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LZ 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 43 HIS Lb 48 HIS ** Ld 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Ld 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lg 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 27 GLN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN D 461 HIS ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.4992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 151486 Z= 0.429 Angle : 0.780 16.386 221974 Z= 0.400 Chirality : 0.043 0.322 27643 Planarity : 0.006 0.097 14813 Dihedral : 23.142 179.877 64437 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 25.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.89 % Favored : 93.01 % Rotamer: Outliers : 4.34 % Allowed : 22.31 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.09), residues: 7994 helix: 0.30 (0.09), residues: 3337 sheet: -0.73 (0.17), residues: 844 loop : -1.08 (0.10), residues: 3813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.003 TRP B 700 HIS 0.011 0.002 HISLe 88 PHE 0.048 0.003 PHELP 26 TYR 0.038 0.003 TYRLj 39 ARG 0.013 0.001 ARGLV 32 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 299 poor density : 1140 time to evaluate : 6.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LEU cc_start: 0.7374 (pp) cc_final: 0.7127 (pt) REVERT: B 223 ASN cc_start: 0.5542 (m110) cc_final: 0.5157 (t0) REVERT: B 351 MET cc_start: 0.4914 (ttt) cc_final: 0.2719 (tmm) REVERT: B 462 PHE cc_start: 0.8151 (OUTLIER) cc_final: 0.7142 (m-80) REVERT: B 532 MET cc_start: 0.5633 (OUTLIER) cc_final: 0.5097 (mmm) REVERT: B 724 ASP cc_start: 0.8141 (m-30) cc_final: 0.7840 (t70) REVERT: B 736 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7537 (mmtt) REVERT: B 775 LYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6181 (tptp) REVERT: LA 69 TYR cc_start: 0.7320 (t80) cc_final: 0.6938 (t80) REVERT: LA 133 TYR cc_start: 0.9093 (p90) cc_final: 0.8622 (p90) REVERT: LA 149 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7805 (mmt-90) REVERT: LB 167 ARG cc_start: 0.9007 (OUTLIER) cc_final: 0.8670 (ptm-80) REVERT: LB 298 PHE cc_start: 0.8867 (m-80) cc_final: 0.8564 (m-10) REVERT: LB 308 MET cc_start: 0.8873 (mmm) cc_final: 0.7848 (mpp) REVERT: LB 345 ASN cc_start: 0.8597 (t0) cc_final: 0.7838 (t0) REVERT: LB 349 LYS cc_start: 0.9578 (OUTLIER) cc_final: 0.9244 (ttmt) REVERT: LC 41 SER cc_start: 0.9731 (m) cc_final: 0.9399 (p) REVERT: LC 93 MET cc_start: 0.9101 (pmm) cc_final: 0.8857 (pmm) REVERT: LC 99 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.7647 (ppp) REVERT: LC 177 ASP cc_start: 0.8768 (p0) cc_final: 0.8480 (p0) REVERT: LD 31 TYR cc_start: 0.9029 (t80) cc_final: 0.8417 (t80) REVERT: LD 93 THR cc_start: 0.8671 (OUTLIER) cc_final: 0.8361 (m) REVERT: LD 111 GLN cc_start: 0.9367 (tm-30) cc_final: 0.9095 (tm-30) REVERT: LD 180 PHE cc_start: 0.9033 (m-80) cc_final: 0.8773 (m-80) REVERT: LE 4 GLN cc_start: 0.8190 (tt0) cc_final: 0.7813 (tm-30) REVERT: LE 9 TRP cc_start: 0.7426 (t60) cc_final: 0.6838 (t60) REVERT: LE 77 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6328 (tpt-90) REVERT: LF 173 LEU cc_start: 0.9490 (OUTLIER) cc_final: 0.9233 (mm) REVERT: LG 152 LEU cc_start: 0.9067 (mt) cc_final: 0.8857 (mm) REVERT: LH 23 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7353 (mtp85) REVERT: LH 111 PHE cc_start: 0.8581 (m-80) cc_final: 0.7958 (t80) REVERT: LH 177 ASP cc_start: 0.8628 (OUTLIER) cc_final: 0.8156 (m-30) REVERT: LI 123 HIS cc_start: 0.8226 (OUTLIER) cc_final: 0.7585 (p90) REVERT: LI 181 TYR cc_start: 0.8276 (t80) cc_final: 0.8010 (t80) REVERT: LJ 38 GLU cc_start: 0.8236 (pt0) cc_final: 0.7644 (tp30) REVERT: LJ 88 GLU cc_start: 0.9109 (tm-30) cc_final: 0.8892 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8449 (m-40) cc_final: 0.7961 (m-40) REVERT: LJ 123 PHE cc_start: 0.6604 (m-80) cc_final: 0.6334 (m-10) REVERT: LL 172 LEU cc_start: 0.9364 (pp) cc_final: 0.8972 (mt) REVERT: LM 14 LEU cc_start: 0.9198 (mm) cc_final: 0.8695 (mm) REVERT: LM 16 GLU cc_start: 0.8725 (pt0) cc_final: 0.8073 (pm20) REVERT: LM 41 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.6968 (tm-30) REVERT: LM 42 LYS cc_start: 0.8207 (mttt) cc_final: 0.7939 (mttt) REVERT: LM 47 ASP cc_start: 0.7047 (OUTLIER) cc_final: 0.6419 (m-30) REVERT: LM 94 TRP cc_start: 0.9311 (t-100) cc_final: 0.8922 (t-100) REVERT: LN 11 GLN cc_start: 0.9098 (tp40) cc_final: 0.8648 (mm-40) REVERT: LN 91 GLU cc_start: 0.8322 (tt0) cc_final: 0.7620 (tm-30) REVERT: LN 104 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8398 (mt-10) REVERT: LN 175 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8412 (m-40) REVERT: LO 65 ASN cc_start: 0.8373 (t0) cc_final: 0.8142 (t0) REVERT: LO 112 TYR cc_start: 0.8883 (m-80) cc_final: 0.8649 (m-80) REVERT: LP 140 GLU cc_start: 0.8117 (pm20) cc_final: 0.7633 (pm20) REVERT: LQ 66 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8698 (mmt-90) REVERT: LQ 137 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8247 (p) REVERT: LR 25 ASP cc_start: 0.8732 (p0) cc_final: 0.8504 (p0) REVERT: LR 27 ASN cc_start: 0.9306 (m110) cc_final: 0.8601 (t0) REVERT: LR 68 GLN cc_start: 0.9070 (tp40) cc_final: 0.8664 (tm-30) REVERT: LR 95 TRP cc_start: 0.9414 (t-100) cc_final: 0.9053 (t-100) REVERT: LS 25 PHE cc_start: 0.8054 (m-10) cc_final: 0.7642 (m-80) REVERT: LS 172 TYR cc_start: 0.9025 (t80) cc_final: 0.8787 (t80) REVERT: LV 11 PHE cc_start: 0.8377 (m-80) cc_final: 0.7909 (m-80) REVERT: LV 12 ARG cc_start: 0.8587 (ttt-90) cc_final: 0.8056 (ttt-90) REVERT: LV 15 LEU cc_start: 0.9358 (mm) cc_final: 0.8962 (mm) REVERT: LV 32 ARG cc_start: 0.7823 (mtm-85) cc_final: 0.7602 (mtm-85) REVERT: LV 40 LYS cc_start: 0.9366 (mmmt) cc_final: 0.8955 (mmmt) REVERT: LV 92 PHE cc_start: 0.9006 (m-80) cc_final: 0.8591 (m-10) REVERT: LW 12 LYS cc_start: 0.9368 (OUTLIER) cc_final: 0.9033 (mtmm) REVERT: LX 115 ARG cc_start: 0.8913 (mtp85) cc_final: 0.8562 (mtp85) REVERT: LY 53 ASP cc_start: 0.8467 (m-30) cc_final: 0.7740 (t0) REVERT: LY 99 LEU cc_start: 0.8878 (OUTLIER) cc_final: 0.8508 (mm) REVERT: LZ 90 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7800 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8731 (tt0) cc_final: 0.8231 (mm-30) REVERT: La 64 GLN cc_start: 0.8638 (pt0) cc_final: 0.8329 (pt0) REVERT: La 69 TRP cc_start: 0.8774 (t60) cc_final: 0.7944 (t60) REVERT: Ld 11 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7971 (mm-30) REVERT: Ld 35 GLU cc_start: 0.8236 (tm-30) cc_final: 0.8032 (tm-30) REVERT: Lf 39 GLN cc_start: 0.8846 (mp10) cc_final: 0.8504 (mp10) REVERT: Lf 92 LYS cc_start: 0.9468 (tttm) cc_final: 0.8807 (tptp) REVERT: Lf 97 SER cc_start: 0.9201 (t) cc_final: 0.8790 (p) REVERT: Lh 14 LYS cc_start: 0.8282 (mmtt) cc_final: 0.7783 (mtpt) REVERT: Lh 60 GLU cc_start: 0.9150 (pt0) cc_final: 0.8755 (pt0) REVERT: Li 13 LYS cc_start: 0.8446 (pttt) cc_final: 0.7996 (pptt) REVERT: Li 98 ARG cc_start: 0.8265 (mmp-170) cc_final: 0.7906 (mmm160) REVERT: Ll 19 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8006 (pt0) REVERT: Ll 27 ILE cc_start: 0.8646 (mm) cc_final: 0.8385 (mm) REVERT: Lm 113 ARG cc_start: 0.8226 (mtp-110) cc_final: 0.7471 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8902 (mt0) cc_final: 0.8598 (mp10) REVERT: Ln 4 LYS cc_start: 0.3772 (mptt) cc_final: 0.3165 (tttt) REVERT: Ln 9 ARG cc_start: 0.8413 (ttm170) cc_final: 0.7607 (ttp-110) REVERT: Lo 29 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7640 (ptpp) REVERT: Lo 79 THR cc_start: 0.8599 (m) cc_final: 0.8162 (p) REVERT: Lp 17 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.7699 (ptt90) REVERT: Lp 81 SER cc_start: 0.9525 (t) cc_final: 0.9279 (p) REVERT: D 532 MET cc_start: 0.6442 (mmt) cc_final: 0.4132 (tpp) REVERT: D 690 MET cc_start: 0.2589 (mmm) cc_final: 0.1658 (ptt) outliers start: 299 outliers final: 237 residues processed: 1318 average time/residue: 1.1818 time to fit residues: 2763.4506 Evaluate side-chains 1359 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1098 time to evaluate : 8.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 22 TYR Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 462 PHE Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 682 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain LA residue 24 GLN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 322 ILE Chi-restraints excluded: chain LB residue 324 VAL Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 182 LEU Chi-restraints excluded: chain LC residue 196 ASN Chi-restraints excluded: chain LC residue 222 VAL Chi-restraints excluded: chain LC residue 244 LEU Chi-restraints excluded: chain LC residue 327 LEU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 95 TRP Chi-restraints excluded: chain LD residue 153 THR Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 77 ARG Chi-restraints excluded: chain LE residue 84 VAL Chi-restraints excluded: chain LF residue 62 ILE Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 173 LEU Chi-restraints excluded: chain LF residue 190 THR Chi-restraints excluded: chain LF residue 211 SER Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 71 VAL Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 149 ASN Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 24 ARG Chi-restraints excluded: chain LI residue 44 ASP Chi-restraints excluded: chain LI residue 123 HIS Chi-restraints excluded: chain LI residue 138 VAL Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LI residue 190 VAL Chi-restraints excluded: chain LJ residue 32 ARG Chi-restraints excluded: chain LJ residue 80 LEU Chi-restraints excluded: chain LJ residue 93 ASP Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 80 VAL Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LL residue 129 ASN Chi-restraints excluded: chain LL residue 147 ILE Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 21 VAL Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 41 GLN Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 29 GLU Chi-restraints excluded: chain LN residue 49 ARG Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 27 LEU Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LO residue 182 ASN Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 32 THR Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 48 LEU Chi-restraints excluded: chain LP residue 49 GLU Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 66 ARG Chi-restraints excluded: chain LQ residue 86 THR Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LQ residue 137 THR Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 96 ILE Chi-restraints excluded: chain LR residue 122 VAL Chi-restraints excluded: chain LR residue 139 VAL Chi-restraints excluded: chain LS residue 19 VAL Chi-restraints excluded: chain LS residue 36 ILE Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 37 LEU Chi-restraints excluded: chain LU residue 47 VAL Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 62 VAL Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 71 PHE Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LW residue 52 THR Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 81 GLN Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LY residue 99 LEU Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 26 VAL Chi-restraints excluded: chain LZ residue 87 LEU Chi-restraints excluded: chain LZ residue 98 THR Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 130 VAL Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 11 ASN Chi-restraints excluded: chain Lc residue 29 SER Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Ld residue 8 VAL Chi-restraints excluded: chain Ld residue 51 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 84 ASP Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 23 ASP Chi-restraints excluded: chain Le residue 31 ASN Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 41 VAL Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lg residue 6 THR Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 22 VAL Chi-restraints excluded: chain Lg residue 29 ILE Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lh residue 28 LEU Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Li residue 20 MET Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 24 THR Chi-restraints excluded: chain Lk residue 72 THR Chi-restraints excluded: chain Lk residue 76 ASN Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 29 LEU Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 29 LYS Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 57 VAL Chi-restraints excluded: chain Lo residue 64 THR Chi-restraints excluded: chain Lo residue 88 CYS Chi-restraints excluded: chain Lp residue 17 ARG Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 237 LEU Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 493 ASP Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 704 HIS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 744 ASP Chi-restraints excluded: chain D residue 796 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 674 optimal weight: 10.0000 chunk 1086 optimal weight: 10.0000 chunk 663 optimal weight: 9.9990 chunk 515 optimal weight: 0.9990 chunk 755 optimal weight: 20.0000 chunk 1139 optimal weight: 8.9990 chunk 1048 optimal weight: 20.0000 chunk 907 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 701 optimal weight: 6.9990 chunk 556 optimal weight: 8.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** LM 27 GLN ** LN 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LQ 45 ASN ** LS 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN ** LY 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Lb 43 HIS ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lg 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 142 ASN D 181 GLN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 659 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.5007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 151486 Z= 0.263 Angle : 0.666 17.819 221974 Z= 0.345 Chirality : 0.038 0.327 27643 Planarity : 0.005 0.094 14813 Dihedral : 23.147 179.659 64437 Min Nonbonded Distance : 1.079 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.83 % Favored : 94.07 % Rotamer: Outliers : 3.72 % Allowed : 23.47 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.35 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.09), residues: 7994 helix: 0.46 (0.09), residues: 3341 sheet: -0.72 (0.17), residues: 873 loop : -1.01 (0.10), residues: 3780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.069 0.002 TRP B 700 HIS 0.008 0.001 HISLe 88 PHE 0.042 0.002 PHELJ 163 TYR 0.036 0.002 TYRLU 36 ARG 0.014 0.001 ARGLG 57 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15988 Ramachandran restraints generated. 7994 Oldfield, 0 Emsley, 7994 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1421 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1165 time to evaluate : 7.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 223 ASN cc_start: 0.5728 (m110) cc_final: 0.5365 (t0) REVERT: B 351 MET cc_start: 0.5052 (ttt) cc_final: 0.3100 (tmm) REVERT: B 478 MET cc_start: 0.4894 (tmm) cc_final: 0.4467 (tmm) REVERT: B 532 MET cc_start: 0.5618 (OUTLIER) cc_final: 0.5142 (mmm) REVERT: B 724 ASP cc_start: 0.8097 (m-30) cc_final: 0.7797 (t70) REVERT: B 736 LYS cc_start: 0.7939 (OUTLIER) cc_final: 0.7529 (mmtt) REVERT: B 775 LYS cc_start: 0.7118 (OUTLIER) cc_final: 0.6266 (tptp) REVERT: LA 69 TYR cc_start: 0.7211 (t80) cc_final: 0.6702 (t80) REVERT: LA 133 TYR cc_start: 0.9007 (p90) cc_final: 0.8572 (p90) REVERT: LA 149 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7794 (mmt-90) REVERT: LB 167 ARG cc_start: 0.9032 (OUTLIER) cc_final: 0.8694 (ptm-80) REVERT: LB 298 PHE cc_start: 0.8867 (m-80) cc_final: 0.8573 (m-10) REVERT: LB 308 MET cc_start: 0.8842 (mmm) cc_final: 0.7848 (mpp) REVERT: LB 345 ASN cc_start: 0.8499 (t0) cc_final: 0.7753 (t0) REVERT: LB 349 LYS cc_start: 0.9554 (OUTLIER) cc_final: 0.9236 (ttmt) REVERT: LC 41 SER cc_start: 0.9680 (m) cc_final: 0.9336 (p) REVERT: LC 93 MET cc_start: 0.9149 (pmm) cc_final: 0.8919 (pmm) REVERT: LC 99 MET cc_start: 0.8778 (OUTLIER) cc_final: 0.7626 (ppp) REVERT: LC 177 ASP cc_start: 0.8600 (p0) cc_final: 0.8308 (p0) REVERT: LC 274 TYR cc_start: 0.8791 (t80) cc_final: 0.8493 (t80) REVERT: LD 31 TYR cc_start: 0.8948 (t80) cc_final: 0.8415 (t80) REVERT: LD 93 THR cc_start: 0.8545 (OUTLIER) cc_final: 0.8254 (m) REVERT: LD 111 GLN cc_start: 0.9329 (tm-30) cc_final: 0.9073 (tm-30) REVERT: LD 180 PHE cc_start: 0.8996 (m-80) cc_final: 0.8776 (m-80) REVERT: LE 4 GLN cc_start: 0.8237 (tt0) cc_final: 0.7793 (tm-30) REVERT: LE 9 TRP cc_start: 0.7369 (t60) cc_final: 0.6817 (t60) REVERT: LE 77 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6361 (tpt-90) REVERT: LG 152 LEU cc_start: 0.9072 (mt) cc_final: 0.8825 (mm) REVERT: LH 23 ARG cc_start: 0.8403 (OUTLIER) cc_final: 0.7263 (mtp85) REVERT: LH 177 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: LJ 38 GLU cc_start: 0.8215 (pt0) cc_final: 0.7622 (tp30) REVERT: LJ 88 GLU cc_start: 0.9072 (tm-30) cc_final: 0.8842 (tm-30) REVERT: LJ 101 ASN cc_start: 0.8478 (m-40) cc_final: 0.8086 (m-40) REVERT: LJ 116 TYR cc_start: 0.6840 (t80) cc_final: 0.4778 (m-80) REVERT: LJ 117 ASP cc_start: 0.8454 (t0) cc_final: 0.8012 (t0) REVERT: LJ 123 PHE cc_start: 0.6495 (m-80) cc_final: 0.6109 (m-10) REVERT: LL 172 LEU cc_start: 0.9318 (pp) cc_final: 0.8978 (mt) REVERT: LM 14 LEU cc_start: 0.9189 (mm) cc_final: 0.8680 (mm) REVERT: LM 16 GLU cc_start: 0.8730 (pt0) cc_final: 0.8031 (pm20) REVERT: LM 41 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.6874 (tm-30) REVERT: LM 42 LYS cc_start: 0.8093 (mttt) cc_final: 0.7777 (mttt) REVERT: LM 47 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6542 (m-30) REVERT: LM 94 TRP cc_start: 0.9259 (t-100) cc_final: 0.8869 (t-100) REVERT: LN 91 GLU cc_start: 0.8271 (tt0) cc_final: 0.7577 (tm-30) REVERT: LN 123 GLN cc_start: 0.8901 (pt0) cc_final: 0.8539 (pt0) REVERT: LN 160 GLU cc_start: 0.8310 (pm20) cc_final: 0.7802 (pm20) REVERT: LN 175 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8280 (m110) REVERT: LO 28 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9134 (mm) REVERT: LO 65 ASN cc_start: 0.8245 (t0) cc_final: 0.7968 (t0) REVERT: LO 112 TYR cc_start: 0.8836 (m-80) cc_final: 0.8606 (m-80) REVERT: LP 140 GLU cc_start: 0.7972 (pm20) cc_final: 0.7498 (pm20) REVERT: LQ 155 MET cc_start: 0.7275 (tpp) cc_final: 0.7059 (tpp) REVERT: LR 25 ASP cc_start: 0.8581 (p0) cc_final: 0.8363 (p0) REVERT: LR 27 ASN cc_start: 0.9292 (m110) cc_final: 0.8720 (t0) REVERT: LR 68 GLN cc_start: 0.9106 (tp40) cc_final: 0.8684 (tm-30) REVERT: LR 95 TRP cc_start: 0.9332 (t-100) cc_final: 0.8770 (t-100) REVERT: LS 8 GLN cc_start: 0.9168 (pt0) cc_final: 0.8360 (pp30) REVERT: LS 25 PHE cc_start: 0.7970 (m-10) cc_final: 0.7506 (m-80) REVERT: LS 104 GLU cc_start: 0.9110 (tt0) cc_final: 0.8497 (mt-10) REVERT: LS 172 TYR cc_start: 0.8954 (t80) cc_final: 0.8701 (t80) REVERT: LT 19 PHE cc_start: 0.8679 (t80) cc_final: 0.8330 (t80) REVERT: LT 107 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9002 (pt0) REVERT: LV 11 PHE cc_start: 0.8358 (m-80) cc_final: 0.7935 (m-80) REVERT: LV 15 LEU cc_start: 0.9277 (mm) cc_final: 0.8783 (mm) REVERT: LV 32 ARG cc_start: 0.7808 (mtm-85) cc_final: 0.7108 (mtm-85) REVERT: LV 40 LYS cc_start: 0.9350 (mmmt) cc_final: 0.8939 (mmmt) REVERT: LV 92 PHE cc_start: 0.8951 (m-80) cc_final: 0.8551 (m-10) REVERT: LW 12 LYS cc_start: 0.9340 (OUTLIER) cc_final: 0.9005 (mtmm) REVERT: LX 65 GLN cc_start: 0.8931 (pm20) cc_final: 0.8673 (pm20) REVERT: LX 115 ARG cc_start: 0.8854 (mtp85) cc_final: 0.8582 (mtp85) REVERT: LY 53 ASP cc_start: 0.8446 (m-30) cc_final: 0.7679 (t0) REVERT: LY 99 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8492 (mm) REVERT: LZ 90 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7709 (tm-30) REVERT: LZ 119 GLU cc_start: 0.8729 (tt0) cc_final: 0.8215 (mm-30) REVERT: La 58 MET cc_start: 0.7629 (tpt) cc_final: 0.7319 (tpt) REVERT: La 64 GLN cc_start: 0.8538 (pt0) cc_final: 0.8239 (pt0) REVERT: La 69 TRP cc_start: 0.8763 (t60) cc_final: 0.7963 (t60) REVERT: Lb 18 ARG cc_start: 0.7933 (tpp80) cc_final: 0.7393 (ttm170) REVERT: Lc 65 THR cc_start: 0.9226 (m) cc_final: 0.8884 (p) REVERT: Ld 11 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8037 (mm-30) REVERT: Lf 39 GLN cc_start: 0.8829 (mp10) cc_final: 0.8461 (mp10) REVERT: Lf 92 LYS cc_start: 0.9415 (tttm) cc_final: 0.8888 (tptp) REVERT: Lf 97 SER cc_start: 0.9150 (t) cc_final: 0.8788 (p) REVERT: Lh 60 GLU cc_start: 0.9094 (pt0) cc_final: 0.8697 (pt0) REVERT: Li 13 LYS cc_start: 0.8379 (pttt) cc_final: 0.7982 (pptt) REVERT: Li 54 GLU cc_start: 0.8589 (pt0) cc_final: 0.8263 (pm20) REVERT: Li 63 ASN cc_start: 0.8557 (m110) cc_final: 0.8221 (p0) REVERT: Li 68 ARG cc_start: 0.8335 (mmt180) cc_final: 0.7966 (mmt180) REVERT: Li 98 ARG cc_start: 0.8280 (mmp-170) cc_final: 0.7913 (mmm160) REVERT: Ll 19 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8130 (pt0) REVERT: Lm 113 ARG cc_start: 0.8209 (mtp-110) cc_final: 0.7472 (ttp80) REVERT: Lm 120 GLN cc_start: 0.8894 (mt0) cc_final: 0.8576 (mp10) REVERT: Ln 4 LYS cc_start: 0.3644 (mptt) cc_final: 0.3164 (tttt) REVERT: Ln 9 ARG cc_start: 0.8402 (ttm170) cc_final: 0.7612 (ttp-110) REVERT: Lo 79 THR cc_start: 0.8635 (m) cc_final: 0.8185 (p) REVERT: Lp 81 SER cc_start: 0.9500 (t) cc_final: 0.9237 (p) REVERT: C 1 MET cc_start: 0.2121 (mmm) cc_final: 0.1816 (mmm) REVERT: C 63 MET cc_start: 0.4831 (ppp) cc_final: 0.4448 (ppp) REVERT: D 532 MET cc_start: 0.6328 (mmt) cc_final: 0.4160 (tpp) REVERT: D 690 MET cc_start: 0.2262 (mmm) cc_final: 0.1343 (ptt) outliers start: 256 outliers final: 219 residues processed: 1313 average time/residue: 1.2091 time to fit residues: 2804.5716 Evaluate side-chains 1374 residues out of total 6934 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1137 time to evaluate : 7.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain B residue 202 LEU Chi-restraints excluded: chain B residue 206 PHE Chi-restraints excluded: chain B residue 261 LEU Chi-restraints excluded: chain B residue 280 SER Chi-restraints excluded: chain B residue 378 ILE Chi-restraints excluded: chain B residue 381 TYR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 392 SER Chi-restraints excluded: chain B residue 423 LEU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 464 ASN Chi-restraints excluded: chain B residue 494 PHE Chi-restraints excluded: chain B residue 532 MET Chi-restraints excluded: chain B residue 542 SER Chi-restraints excluded: chain B residue 588 ASN Chi-restraints excluded: chain B residue 600 GLN Chi-restraints excluded: chain B residue 610 TYR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 703 SER Chi-restraints excluded: chain B residue 736 LYS Chi-restraints excluded: chain B residue 775 LYS Chi-restraints excluded: chain B residue 779 VAL Chi-restraints excluded: chain B residue 784 ASN Chi-restraints excluded: chain LA residue 61 VAL Chi-restraints excluded: chain LA residue 101 VAL Chi-restraints excluded: chain LA residue 106 SER Chi-restraints excluded: chain LA residue 112 ILE Chi-restraints excluded: chain LA residue 149 ARG Chi-restraints excluded: chain LA residue 199 THR Chi-restraints excluded: chain LB residue 56 ILE Chi-restraints excluded: chain LB residue 167 ARG Chi-restraints excluded: chain LB residue 235 THR Chi-restraints excluded: chain LB residue 282 ILE Chi-restraints excluded: chain LB residue 322 ILE Chi-restraints excluded: chain LB residue 324 VAL Chi-restraints excluded: chain LB residue 349 LYS Chi-restraints excluded: chain LB residue 377 HIS Chi-restraints excluded: chain LC residue 5 GLN Chi-restraints excluded: chain LC residue 99 MET Chi-restraints excluded: chain LC residue 196 ASN Chi-restraints excluded: chain LC residue 222 VAL Chi-restraints excluded: chain LC residue 244 LEU Chi-restraints excluded: chain LC residue 327 LEU Chi-restraints excluded: chain LC residue 362 ASP Chi-restraints excluded: chain LD residue 17 GLN Chi-restraints excluded: chain LD residue 93 THR Chi-restraints excluded: chain LD residue 153 THR Chi-restraints excluded: chain LE residue 39 VAL Chi-restraints excluded: chain LE residue 41 ILE Chi-restraints excluded: chain LE residue 53 VAL Chi-restraints excluded: chain LE residue 71 VAL Chi-restraints excluded: chain LE residue 77 ARG Chi-restraints excluded: chain LE residue 84 VAL Chi-restraints excluded: chain LF residue 112 ASN Chi-restraints excluded: chain LF residue 120 THR Chi-restraints excluded: chain LF residue 190 THR Chi-restraints excluded: chain LG residue 74 THR Chi-restraints excluded: chain LG residue 78 PHE Chi-restraints excluded: chain LG residue 79 GLN Chi-restraints excluded: chain LG residue 83 ASP Chi-restraints excluded: chain LG residue 151 VAL Chi-restraints excluded: chain LG residue 156 ASP Chi-restraints excluded: chain LG residue 158 ASP Chi-restraints excluded: chain LG residue 190 VAL Chi-restraints excluded: chain LG residue 194 THR Chi-restraints excluded: chain LH residue 23 ARG Chi-restraints excluded: chain LH residue 42 ASP Chi-restraints excluded: chain LH residue 57 VAL Chi-restraints excluded: chain LH residue 71 VAL Chi-restraints excluded: chain LH residue 92 TYR Chi-restraints excluded: chain LH residue 130 ASP Chi-restraints excluded: chain LH residue 144 ILE Chi-restraints excluded: chain LH residue 149 ASN Chi-restraints excluded: chain LH residue 177 ASP Chi-restraints excluded: chain LI residue 8 CYS Chi-restraints excluded: chain LI residue 24 ARG Chi-restraints excluded: chain LI residue 147 VAL Chi-restraints excluded: chain LI residue 166 ILE Chi-restraints excluded: chain LI residue 174 THR Chi-restraints excluded: chain LI residue 190 VAL Chi-restraints excluded: chain LJ residue 32 ARG Chi-restraints excluded: chain LJ residue 80 LEU Chi-restraints excluded: chain LJ residue 172 LEU Chi-restraints excluded: chain LL residue 34 SER Chi-restraints excluded: chain LL residue 53 LEU Chi-restraints excluded: chain LL residue 77 LEU Chi-restraints excluded: chain LL residue 80 VAL Chi-restraints excluded: chain LL residue 86 THR Chi-restraints excluded: chain LL residue 129 ASN Chi-restraints excluded: chain LM residue 3 THR Chi-restraints excluded: chain LM residue 21 VAL Chi-restraints excluded: chain LM residue 27 GLN Chi-restraints excluded: chain LM residue 35 ILE Chi-restraints excluded: chain LM residue 41 GLN Chi-restraints excluded: chain LM residue 47 ASP Chi-restraints excluded: chain LM residue 70 PHE Chi-restraints excluded: chain LM residue 114 ASP Chi-restraints excluded: chain LN residue 10 LEU Chi-restraints excluded: chain LN residue 18 VAL Chi-restraints excluded: chain LN residue 29 GLU Chi-restraints excluded: chain LN residue 49 ARG Chi-restraints excluded: chain LN residue 66 VAL Chi-restraints excluded: chain LN residue 175 ASN Chi-restraints excluded: chain LN residue 183 THR Chi-restraints excluded: chain LN residue 196 THR Chi-restraints excluded: chain LO residue 28 LEU Chi-restraints excluded: chain LO residue 150 GLU Chi-restraints excluded: chain LO residue 175 THR Chi-restraints excluded: chain LP residue 7 THR Chi-restraints excluded: chain LP residue 36 ILE Chi-restraints excluded: chain LP residue 54 HIS Chi-restraints excluded: chain LP residue 114 VAL Chi-restraints excluded: chain LQ residue 30 VAL Chi-restraints excluded: chain LQ residue 86 THR Chi-restraints excluded: chain LQ residue 114 ILE Chi-restraints excluded: chain LQ residue 123 THR Chi-restraints excluded: chain LQ residue 124 LEU Chi-restraints excluded: chain LR residue 29 THR Chi-restraints excluded: chain LR residue 57 VAL Chi-restraints excluded: chain LR residue 69 SER Chi-restraints excluded: chain LR residue 93 VAL Chi-restraints excluded: chain LR residue 122 VAL Chi-restraints excluded: chain LR residue 139 VAL Chi-restraints excluded: chain LS residue 19 VAL Chi-restraints excluded: chain LS residue 36 ILE Chi-restraints excluded: chain LS residue 59 VAL Chi-restraints excluded: chain LS residue 60 SER Chi-restraints excluded: chain LS residue 61 ILE Chi-restraints excluded: chain LS residue 65 ASN Chi-restraints excluded: chain LS residue 82 ASP Chi-restraints excluded: chain LS residue 97 VAL Chi-restraints excluded: chain LT residue 52 MET Chi-restraints excluded: chain LT residue 86 GLU Chi-restraints excluded: chain LT residue 90 ASN Chi-restraints excluded: chain LT residue 124 VAL Chi-restraints excluded: chain LT residue 151 LEU Chi-restraints excluded: chain LU residue 61 THR Chi-restraints excluded: chain LU residue 62 VAL Chi-restraints excluded: chain LU residue 65 VAL Chi-restraints excluded: chain LU residue 91 ASP Chi-restraints excluded: chain LU residue 100 THR Chi-restraints excluded: chain LV residue 14 SER Chi-restraints excluded: chain LV residue 23 MET Chi-restraints excluded: chain LV residue 27 ASP Chi-restraints excluded: chain LV residue 73 VAL Chi-restraints excluded: chain LV residue 98 ASN Chi-restraints excluded: chain LV residue 112 SER Chi-restraints excluded: chain LW residue 7 SER Chi-restraints excluded: chain LW residue 12 LYS Chi-restraints excluded: chain LX residue 87 SER Chi-restraints excluded: chain LY residue 7 ASP Chi-restraints excluded: chain LY residue 11 ASP Chi-restraints excluded: chain LY residue 21 THR Chi-restraints excluded: chain LY residue 29 VAL Chi-restraints excluded: chain LY residue 54 ASP Chi-restraints excluded: chain LY residue 59 VAL Chi-restraints excluded: chain LY residue 81 GLN Chi-restraints excluded: chain LY residue 85 VAL Chi-restraints excluded: chain LY residue 86 THR Chi-restraints excluded: chain LY residue 98 ASN Chi-restraints excluded: chain LY residue 99 LEU Chi-restraints excluded: chain LZ residue 10 VAL Chi-restraints excluded: chain LZ residue 12 VAL Chi-restraints excluded: chain LZ residue 26 VAL Chi-restraints excluded: chain LZ residue 98 THR Chi-restraints excluded: chain La residue 104 THR Chi-restraints excluded: chain La residue 124 ILE Chi-restraints excluded: chain La residue 145 VAL Chi-restraints excluded: chain Lb residue 8 THR Chi-restraints excluded: chain Lb residue 35 VAL Chi-restraints excluded: chain Lc residue 29 SER Chi-restraints excluded: chain Lc residue 50 VAL Chi-restraints excluded: chain Lc residue 56 LEU Chi-restraints excluded: chain Lc residue 57 GLU Chi-restraints excluded: chain Lc residue 74 ASN Chi-restraints excluded: chain Lc residue 93 LEU Chi-restraints excluded: chain Ld residue 51 LEU Chi-restraints excluded: chain Ld residue 71 LEU Chi-restraints excluded: chain Ld residue 84 ASP Chi-restraints excluded: chain Ld residue 94 GLU Chi-restraints excluded: chain Le residue 3 SER Chi-restraints excluded: chain Le residue 23 ASP Chi-restraints excluded: chain Le residue 40 SER Chi-restraints excluded: chain Le residue 42 VAL Chi-restraints excluded: chain Le residue 51 SER Chi-restraints excluded: chain Le residue 73 THR Chi-restraints excluded: chain Le residue 81 ASP Chi-restraints excluded: chain Lf residue 15 SER Chi-restraints excluded: chain Lg residue 6 THR Chi-restraints excluded: chain Lg residue 15 THR Chi-restraints excluded: chain Lg residue 22 VAL Chi-restraints excluded: chain Lg residue 29 ILE Chi-restraints excluded: chain Lg residue 68 THR Chi-restraints excluded: chain Lg residue 73 SER Chi-restraints excluded: chain Lh residue 28 LEU Chi-restraints excluded: chain Lh residue 85 THR Chi-restraints excluded: chain Li residue 18 THR Chi-restraints excluded: chain Li residue 20 MET Chi-restraints excluded: chain Li residue 81 THR Chi-restraints excluded: chain Lj residue 29 VAL Chi-restraints excluded: chain Lj residue 33 THR Chi-restraints excluded: chain Lj residue 44 THR Chi-restraints excluded: chain Lj residue 52 LYS Chi-restraints excluded: chain Lj residue 70 VAL Chi-restraints excluded: chain Lk residue 24 THR Chi-restraints excluded: chain Lk residue 72 THR Chi-restraints excluded: chain Lk residue 76 ASN Chi-restraints excluded: chain Ll residue 19 GLN Chi-restraints excluded: chain Ll residue 29 LEU Chi-restraints excluded: chain Ll residue 31 THR Chi-restraints excluded: chain Ll residue 32 ASN Chi-restraints excluded: chain Lm residue 85 LEU Chi-restraints excluded: chain Lo residue 26 THR Chi-restraints excluded: chain Lo residue 54 THR Chi-restraints excluded: chain Lo residue 57 VAL Chi-restraints excluded: chain Lo residue 88 CYS Chi-restraints excluded: chain Lp residue 46 THR Chi-restraints excluded: chain Lp residue 60 CYS Chi-restraints excluded: chain D residue 13 VAL Chi-restraints excluded: chain D residue 44 TYR Chi-restraints excluded: chain D residue 114 TRP Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 142 ASN Chi-restraints excluded: chain D residue 399 CYS Chi-restraints excluded: chain D residue 439 PHE Chi-restraints excluded: chain D residue 440 ASP Chi-restraints excluded: chain D residue 614 ASN Chi-restraints excluded: chain D residue 704 HIS Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain D residue 744 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1144 random chunks: chunk 720 optimal weight: 20.0000 chunk 966 optimal weight: 20.0000 chunk 278 optimal weight: 8.9990 chunk 836 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 252 optimal weight: 8.9990 chunk 909 optimal weight: 20.0000 chunk 380 optimal weight: 10.0000 chunk 933 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 167 optimal weight: 7.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 296 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LC 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LD 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LE 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LF 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LH 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LI 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LJ 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LL 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LM 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LN 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LO 42 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** LP 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LQ 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LS 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LT 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LV 24 ASN ** LX 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LY 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** La 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lb 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Le 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lh 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lj 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Lo 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.069849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.051515 restraints weight = 815572.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.052719 restraints weight = 305750.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.053337 restraints weight = 169415.923| |-----------------------------------------------------------------------------| r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3044 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3044 r_free = 0.3044 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.5015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.295 151486 Z= 0.309 Angle : 0.696 59.142 221974 Z= 0.367 Chirality : 0.039 0.796 27643 Planarity : 0.005 0.169 14813 Dihedral : 23.145 179.673 64437 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 21.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.99 % Favored : 93.90 % Rotamer: Outliers : 3.75 % Allowed : 23.73 % Favored : 72.52 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 3.48 % Cis-general : 0.00 % Twisted Proline : 0.35 % 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: -0.57 (0.09), residues: 7994 helix: 0.47 (0.09), residues: 3342 sheet: -0.72 (0.17), residues: 873 loop : -1.01 (0.10), residues: 3779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP B 700 HIS 0.010 0.001 HISLb 43 PHE 0.034 0.002 PHELP 26 TYR 0.039 0.002 TYRLI 181 ARG 0.041 0.001 ARGLV 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44344.40 seconds wall clock time: 772 minutes 47.99 seconds (46367.99 seconds total)