Starting phenix.real_space_refine on Sat Dec 28 19:03:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y38_33591/12_2024/7y38_33591.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y38_33591/12_2024/7y38_33591.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y38_33591/12_2024/7y38_33591.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y38_33591/12_2024/7y38_33591.map" model { file = "/net/cci-nas-00/data/ceres_data/7y38_33591/12_2024/7y38_33591.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y38_33591/12_2024/7y38_33591.cif" } resolution = 2.8 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= -0.000 sd= 0.030 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: 6 Type Number sf(0) Gaussians Zn 12 6.06 5 P 75 5.49 5 S 397 5.16 5 C 33324 2.51 5 N 9266 2.21 5 O 10061 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 53135 Number of models: 1 Model: "" Number of chains: 27 Chain: "A" Number of atoms: 3677 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3671 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3671 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'CIS': 1, 'PTRANS': 24, 'TRANS': 445} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 23 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3743 Chain: "B" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "C" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "D" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "E" Number of atoms: 3673 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 471, 3667 Classifications: {'peptide': 471} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3739 Chain: "F" Number of atoms: 3639 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 468, 3633 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 Conformer: "B" Number of residues, atoms: 468, 3633 Classifications: {'peptide': 468} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 24, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 25 bond proxies already assigned to first conformer: 3703 Chain: "G" Number of atoms: 3668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3734 Chain: "H" Number of atoms: 3640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3634 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 467, 3634 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3704 Chain: "I" Number of atoms: 3616 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 464, 3610 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 Conformer: "B" Number of residues, atoms: 464, 3610 Classifications: {'peptide': 464} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 440} Chain breaks: 1 Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 bond proxies already assigned to first conformer: 3679 Chain: "J" Number of atoms: 3633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 466, 3627 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 466, 3627 Classifications: {'peptide': 466} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain breaks: 1 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3698 Chain: "K" Number of atoms: 3648 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 467, 3642 Classifications: {'peptide': 467} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 22, 'TRANS': 444} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3713 Chain: "L" Number of atoms: 3668 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Conformer: "B" Number of residues, atoms: 470, 3662 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 23, 'TRANS': 446} Chain breaks: 1 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 bond proxies already assigned to first conformer: 3734 Chain: "X" Number of atoms: 4782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 611, 4782 Classifications: {'peptide': 611} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 32, 'TRANS': 578} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3642 Classifications: {'peptide': 466} Link IDs: {'PTRANS': 22, 'TRANS': 443} Chain: "Z" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 64 Unusual residues: {' ZN': 1, 'ATP': 1, 'GTP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1006 SG CYS A 134 94.319 18.849 67.092 1.00138.69 S ATOM 1058 SG CYS A 141 98.232 17.537 67.191 1.00120.54 S ATOM 4683 SG CYS B 134 139.320 25.510 64.633 1.00143.97 S ATOM 4735 SG CYS B 141 143.226 26.325 65.211 1.00114.99 S ATOM 8356 SG CYS C 134 176.816 52.385 62.609 1.00142.28 S ATOM 8408 SG CYS C 141 178.393 56.191 62.650 1.00120.87 S ATOM 12029 SG CYS D 134 192.237 95.890 60.986 1.00144.77 S ATOM 12081 SG CYS D 141 193.712 99.581 61.580 1.00126.42 S ATOM 15702 SG CYS E 134 185.946 141.119 60.653 1.00138.69 S ATOM 15754 SG CYS E 141 185.534 145.184 61.324 1.00117.05 S ATOM 19375 SG CYS F 134 158.993 178.231 62.249 1.00135.33 S ATOM 19427 SG CYS F 141 155.578 180.370 62.715 1.00121.33 S ATOM 23009 SG CYS G 134 116.184 195.994 63.541 1.00131.75 S ATOM 23061 SG CYS G 141 112.419 195.458 64.461 1.00104.53 S ATOM 26677 SG CYS H 134 70.334 188.867 66.152 1.00135.03 S ATOM 26729 SG CYS H 141 67.094 186.639 66.611 1.00114.42 S ATOM 30322 SG CYS I 134 33.548 160.276 68.134 1.00140.36 S ATOM 30374 SG CYS I 141 31.929 157.237 68.505 1.00124.62 S ATOM 33933 SG CYS J 134 17.712 117.240 69.338 1.00124.83 S ATOM 33985 SG CYS J 141 16.514 113.357 70.167 1.00117.81 S ATOM 37566 SG CYS K 134 24.285 72.175 69.736 1.00159.69 S ATOM 37618 SG CYS K 141 24.643 67.961 70.092 1.00119.96 S ATOM 41214 SG CYS L 134 52.078 36.040 68.777 1.00136.88 S ATOM 41266 SG CYS L 141 54.762 33.012 69.489 1.00116.90 S Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ACYS A 236 " occ=0.66 ... (10 atoms not shown) pdb=" SG BCYS A 236 " occ=0.34 residue: pdb=" N ACYS B 236 " occ=0.61 ... (10 atoms not shown) pdb=" SG BCYS B 236 " occ=0.39 residue: pdb=" N ACYS C 236 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS C 236 " occ=0.43 residue: pdb=" N ACYS D 236 " occ=0.51 ... (10 atoms not shown) pdb=" SG BCYS D 236 " occ=0.49 residue: pdb=" N ACYS E 236 " occ=0.67 ... (10 atoms not shown) pdb=" SG BCYS E 236 " occ=0.33 residue: pdb=" N ACYS F 236 " occ=0.63 ... (10 atoms not shown) pdb=" SG BCYS F 236 " occ=0.37 residue: pdb=" N ACYS G 236 " occ=0.58 ... (10 atoms not shown) pdb=" SG BCYS G 236 " occ=0.41 residue: pdb=" N ACYS H 236 " occ=0.57 ... (10 atoms not shown) pdb=" SG BCYS H 236 " occ=0.43 residue: pdb=" N ACYS I 236 " occ=0.54 ... (10 atoms not shown) pdb=" SG BCYS I 236 " occ=0.46 residue: pdb=" N ACYS J 236 " occ=0.53 ... (10 atoms not shown) pdb=" SG BCYS J 236 " occ=0.47 residue: pdb=" N ACYS K 236 " occ=0.76 ... (10 atoms not shown) pdb=" SG BCYS K 236 " occ=0.24 residue: pdb=" N ACYS L 236 " occ=0.73 ... (10 atoms not shown) pdb=" SG BCYS L 236 " occ=0.27 Time building chain proxies: 37.52, per 1000 atoms: 0.71 Number of scatterers: 53135 At special positions: 0 Unit cell: (212.3, 211.2, 139.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 12 29.99 S 397 16.00 P 75 15.00 O 10061 8.00 N 9266 7.00 C 33324 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.27 Conformation dependent library (CDL) restraints added in 8.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb=" ZN B1001 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 141 " pdb="ZN ZN B1001 " - pdb=" NE2 HIS B 79 " pdb="ZN ZN B1001 " - pdb=" SG CYS B 134 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb=" ZN D1001 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 141 " pdb="ZN ZN D1001 " - pdb=" SG CYS D 134 " pdb="ZN ZN D1001 " - pdb=" NE2 HIS D 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb=" ZN F1001 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 141 " pdb="ZN ZN F1001 " - pdb=" NE2 HIS F 79 " pdb="ZN ZN F1001 " - pdb=" SG CYS F 134 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb=" ZN H1001 " pdb="ZN ZN H1001 " - pdb=" NE2 HIS H 79 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 141 " pdb="ZN ZN H1001 " - pdb=" SG CYS H 134 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb=" ZN J1001 " pdb="ZN ZN J1001 " - pdb=" NE2 HIS J 79 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 141 " pdb="ZN ZN J1001 " - pdb=" SG CYS J 134 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb=" ZN L1001 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 141 " pdb="ZN ZN L1001 " - pdb=" NE2 HIS L 79 " pdb="ZN ZN L1001 " - pdb=" SG CYS L 134 " 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12742 Finding SS restraints... Secondary structure from input PDB file: 229 helices and 72 sheets defined 34.2% alpha, 19.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.45 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.276A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 55 removed outlier: 6.535A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 49 " --> pdb=" O HIS A 45 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLU A 54 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 3.568A pdb=" N ARG A 70 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N MET A 72 " --> pdb=" O ALA A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 104 Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 180 through 185 removed outlier: 3.593A pdb=" N MET A 184 " --> pdb=" O THR A 180 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 185' Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 341 removed outlier: 3.631A pdb=" N CYS A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 343 No H-bonds generated for 'chain 'A' and resid 342 through 343' Processing helix chain 'A' and resid 344 through 348 removed outlier: 3.598A pdb=" N THR A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 363 Processing helix chain 'A' and resid 383 through 403 removed outlier: 3.521A pdb=" N LYS A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS A 400 " --> pdb=" O LYS A 396 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ASP A 401 " --> pdb=" O GLU A 397 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N MET A 402 " --> pdb=" O CYS A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 472 Processing helix chain 'B' and resid 14 through 22 Processing helix chain 'B' and resid 37 through 52 removed outlier: 3.570A pdb=" N PHE B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LYS B 49 " --> pdb=" O HIS B 45 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 104 Processing helix chain 'B' and resid 111 through 125 removed outlier: 3.516A pdb=" N VAL B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 167 Processing helix chain 'B' and resid 180 through 185 removed outlier: 3.570A pdb=" N MET B 184 " --> pdb=" O THR B 180 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR B 185 " --> pdb=" O THR B 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 180 through 185' Processing helix chain 'B' and resid 203 through 205 No H-bonds generated for 'chain 'B' and resid 203 through 205' Processing helix chain 'B' and resid 251 through 257 Processing helix chain 'B' and resid 335 through 341 Processing helix chain 'B' and resid 342 through 343 No H-bonds generated for 'chain 'B' and resid 342 through 343' Processing helix chain 'B' and resid 344 through 348 removed outlier: 3.607A pdb=" N THR B 348 " --> pdb=" O ILE B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 363 Processing helix chain 'B' and resid 380 through 382 No H-bonds generated for 'chain 'B' and resid 380 through 382' Processing helix chain 'B' and resid 383 through 403 removed outlier: 3.500A pdb=" N MET B 402 " --> pdb=" O CYS B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 474 removed outlier: 4.314A pdb=" N LYS B 474 " --> pdb=" O TRP B 470 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.234A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 Processing helix chain 'C' and resid 88 through 103 removed outlier: 3.730A pdb=" N ALA C 103 " --> pdb=" O LYS C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 157 through 168 removed outlier: 3.885A pdb=" N LYS C 168 " --> pdb=" O HIS C 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 185 removed outlier: 3.565A pdb=" N MET C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N TYR C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 180 through 185' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 removed outlier: 3.506A pdb=" N CYS C 339 " --> pdb=" O PRO C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.571A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA C 347 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 343 through 348' Processing helix chain 'C' and resid 351 through 366 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 401 removed outlier: 3.639A pdb=" N LYS C 400 " --> pdb=" O LYS C 396 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP C 401 " --> pdb=" O GLU C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 461 through 472 Processing helix chain 'D' and resid 13 through 22 removed outlier: 4.321A pdb=" N ALA D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 54 removed outlier: 3.556A pdb=" N ARG D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE D 43 " --> pdb=" O ASN D 39 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N SER D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 103 removed outlier: 3.543A pdb=" N ARG D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 157 through 168 removed outlier: 3.780A pdb=" N LYS D 168 " --> pdb=" O HIS D 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 185 removed outlier: 3.547A pdb=" N TYR D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 195 No H-bonds generated for 'chain 'D' and resid 193 through 195' Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 335 through 342 Processing helix chain 'D' and resid 343 through 348 removed outlier: 3.812A pdb=" N LEU D 346 " --> pdb=" O THR D 343 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA D 347 " --> pdb=" O GLY D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 351 through 364 Processing helix chain 'D' and resid 380 through 382 No H-bonds generated for 'chain 'D' and resid 380 through 382' Processing helix chain 'D' and resid 383 through 404 removed outlier: 3.759A pdb=" N ARG D 399 " --> pdb=" O ALA D 395 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS D 400 " --> pdb=" O LYS D 396 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ASP D 401 " --> pdb=" O GLU D 397 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N MET D 402 " --> pdb=" O CYS D 398 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLU D 403 " --> pdb=" O ARG D 399 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP D 404 " --> pdb=" O LYS D 400 " (cutoff:3.500A) Processing helix chain 'D' and resid 461 through 472 Processing helix chain 'E' and resid 14 through 22 Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.623A pdb=" N ARG E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N PHE E 43 " --> pdb=" O ASN E 39 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 3.649A pdb=" N MET E 72 " --> pdb=" O ALA E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 102 Processing helix chain 'E' and resid 111 through 125 removed outlier: 3.728A pdb=" N VAL E 125 " --> pdb=" O ALA E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 180 through 185 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 342 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.943A pdb=" N ALA E 347 " --> pdb=" O GLY E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 351 through 363 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 401 removed outlier: 3.565A pdb=" N LYS E 400 " --> pdb=" O LYS E 396 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASP E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 473 Processing helix chain 'F' and resid 13 through 22 removed outlier: 4.291A pdb=" N ALA F 17 " --> pdb=" O ALA F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 55 removed outlier: 3.588A pdb=" N PHE F 43 " --> pdb=" O ASN F 39 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N SER F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LYS F 49 " --> pdb=" O HIS F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 72 removed outlier: 3.706A pdb=" N MET F 72 " --> pdb=" O ALA F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 103 Processing helix chain 'F' and resid 111 through 125 removed outlier: 3.662A pdb=" N LYS F 115 " --> pdb=" O ASN F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 157 through 167 Processing helix chain 'F' and resid 180 through 185 removed outlier: 3.680A pdb=" N MET F 184 " --> pdb=" O THR F 180 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N TYR F 185 " --> pdb=" O THR F 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 180 through 185' Processing helix chain 'F' and resid 203 through 205 No H-bonds generated for 'chain 'F' and resid 203 through 205' Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 335 through 342 removed outlier: 3.561A pdb=" N MET F 342 " --> pdb=" O ILE F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 343 through 348 removed outlier: 3.659A pdb=" N LEU F 346 " --> pdb=" O THR F 343 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR F 348 " --> pdb=" O ILE F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 351 through 365 Processing helix chain 'F' and resid 380 through 382 No H-bonds generated for 'chain 'F' and resid 380 through 382' Processing helix chain 'F' and resid 383 through 403 removed outlier: 3.667A pdb=" N LYS F 400 " --> pdb=" O LYS F 396 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP F 401 " --> pdb=" O GLU F 397 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N MET F 402 " --> pdb=" O CYS F 398 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLU F 403 " --> pdb=" O ARG F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 461 through 472 Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.206A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 54 removed outlier: 3.695A pdb=" N PHE G 43 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N SER G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N LYS G 49 " --> pdb=" O HIS G 45 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N GLU G 54 " --> pdb=" O LEU G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 3.719A pdb=" N MET G 72 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.668A pdb=" N ARG G 92 " --> pdb=" O GLU G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 180 through 185 removed outlier: 3.529A pdb=" N TYR G 185 " --> pdb=" O THR G 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 341 Processing helix chain 'G' and resid 342 through 343 No H-bonds generated for 'chain 'G' and resid 342 through 343' Processing helix chain 'G' and resid 344 through 348 removed outlier: 3.519A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 351 through 365 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 removed outlier: 3.587A pdb=" N LYS G 400 " --> pdb=" O LYS G 396 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP G 401 " --> pdb=" O GLU G 397 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N MET G 402 " --> pdb=" O CYS G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 461 through 474 removed outlier: 3.506A pdb=" N ARG G 467 " --> pdb=" O PRO G 463 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS G 474 " --> pdb=" O TRP G 470 " (cutoff:3.500A) Processing helix chain 'H' and resid 13 through 22 removed outlier: 4.120A pdb=" N ALA H 17 " --> pdb=" O ALA H 13 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 53 removed outlier: 3.604A pdb=" N GLN H 53 " --> pdb=" O LYS H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 removed outlier: 3.549A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 101 removed outlier: 3.508A pdb=" N ARG H 92 " --> pdb=" O GLU H 88 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 157 through 167 Processing helix chain 'H' and resid 180 through 185 removed outlier: 3.610A pdb=" N MET H 184 " --> pdb=" O THR H 180 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N TYR H 185 " --> pdb=" O THR H 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 180 through 185' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 203 through 205 No H-bonds generated for 'chain 'H' and resid 203 through 205' Processing helix chain 'H' and resid 251 through 257 Processing helix chain 'H' and resid 335 through 342 removed outlier: 3.566A pdb=" N GLN H 341 " --> pdb=" O THR H 337 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N MET H 342 " --> pdb=" O ILE H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 348 removed outlier: 3.588A pdb=" N LEU H 346 " --> pdb=" O THR H 343 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 348 " --> pdb=" O ILE H 345 " (cutoff:3.500A) Processing helix chain 'H' and resid 351 through 364 removed outlier: 3.610A pdb=" N GLN H 364 " --> pdb=" O VAL H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 382 No H-bonds generated for 'chain 'H' and resid 380 through 382' Processing helix chain 'H' and resid 383 through 404 removed outlier: 3.519A pdb=" N GLN H 389 " --> pdb=" O PRO H 385 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG H 399 " --> pdb=" O ALA H 395 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS H 400 " --> pdb=" O LYS H 396 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N MET H 402 " --> pdb=" O CYS H 398 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP H 404 " --> pdb=" O LYS H 400 " (cutoff:3.500A) Processing helix chain 'H' and resid 461 through 472 Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.354A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.567A pdb=" N PHE I 43 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 53 " --> pdb=" O LYS I 49 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU I 54 " --> pdb=" O LEU I 50 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE I 55 " --> pdb=" O ILE I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 71 Processing helix chain 'I' and resid 88 through 103 Processing helix chain 'I' and resid 111 through 116 Processing helix chain 'I' and resid 117 through 125 removed outlier: 3.782A pdb=" N ALA I 121 " --> pdb=" O GLY I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 168 removed outlier: 3.772A pdb=" N LYS I 168 " --> pdb=" O HIS I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 185 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 251 through 257 Processing helix chain 'I' and resid 335 through 342 removed outlier: 3.525A pdb=" N MET I 342 " --> pdb=" O ILE I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 351 through 363 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 403 removed outlier: 3.579A pdb=" N SER I 392 " --> pdb=" O ALA I 388 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET I 402 " --> pdb=" O CYS I 398 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU I 403 " --> pdb=" O ARG I 399 " (cutoff:3.500A) Processing helix chain 'I' and resid 461 through 472 Processing helix chain 'J' and resid 13 through 22 removed outlier: 4.312A pdb=" N ALA J 17 " --> pdb=" O ALA J 13 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 55 removed outlier: 3.604A pdb=" N SER J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE J 55 " --> pdb=" O ILE J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.810A pdb=" N MET J 72 " --> pdb=" O ALA J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 87 through 102 removed outlier: 4.630A pdb=" N GLU J 91 " --> pdb=" O ALA J 87 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 157 through 167 Processing helix chain 'J' and resid 180 through 185 removed outlier: 3.606A pdb=" N MET J 184 " --> pdb=" O THR J 180 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR J 185 " --> pdb=" O THR J 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 180 through 185' Processing helix chain 'J' and resid 193 through 195 No H-bonds generated for 'chain 'J' and resid 193 through 195' Processing helix chain 'J' and resid 203 through 205 No H-bonds generated for 'chain 'J' and resid 203 through 205' Processing helix chain 'J' and resid 252 through 257 Processing helix chain 'J' and resid 335 through 341 Processing helix chain 'J' and resid 351 through 362 Processing helix chain 'J' and resid 380 through 382 No H-bonds generated for 'chain 'J' and resid 380 through 382' Processing helix chain 'J' and resid 383 through 401 removed outlier: 3.539A pdb=" N GLN J 389 " --> pdb=" O PRO J 385 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS J 400 " --> pdb=" O LYS J 396 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASP J 401 " --> pdb=" O GLU J 397 " (cutoff:3.500A) Processing helix chain 'J' and resid 461 through 473 Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.204A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.617A pdb=" N PHE K 43 " --> pdb=" O ASN K 39 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLU K 54 " --> pdb=" O LEU K 50 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE K 55 " --> pdb=" O ILE K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 3.765A pdb=" N MET K 72 " --> pdb=" O ALA K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 88 through 103 Processing helix chain 'K' and resid 111 through 125 removed outlier: 3.976A pdb=" N LYS K 115 " --> pdb=" O ASN K 111 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL K 122 " --> pdb=" O ASP K 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 180 through 185 removed outlier: 3.532A pdb=" N MET K 184 " --> pdb=" O THR K 180 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TYR K 185 " --> pdb=" O THR K 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 180 through 185' Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 251 through 257 Processing helix chain 'K' and resid 335 through 342 removed outlier: 3.520A pdb=" N MET K 342 " --> pdb=" O ILE K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 343 through 348 removed outlier: 3.742A pdb=" N LEU K 346 " --> pdb=" O THR K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 351 through 364 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 403 removed outlier: 3.566A pdb=" N ARG K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS K 400 " --> pdb=" O LYS K 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU K 403 " --> pdb=" O ARG K 399 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 473 Processing helix chain 'L' and resid 13 through 22 removed outlier: 4.473A pdb=" N ALA L 17 " --> pdb=" O ALA L 13 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 53 removed outlier: 3.538A pdb=" N SER L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS L 49 " --> pdb=" O HIS L 45 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 103 Processing helix chain 'L' and resid 111 through 125 Processing helix chain 'L' and resid 157 through 167 Processing helix chain 'L' and resid 181 through 185 Processing helix chain 'L' and resid 193 through 195 No H-bonds generated for 'chain 'L' and resid 193 through 195' Processing helix chain 'L' and resid 203 through 205 No H-bonds generated for 'chain 'L' and resid 203 through 205' Processing helix chain 'L' and resid 252 through 257 Processing helix chain 'L' and resid 335 through 342 removed outlier: 3.507A pdb=" N MET L 342 " --> pdb=" O ILE L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 343 through 348 removed outlier: 3.717A pdb=" N LEU L 346 " --> pdb=" O THR L 343 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA L 347 " --> pdb=" O GLY L 344 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N THR L 348 " --> pdb=" O ILE L 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 343 through 348' Processing helix chain 'L' and resid 351 through 362 Processing helix chain 'L' and resid 380 through 382 No H-bonds generated for 'chain 'L' and resid 380 through 382' Processing helix chain 'L' and resid 383 through 402 removed outlier: 3.540A pdb=" N LYS L 400 " --> pdb=" O LYS L 396 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP L 401 " --> pdb=" O GLU L 397 " (cutoff:3.500A) Processing helix chain 'L' and resid 461 through 474 removed outlier: 3.861A pdb=" N LYS L 474 " --> pdb=" O TRP L 470 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 55 removed outlier: 3.556A pdb=" N GLU X 54 " --> pdb=" O LYS X 50 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER X 55 " --> pdb=" O ARG X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 84 removed outlier: 4.149A pdb=" N SER X 62 " --> pdb=" O THR X 58 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N TYR X 64 " --> pdb=" O ASN X 60 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU X 82 " --> pdb=" O HIS X 78 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY X 83 " --> pdb=" O ARG X 79 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N CYS X 84 " --> pdb=" O LEU X 80 " (cutoff:3.500A) Processing helix chain 'X' and resid 117 through 133 removed outlier: 3.635A pdb=" N ALA X 121 " --> pdb=" O ASN X 117 " (cutoff:3.500A) Processing helix chain 'X' and resid 135 through 139 removed outlier: 3.735A pdb=" N TYR X 139 " --> pdb=" O VAL X 136 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 153 removed outlier: 3.629A pdb=" N ASP X 153 " --> pdb=" O LEU X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 165 through 169 Processing helix chain 'X' and resid 194 through 202 Processing helix chain 'X' and resid 214 through 232 Processing helix chain 'X' and resid 237 through 244 removed outlier: 3.593A pdb=" N SER X 243 " --> pdb=" O ARG X 239 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER X 244 " --> pdb=" O GLU X 240 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 259 removed outlier: 3.525A pdb=" N LYS X 259 " --> pdb=" O THR X 255 " (cutoff:3.500A) Processing helix chain 'X' and resid 261 through 270 Processing helix chain 'X' and resid 277 through 281 Processing helix chain 'X' and resid 318 through 323 removed outlier: 3.934A pdb=" N LEU X 323 " --> pdb=" O ALA X 319 " (cutoff:3.500A) Processing helix chain 'X' and resid 326 through 338 removed outlier: 3.515A pdb=" N VAL X 337 " --> pdb=" O ARG X 333 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU X 338 " --> pdb=" O LEU X 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 349 through 357 removed outlier: 3.540A pdb=" N ILE X 357 " --> pdb=" O PHE X 353 " (cutoff:3.500A) Processing helix chain 'X' and resid 381 through 395 removed outlier: 3.523A pdb=" N LEU X 385 " --> pdb=" O ASP X 381 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N ALA X 387 " --> pdb=" O LEU X 383 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLY X 395 " --> pdb=" O LEU X 391 " (cutoff:3.500A) Processing helix chain 'X' and resid 397 through 406 removed outlier: 3.572A pdb=" N ASP X 402 " --> pdb=" O GLN X 398 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU X 403 " --> pdb=" O PRO X 399 " (cutoff:3.500A) Processing helix chain 'X' and resid 407 through 409 No H-bonds generated for 'chain 'X' and resid 407 through 409' Processing helix chain 'X' and resid 435 through 452 Processing helix chain 'X' and resid 453 through 455 No H-bonds generated for 'chain 'X' and resid 453 through 455' Processing helix chain 'X' and resid 476 through 484 removed outlier: 3.806A pdb=" N ALA X 480 " --> pdb=" O ASP X 476 " (cutoff:3.500A) Processing helix chain 'X' and resid 524 through 532 removed outlier: 3.605A pdb=" N ARG X 528 " --> pdb=" O ASP X 524 " (cutoff:3.500A) Processing helix chain 'X' and resid 544 through 558 removed outlier: 3.618A pdb=" N ARG X 548 " --> pdb=" O GLU X 544 " (cutoff:3.500A) Processing helix chain 'X' and resid 562 through 575 Processing helix chain 'X' and resid 579 through 590 Processing helix chain 'X' and resid 591 through 592 No H-bonds generated for 'chain 'X' and resid 591 through 592' Processing helix chain 'X' and resid 593 through 600 removed outlier: 3.703A pdb=" N LYS X 598 " --> pdb=" O ASN X 595 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU X 599 " --> pdb=" O PHE X 596 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG X 600 " --> pdb=" O LYS X 597 " (cutoff:3.500A) Processing helix chain 'Y' and resid 5 through 9 removed outlier: 4.196A pdb=" N GLY Y 8 " --> pdb=" O THR Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 34 removed outlier: 3.533A pdb=" N VAL Y 32 " --> pdb=" O SER Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 40 removed outlier: 3.526A pdb=" N SER Y 39 " --> pdb=" O GLN Y 36 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N LEU Y 40 " --> pdb=" O LYS Y 37 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 49 Processing helix chain 'Y' and resid 78 through 109 removed outlier: 3.631A pdb=" N GLN Y 83 " --> pdb=" O PRO Y 79 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER Y 84 " --> pdb=" O GLU Y 80 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL Y 92 " --> pdb=" O SER Y 88 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU Y 97 " --> pdb=" O TYR Y 93 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE Y 98 " --> pdb=" O ASN Y 94 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL Y 99 " --> pdb=" O GLU Y 95 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 120 Processing helix chain 'Y' and resid 162 through 172 removed outlier: 3.607A pdb=" N ALA Y 165 " --> pdb=" O HIS Y 162 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N TYR Y 166 " --> pdb=" O GLU Y 163 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLU Y 167 " --> pdb=" O PHE Y 164 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU Y 169 " --> pdb=" O TYR Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 198 removed outlier: 3.692A pdb=" N ILE Y 196 " --> pdb=" O LYS Y 192 " (cutoff:3.500A) Processing helix chain 'Y' and resid 210 through 225 removed outlier: 3.659A pdb=" N ILE Y 217 " --> pdb=" O ASN Y 213 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N THR Y 218 " --> pdb=" O CYS Y 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 233 through 240 Processing helix chain 'Y' and resid 258 through 270 removed outlier: 3.551A pdb=" N VAL Y 269 " --> pdb=" O LEU Y 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 315 through 319 Processing helix chain 'Y' and resid 320 through 325 Processing helix chain 'Y' and resid 360 through 362 No H-bonds generated for 'chain 'Y' and resid 360 through 362' Processing helix chain 'Y' and resid 363 through 371 removed outlier: 3.907A pdb=" N GLN Y 368 " --> pdb=" O VAL Y 364 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE Y 369 " --> pdb=" O LYS Y 365 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP Y 370 " --> pdb=" O GLN Y 366 " (cutoff:3.500A) Processing helix chain 'Y' and resid 409 through 413 removed outlier: 3.733A pdb=" N VAL Y 412 " --> pdb=" O HIS Y 409 " (cutoff:3.500A) Processing helix chain 'Y' and resid 432 through 436 removed outlier: 3.675A pdb=" N LEU Y 435 " --> pdb=" O ILE Y 432 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLN Y 436 " --> pdb=" O LYS Y 433 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 432 through 436' Processing helix chain 'Y' and resid 452 through 460 removed outlier: 3.883A pdb=" N MET Y 458 " --> pdb=" O HIS Y 454 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 5.999A pdb=" N VAL A 4 " --> pdb=" O GLU A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.234A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE A 64 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 5.403A pdb=" N GLN A 151 " --> pdb=" O ILE A 64 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLY A 177 " --> pdb=" O VAL A 286 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N PHE A 447 " --> pdb=" O VAL A 263 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N HIS A 265 " --> pdb=" O PHE A 447 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 192 removed outlier: 3.523A pdb=" N TRP A 199 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 308 removed outlier: 3.786A pdb=" N THR A 437 " --> pdb=" O HIS A 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 324 through 333 Processing sheet with id=AA6, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.619A pdb=" N THR A 376 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 365 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N CYS X 414 " --> pdb=" O PHE X 286 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 removed outlier: 6.299A pdb=" N VAL B 4 " --> pdb=" O GLU B 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 133 through 134 removed outlier: 6.703A pdb=" N ILE B 61 " --> pdb=" O HIS B 79 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N VAL B 81 " --> pdb=" O ILE B 61 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP B 63 " --> pdb=" O VAL B 81 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY B 177 " --> pdb=" O VAL B 286 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N VAL B 280 " --> pdb=" O VAL B 287 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG B 289 " --> pdb=" O THR B 278 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N THR B 278 " --> pdb=" O ARG B 289 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N THR B 291 " --> pdb=" O CYS B 276 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N CYS B 276 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 7.492A pdb=" N SER B 293 " --> pdb=" O CYS B 274 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N CYS B 274 " --> pdb=" O SER B 293 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE B 264 " --> pdb=" O CYS B 274 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 246 through 250 removed outlier: 6.808A pdb=" N ALA B 189 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 9.171A pdb=" N TYR B 333 " --> pdb=" O ALA B 189 " (cutoff:3.500A) removed outlier: 8.374A pdb=" N ALA B 191 " --> pdb=" O TYR B 333 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 303 through 308 removed outlier: 3.894A pdb=" N THR B 437 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 365 through 368 Processing sheet with id=AB3, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.046A pdb=" N VAL C 4 " --> pdb=" O GLU C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 133 through 134 removed outlier: 6.543A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL C 147 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE C 64 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N GLN C 151 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY C 177 " --> pdb=" O VAL C 286 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 264 " --> pdb=" O CYS C 274 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N PHE C 447 " --> pdb=" O VAL C 263 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS C 265 " --> pdb=" O PHE C 447 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 246 through 251 removed outlier: 6.864A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.571A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 303 through 308 removed outlier: 4.053A pdb=" N THR C 437 " --> pdb=" O HIS C 308 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 6 removed outlier: 6.217A pdb=" N VAL D 4 " --> pdb=" O GLU D 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.429A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 147 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 177 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N VAL D 280 " --> pdb=" O VAL D 287 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ARG D 289 " --> pdb=" O THR D 278 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N THR D 278 " --> pdb=" O ARG D 289 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 133 through 134 removed outlier: 8.429A pdb=" N CYS D 134 " --> pdb=" O TYR D 78 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N CYS D 80 " --> pdb=" O CYS D 134 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL D 147 " --> pdb=" O THR D 60 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 177 " --> pdb=" O VAL D 286 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N THR D 291 " --> pdb=" O ARG D 275 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE D 264 " --> pdb=" O CYS D 274 " (cutoff:3.500A) removed outlier: 8.927A pdb=" N PHE D 447 " --> pdb=" O VAL D 263 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N HIS D 265 " --> pdb=" O PHE D 447 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 246 through 251 removed outlier: 6.789A pdb=" N ALA D 189 " --> pdb=" O CYS D 331 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N TYR D 333 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 8.424A pdb=" N ALA D 191 " --> pdb=" O TYR D 333 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 303 through 308 removed outlier: 3.915A pdb=" N THR D 437 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 365 through 369 Processing sheet with id=AC4, first strand: chain 'E' and resid 3 through 6 Processing sheet with id=AC5, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.488A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 177 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.488A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY E 177 " --> pdb=" O VAL E 286 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N THR E 291 " --> pdb=" O ARG E 275 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS E 274 " --> pdb=" O PHE E 264 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE E 264 " --> pdb=" O CYS E 274 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE E 447 " --> pdb=" O HIS E 265 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 246 through 251 removed outlier: 6.851A pdb=" N ALA E 189 " --> pdb=" O CYS E 331 " (cutoff:3.500A) removed outlier: 9.257A pdb=" N TYR E 333 " --> pdb=" O ALA E 189 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N ALA E 191 " --> pdb=" O TYR E 333 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 303 through 308 removed outlier: 3.877A pdb=" N THR E 437 " --> pdb=" O HIS E 308 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 366 through 368 Processing sheet with id=AD1, first strand: chain 'F' and resid 4 through 6 removed outlier: 6.052A pdb=" N VAL F 4 " --> pdb=" O GLU F 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'F' and resid 133 through 134 removed outlier: 7.961A pdb=" N CYS F 134 " --> pdb=" O TYR F 78 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N CYS F 80 " --> pdb=" O CYS F 134 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 64 " --> pdb=" O ILE F 149 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLN F 151 " --> pdb=" O ILE F 64 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLY F 177 " --> pdb=" O VAL F 286 " (cutoff:3.500A) removed outlier: 6.887A pdb=" N TYR F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER F 281 " --> pdb=" O TYR F 285 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N VAL F 287 " --> pdb=" O VAL F 279 " (cutoff:3.500A) removed outlier: 8.836A pdb=" N PHE F 447 " --> pdb=" O VAL F 263 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N HIS F 265 " --> pdb=" O PHE F 447 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 189 through 192 removed outlier: 3.604A pdb=" N TRP F 199 " --> pdb=" O GLY F 190 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 303 through 308 removed outlier: 3.950A pdb=" N THR F 437 " --> pdb=" O HIS F 308 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 324 through 334 Processing sheet with id=AD6, first strand: chain 'G' and resid 4 through 6 removed outlier: 6.137A pdb=" N VAL G 4 " --> pdb=" O GLU G 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.177A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE G 64 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLN G 151 " --> pdb=" O ILE G 64 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY G 177 " --> pdb=" O VAL G 286 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N TYR G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N SER G 281 " --> pdb=" O TYR G 285 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N VAL G 287 " --> pdb=" O VAL G 279 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR G 291 " --> pdb=" O ARG G 275 " (cutoff:3.500A) removed outlier: 9.051A pdb=" N PHE G 447 " --> pdb=" O VAL G 263 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N HIS G 265 " --> pdb=" O PHE G 447 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 246 through 251 removed outlier: 6.808A pdb=" N ALA G 189 " --> pdb=" O CYS G 331 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N TYR G 333 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N ALA G 191 " --> pdb=" O TYR G 333 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'G' and resid 303 through 308 removed outlier: 3.875A pdb=" N THR G 437 " --> pdb=" O HIS G 308 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AE2, first strand: chain 'H' and resid 78 through 81 removed outlier: 6.621A pdb=" N ILE H 61 " --> pdb=" O HIS H 79 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N VAL H 81 " --> pdb=" O ILE H 61 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP H 63 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ILE H 64 " --> pdb=" O ILE H 149 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N GLN H 151 " --> pdb=" O ILE H 64 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N TYR H 285 " --> pdb=" O SER H 281 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N SER H 281 " --> pdb=" O TYR H 285 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL H 287 " --> pdb=" O VAL H 279 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR H 291 " --> pdb=" O ARG H 275 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N CYS H 274 " --> pdb=" O PHE H 264 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N PHE H 447 " --> pdb=" O VAL H 263 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N HIS H 265 " --> pdb=" O PHE H 447 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 246 through 250 removed outlier: 6.734A pdb=" N ALA H 189 " --> pdb=" O CYS H 331 " (cutoff:3.500A) removed outlier: 9.098A pdb=" N TYR H 333 " --> pdb=" O ALA H 189 " (cutoff:3.500A) removed outlier: 8.292A pdb=" N ALA H 191 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 303 through 308 removed outlier: 3.853A pdb=" N THR H 437 " --> pdb=" O HIS H 308 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.063A pdb=" N VAL I 4 " --> pdb=" O GLU I 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'I' and resid 133 through 134 removed outlier: 3.713A pdb=" N VAL I 147 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE I 64 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 5.142A pdb=" N GLN I 151 " --> pdb=" O ILE I 64 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY I 177 " --> pdb=" O VAL I 286 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N PHE I 264 " --> pdb=" O CYS I 274 " (cutoff:3.500A) removed outlier: 8.881A pdb=" N PHE I 447 " --> pdb=" O VAL I 263 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N HIS I 265 " --> pdb=" O PHE I 447 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'I' and resid 246 through 250 removed outlier: 6.819A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.176A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'I' and resid 303 through 308 removed outlier: 3.864A pdb=" N THR I 437 " --> pdb=" O HIS I 308 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'I' and resid 364 through 365 removed outlier: 4.364A pdb=" N THR I 376 " --> pdb=" O ARG I 365 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'J' and resid 4 through 6 removed outlier: 6.368A pdb=" N VAL J 4 " --> pdb=" O GLU J 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'J' and resid 133 through 134 removed outlier: 6.366A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J 147 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY J 177 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TYR J 285 " --> pdb=" O SER J 281 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER J 281 " --> pdb=" O TYR J 285 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL J 287 " --> pdb=" O VAL J 279 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'J' and resid 133 through 134 removed outlier: 6.366A pdb=" N ILE J 61 " --> pdb=" O HIS J 79 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N VAL J 81 " --> pdb=" O ILE J 61 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASP J 63 " --> pdb=" O VAL J 81 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N VAL J 147 " --> pdb=" O THR J 60 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLY J 177 " --> pdb=" O VAL J 286 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N THR J 291 " --> pdb=" O ARG J 275 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE J 264 " --> pdb=" O CYS J 274 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N PHE J 447 " --> pdb=" O VAL J 263 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N HIS J 265 " --> pdb=" O PHE J 447 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'J' and resid 246 through 251 removed outlier: 3.523A pdb=" N ALA J 191 " --> pdb=" O CYS J 331 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N TYR J 333 " --> pdb=" O ALA J 191 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'J' and resid 303 through 308 removed outlier: 3.895A pdb=" N THR J 437 " --> pdb=" O HIS J 308 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.291A pdb=" N VAL K 4 " --> pdb=" O GLU K 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF6 Processing sheet with id=AF7, first strand: chain 'K' and resid 61 through 64 removed outlier: 7.039A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'K' and resid 147 through 151 removed outlier: 3.659A pdb=" N GLY K 177 " --> pdb=" O VAL K 286 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N CYS K 274 " --> pdb=" O PHE K 264 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE K 264 " --> pdb=" O CYS K 274 " (cutoff:3.500A) removed outlier: 8.915A pdb=" N PHE K 447 " --> pdb=" O VAL K 263 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N HIS K 265 " --> pdb=" O PHE K 447 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'K' and resid 246 through 250 removed outlier: 6.850A pdb=" N ALA K 189 " --> pdb=" O CYS K 331 " (cutoff:3.500A) removed outlier: 9.195A pdb=" N TYR K 333 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 8.413A pdb=" N ALA K 191 " --> pdb=" O TYR K 333 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'K' and resid 303 through 308 removed outlier: 3.860A pdb=" N THR K 437 " --> pdb=" O HIS K 308 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'K' and resid 365 through 368 removed outlier: 4.070A pdb=" N ILE K 366 " --> pdb=" O GLN K 373 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'L' and resid 4 through 6 removed outlier: 6.258A pdb=" N VAL L 4 " --> pdb=" O GLU L 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'L' and resid 77 through 81 removed outlier: 4.047A pdb=" N VAL L 147 " --> pdb=" O THR L 60 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLN L 151 " --> pdb=" O ILE L 64 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY L 177 " --> pdb=" O VAL L 286 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N TYR L 285 " --> pdb=" O SER L 281 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N SER L 281 " --> pdb=" O TYR L 285 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL L 287 " --> pdb=" O VAL L 279 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N THR L 291 " --> pdb=" O ARG L 275 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 189 through 192 Processing sheet with id=AG6, first strand: chain 'L' and resid 303 through 308 removed outlier: 3.721A pdb=" N THR L 437 " --> pdb=" O HIS L 308 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'L' and resid 324 through 334 Processing sheet with id=AG8, first strand: chain 'L' and resid 371 through 374 removed outlier: 6.208A pdb=" N ILE L 366 " --> pdb=" O GLN L 373 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER X 157 " --> pdb=" O VAL L 367 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'X' and resid 19 through 20 removed outlier: 3.569A pdb=" N ILE X 26 " --> pdb=" O THR X 101 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'X' and resid 176 through 179 Processing sheet with id=AH2, first strand: chain 'X' and resid 342 through 344 Processing sheet with id=AH3, first strand: chain 'X' and resid 508 through 512 Processing sheet with id=AH4, first strand: chain 'Y' and resid 3 through 4 removed outlier: 3.652A pdb=" N GLU Y 4 " --> pdb=" O LYS Y 11 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'Y' and resid 20 through 21 Processing sheet with id=AH6, first strand: chain 'Y' and resid 122 through 123 Processing sheet with id=AH7, first strand: chain 'Y' and resid 133 through 134 Processing sheet with id=AH8, first strand: chain 'Y' and resid 181 through 182 Processing sheet with id=AH9, first strand: chain 'Y' and resid 389 through 390 2063 hydrogen bonds defined for protein. 5778 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.86 Time building geometry restraints manager: 11.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 8574 1.31 - 1.44: 14247 1.44 - 1.56: 30725 1.56 - 1.69: 157 1.69 - 1.82: 593 Bond restraints: 54296 Sorted by residual: bond pdb=" C1' ATP B1003 " pdb=" C2' ATP B1003 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.70e+02 bond pdb=" C1' ATP H1002 " pdb=" C2' ATP H1002 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.69e+02 bond pdb=" C1' ATP F1003 " pdb=" C2' ATP F1003 " ideal model delta sigma weight residual 1.531 1.300 0.231 1.20e-02 6.94e+03 3.69e+02 bond pdb=" C1' ATP G1002 " pdb=" C2' ATP G1002 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.68e+02 bond pdb=" C1' ATP I1002 " pdb=" C2' ATP I1002 " ideal model delta sigma weight residual 1.531 1.301 0.230 1.20e-02 6.94e+03 3.68e+02 ... (remaining 54291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 73272 3.23 - 6.47: 449 6.47 - 9.70: 103 9.70 - 12.94: 18 12.94 - 16.17: 16 Bond angle restraints: 73858 Sorted by residual: angle pdb=" PB ATP L1002 " pdb=" O3B ATP L1002 " pdb=" PG ATP L1002 " ideal model delta sigma weight residual 139.87 123.70 16.17 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP F1003 " pdb=" O3B ATP F1003 " pdb=" PG ATP F1003 " ideal model delta sigma weight residual 139.87 123.73 16.14 1.00e+00 1.00e+00 2.61e+02 angle pdb=" PB ATP B1003 " pdb=" O3B ATP B1003 " pdb=" PG ATP B1003 " ideal model delta sigma weight residual 139.87 123.76 16.11 1.00e+00 1.00e+00 2.60e+02 angle pdb=" PB ATP D1003 " pdb=" O3B ATP D1003 " pdb=" PG ATP D1003 " ideal model delta sigma weight residual 139.87 123.77 16.10 1.00e+00 1.00e+00 2.59e+02 angle pdb=" PB ATP C1003 " pdb=" O3B ATP C1003 " pdb=" PG ATP C1003 " ideal model delta sigma weight residual 139.87 123.78 16.09 1.00e+00 1.00e+00 2.59e+02 ... (remaining 73853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.54: 32451 35.54 - 71.08: 591 71.08 - 106.62: 54 106.62 - 142.16: 17 142.16 - 177.70: 23 Dihedral angle restraints: 33136 sinusoidal: 13436 harmonic: 19700 Sorted by residual: dihedral pdb=" C8 GTP F1002 " pdb=" C1' GTP F1002 " pdb=" N9 GTP F1002 " pdb=" O4' GTP F1002 " ideal model delta sinusoidal sigma weight residual 104.59 -73.11 177.70 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2G GTP E1002 " pdb=" O3B GTP E1002 " pdb=" PG GTP E1002 " pdb=" PB GTP E1002 " ideal model delta sinusoidal sigma weight residual 177.30 -5.49 -177.21 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C8 GTP D1002 " pdb=" C1' GTP D1002 " pdb=" N9 GTP D1002 " pdb=" O4' GTP D1002 " ideal model delta sinusoidal sigma weight residual 104.59 -71.13 175.72 1 2.00e+01 2.50e-03 4.79e+01 ... (remaining 33133 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 7372 0.065 - 0.130: 969 0.130 - 0.195: 12 0.195 - 0.260: 1 0.260 - 0.325: 12 Chirality restraints: 8366 Sorted by residual: chirality pdb=" C2' ATP D1003 " pdb=" C1' ATP D1003 " pdb=" C3' ATP D1003 " pdb=" O2' ATP D1003 " both_signs ideal model delta sigma weight residual False -2.68 -2.35 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" C2' ATP E1003 " pdb=" C1' ATP E1003 " pdb=" C3' ATP E1003 " pdb=" O2' ATP E1003 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C2' ATP A1002 " pdb=" C1' ATP A1002 " pdb=" C3' ATP A1002 " pdb=" O2' ATP A1002 " both_signs ideal model delta sigma weight residual False -2.68 -2.37 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 8363 not shown) Planarity restraints: 9280 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP D 2 " 0.050 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO D 3 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO D 3 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO D 3 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 125 " -0.048 5.00e-02 4.00e+02 7.32e-02 8.56e+00 pdb=" N PRO B 126 " 0.127 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP Y 351 " 0.039 5.00e-02 4.00e+02 5.92e-02 5.61e+00 pdb=" N PRO Y 352 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO Y 352 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO Y 352 " 0.033 5.00e-02 4.00e+02 ... (remaining 9277 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 589 2.67 - 3.23: 45383 3.23 - 3.79: 71552 3.79 - 4.34: 99969 4.34 - 4.90: 170751 Nonbonded interactions: 388244 Sorted by model distance: nonbonded pdb=" OE2 GLU F 129 " pdb="ZN ZN F1001 " model vdw 2.113 2.230 nonbonded pdb=" OE2 GLU B 412 " pdb=" OG1 THR B 414 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR B 130 " pdb=" O PHE B 133 " model vdw 2.178 3.040 nonbonded pdb=" OG1 THR J 130 " pdb=" O PHE J 133 " model vdw 2.186 3.040 nonbonded pdb=" OE2 GLU X 567 " pdb=" OG1 THR X 580 " model vdw 2.213 3.040 ... (remaining 388239 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 235 or resid 237 through 268 or (resid 269 and ( \ name N or name CA or name C or name O or name CB )) or resid 270 through 373 or \ (resid 374 and (name N or name CA or name C or name O or name CB )) or resid 375 \ through 414 or resid 422 through 472 or resid 1001)) selection = (chain 'B' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'C' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'D' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'E' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'F' and (resid 3 through 235 or resid 237 through 472 or resid 1001)) selection = (chain 'G' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'H' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 472 or \ resid 1001)) selection = (chain 'I' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 472 or \ resid 1001)) selection = (chain 'J' and (resid 3 through 235 or resid 237 through 414 or resid 422 throug \ h 472 or resid 1001)) selection = (chain 'K' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) selection = (chain 'L' and (resid 3 through 235 or resid 237 through 373 or (resid 374 and ( \ name N or name CA or name C or name O or name CB )) or resid 375 through 414 or \ resid 422 through 472 or resid 1001)) } 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=0.24 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.650 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: 0.040 Extract box with map and model: 1.540 Check model and map are aligned: 0.280 Set scattering table: 0.360 Process input model: 115.810 Find NCS groups from input model: 2.450 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 134.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 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 : 0.010 0.231 54296 Z= 0.633 Angle : 0.719 16.171 73858 Z= 0.464 Chirality : 0.043 0.325 8366 Planarity : 0.005 0.075 9280 Dihedral : 15.465 177.702 20394 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.15 % Rotamer: Outliers : 0.04 % Allowed : 0.09 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.10), residues: 6688 helix: 1.09 (0.12), residues: 1926 sheet: 0.84 (0.15), residues: 1225 loop : -1.84 (0.09), residues: 3537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 423 HIS 0.004 0.000 HIS Y 130 PHE 0.015 0.001 PHE X 433 TYR 0.020 0.001 TYR Y 336 ARG 0.004 0.000 ARG X 568 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 524 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 522 time to evaluate : 4.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 TYR cc_start: 0.9082 (m-80) cc_final: 0.8796 (m-80) REVERT: D 448 ASP cc_start: 0.8973 (t70) cc_final: 0.8737 (t0) REVERT: E 354 ASP cc_start: 0.8639 (m-30) cc_final: 0.8361 (m-30) REVERT: F 26 GLU cc_start: 0.7522 (pm20) cc_final: 0.7305 (pm20) REVERT: G 28 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8446 (mt-10) REVERT: G 423 PHE cc_start: 0.8654 (p90) cc_final: 0.8362 (p90) REVERT: H 88 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8374 (mt-10) REVERT: H 221 ARG cc_start: 0.8199 (tmm160) cc_final: 0.7710 (tmm160) REVERT: H 383 MET cc_start: 0.8853 (mmm) cc_final: 0.8626 (mmt) REVERT: H 423 PHE cc_start: 0.8624 (p90) cc_final: 0.8293 (p90) REVERT: I 11 ASP cc_start: 0.8321 (p0) cc_final: 0.8017 (p0) REVERT: I 277 ASP cc_start: 0.8203 (m-30) cc_final: 0.7886 (m-30) REVERT: I 364 GLN cc_start: 0.8088 (pp30) cc_final: 0.7855 (pp30) REVERT: I 404 ASP cc_start: 0.7975 (t0) cc_final: 0.7506 (t0) REVERT: J 11 ASP cc_start: 0.7968 (t70) cc_final: 0.7490 (t0) REVERT: J 277 ASP cc_start: 0.8237 (m-30) cc_final: 0.7987 (m-30) REVERT: L 11 ASP cc_start: 0.9179 (m-30) cc_final: 0.8967 (m-30) REVERT: L 404 ASP cc_start: 0.8472 (t70) cc_final: 0.8013 (t0) REVERT: X 280 GLU cc_start: 0.7331 (tp30) cc_final: 0.7066 (tp30) outliers start: 2 outliers final: 0 residues processed: 523 average time/residue: 1.5353 time to fit residues: 983.9077 Evaluate side-chains 397 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 562 optimal weight: 8.9990 chunk 504 optimal weight: 1.9990 chunk 280 optimal weight: 0.4980 chunk 172 optimal weight: 5.9990 chunk 340 optimal weight: 9.9990 chunk 269 optimal weight: 5.9990 chunk 522 optimal weight: 5.9990 chunk 202 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 388 optimal weight: 5.9990 chunk 604 optimal weight: 0.4980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 441 GLN D 381 ASN F 377 ASN G 95 ASN I 441 GLN ** L 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 65 GLN X 439 ASN Y 47 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 54296 Z= 0.278 Angle : 0.665 16.564 73858 Z= 0.339 Chirality : 0.045 0.319 8366 Planarity : 0.005 0.068 9280 Dihedral : 13.307 177.911 7973 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer: Outliers : 0.88 % Allowed : 6.22 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 6688 helix: 1.67 (0.12), residues: 1956 sheet: 0.68 (0.15), residues: 1213 loop : -1.93 (0.09), residues: 3519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 470 HIS 0.005 0.001 HIS F 429 PHE 0.017 0.002 PHE H 264 TYR 0.034 0.002 TYR Y 403 ARG 0.009 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 470 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 420 time to evaluate : 4.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8635 (t0) cc_final: 0.8425 (t0) REVERT: A 84 MET cc_start: 0.9156 (mmp) cc_final: 0.8830 (mmp) REVERT: B 53 GLN cc_start: 0.9189 (OUTLIER) cc_final: 0.8849 (tt0) REVERT: B 285 TYR cc_start: 0.9271 (OUTLIER) cc_final: 0.8309 (m-80) REVERT: C 285 TYR cc_start: 0.9129 (OUTLIER) cc_final: 0.7297 (m-80) REVERT: C 404 ASP cc_start: 0.8699 (t0) cc_final: 0.8453 (t0) REVERT: D 389 GLN cc_start: 0.8197 (tp40) cc_final: 0.7935 (mm-40) REVERT: D 448 ASP cc_start: 0.8957 (t70) cc_final: 0.8734 (t0) REVERT: E 369 ASN cc_start: 0.7521 (t0) cc_final: 0.7211 (t0) REVERT: F 26 GLU cc_start: 0.7408 (pm20) cc_final: 0.7085 (pm20) REVERT: G 28 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8430 (mt-10) REVERT: G 423 PHE cc_start: 0.8763 (p90) cc_final: 0.8493 (p90) REVERT: G 474 LYS cc_start: 0.8543 (mmpt) cc_final: 0.8166 (tmtm) REVERT: H 88 GLU cc_start: 0.8750 (mt-10) cc_final: 0.8491 (mt-10) REVERT: H 221 ARG cc_start: 0.8236 (tmm160) cc_final: 0.7561 (tmm160) REVERT: H 228 MET cc_start: 0.7054 (tpp) cc_final: 0.6631 (tpt) REVERT: H 383 MET cc_start: 0.8681 (mmm) cc_final: 0.8296 (mmt) REVERT: H 423 PHE cc_start: 0.8682 (p90) cc_final: 0.8359 (p90) REVERT: I 232 LYS cc_start: 0.7865 (mmmt) cc_final: 0.6920 (mppt) REVERT: I 364 GLN cc_start: 0.8519 (pp30) cc_final: 0.8305 (pp30) REVERT: J 11 ASP cc_start: 0.7988 (t70) cc_final: 0.7535 (t0) REVERT: J 28 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8798 (mm-30) REVERT: J 228 MET cc_start: 0.6034 (OUTLIER) cc_final: 0.5629 (tpt) REVERT: J 277 ASP cc_start: 0.8205 (m-30) cc_final: 0.7970 (m-30) REVERT: J 285 TYR cc_start: 0.9219 (OUTLIER) cc_final: 0.8903 (m-80) REVERT: J 412 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8292 (mm-30) REVERT: K 232 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8652 (mmmm) REVERT: L 221 ARG cc_start: 0.6817 (OUTLIER) cc_final: 0.6527 (ptm160) REVERT: L 404 ASP cc_start: 0.8621 (t70) cc_final: 0.7926 (t0) REVERT: Y 377 MET cc_start: 0.3232 (OUTLIER) cc_final: 0.2142 (mmm) outliers start: 50 outliers final: 15 residues processed: 447 average time/residue: 1.5006 time to fit residues: 831.2508 Evaluate side-chains 408 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 385 time to evaluate : 4.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain X residue 82 GLU Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 432 MET Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 114 ASN Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 289 MET Chi-restraints excluded: chain Y residue 377 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 336 optimal weight: 0.7980 chunk 187 optimal weight: 8.9990 chunk 503 optimal weight: 5.9990 chunk 411 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 chunk 605 optimal weight: 9.9990 chunk 654 optimal weight: 0.0010 chunk 539 optimal weight: 3.9990 chunk 600 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 486 optimal weight: 0.6980 overall best weight: 1.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN F 377 ASN G 364 GLN L 389 GLN Y 47 GLN Y 104 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54296 Z= 0.186 Angle : 0.600 16.068 73858 Z= 0.299 Chirality : 0.043 0.291 8366 Planarity : 0.005 0.065 9280 Dihedral : 12.600 178.661 7973 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.31 % Favored : 95.63 % Rotamer: Outliers : 0.91 % Allowed : 7.66 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 6688 helix: 1.99 (0.13), residues: 1967 sheet: 0.77 (0.14), residues: 1236 loop : -1.90 (0.10), residues: 3485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 470 HIS 0.004 0.001 HIS H 79 PHE 0.017 0.001 PHE G 264 TYR 0.023 0.001 TYR Y 403 ARG 0.006 0.000 ARG D 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 411 time to evaluate : 4.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8613 (t0) cc_final: 0.8360 (t0) REVERT: A 354 ASP cc_start: 0.8681 (m-30) cc_final: 0.8426 (m-30) REVERT: B 285 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.8127 (m-80) REVERT: C 285 TYR cc_start: 0.9144 (OUTLIER) cc_final: 0.7069 (m-80) REVERT: C 405 GLU cc_start: 0.8851 (tt0) cc_final: 0.8277 (pm20) REVERT: D 389 GLN cc_start: 0.8203 (tp40) cc_final: 0.7942 (mm-40) REVERT: E 349 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8303 (mp0) REVERT: E 369 ASN cc_start: 0.7625 (t0) cc_final: 0.7307 (t0) REVERT: E 470 TRP cc_start: 0.8910 (t-100) cc_final: 0.8620 (t-100) REVERT: G 28 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8431 (mt-10) REVERT: G 423 PHE cc_start: 0.8731 (p90) cc_final: 0.8451 (p90) REVERT: G 474 LYS cc_start: 0.8527 (mmpt) cc_final: 0.8137 (tmtm) REVERT: H 88 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8537 (mt-10) REVERT: H 221 ARG cc_start: 0.8204 (tmm160) cc_final: 0.7543 (tmm160) REVERT: H 228 MET cc_start: 0.7295 (tpp) cc_final: 0.6839 (tpt) REVERT: H 423 PHE cc_start: 0.8715 (p90) cc_final: 0.8419 (p90) REVERT: I 364 GLN cc_start: 0.8507 (pp30) cc_final: 0.8267 (pp30) REVERT: I 404 ASP cc_start: 0.8215 (t0) cc_final: 0.7668 (t0) REVERT: J 11 ASP cc_start: 0.7952 (t70) cc_final: 0.7529 (t0) REVERT: J 28 GLU cc_start: 0.9083 (mm-30) cc_final: 0.8809 (mm-30) REVERT: J 228 MET cc_start: 0.6028 (OUTLIER) cc_final: 0.5616 (tpt) REVERT: J 277 ASP cc_start: 0.8201 (m-30) cc_final: 0.7964 (m-30) REVERT: J 285 TYR cc_start: 0.9261 (OUTLIER) cc_final: 0.8689 (m-80) REVERT: K 232 LYS cc_start: 0.8982 (OUTLIER) cc_final: 0.8623 (mmmm) REVERT: K 424 LYS cc_start: 0.9057 (mtpp) cc_final: 0.8222 (tptt) REVERT: L 404 ASP cc_start: 0.8399 (t70) cc_final: 0.7767 (t0) REVERT: X 212 MET cc_start: 0.3235 (mmt) cc_final: 0.2560 (mpp) REVERT: Y 137 ASP cc_start: 0.5625 (p0) cc_final: 0.5406 (OUTLIER) REVERT: Y 338 LYS cc_start: 0.2508 (OUTLIER) cc_final: 0.1113 (mptt) REVERT: Y 377 MET cc_start: 0.3291 (OUTLIER) cc_final: 0.2314 (mmm) outliers start: 52 outliers final: 12 residues processed: 439 average time/residue: 1.4707 time to fit residues: 803.5004 Evaluate side-chains 400 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 382 time to evaluate : 4.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 114 ASN Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 598 optimal weight: 7.9990 chunk 455 optimal weight: 0.9990 chunk 314 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 289 optimal weight: 4.9990 chunk 406 optimal weight: 6.9990 chunk 608 optimal weight: 8.9990 chunk 643 optimal weight: 4.9990 chunk 317 optimal weight: 5.9990 chunk 576 optimal weight: 0.6980 chunk 173 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 444 GLN B 375 ASN C 203 GLN F 377 ASN X 471 HIS Y 47 GLN Y 298 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 54296 Z= 0.361 Angle : 0.683 17.476 73858 Z= 0.347 Chirality : 0.047 0.357 8366 Planarity : 0.006 0.065 9280 Dihedral : 12.485 178.899 7973 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.10 % Favored : 93.84 % Rotamer: Outliers : 1.19 % Allowed : 8.73 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.10), residues: 6688 helix: 2.03 (0.13), residues: 1963 sheet: 0.68 (0.15), residues: 1186 loop : -2.05 (0.09), residues: 3539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 470 HIS 0.008 0.001 HIS C 259 PHE 0.017 0.002 PHE F 423 TYR 0.020 0.002 TYR Y 403 ARG 0.006 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 393 time to evaluate : 4.643 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8717 (t0) cc_final: 0.8480 (t0) REVERT: A 84 MET cc_start: 0.9239 (mmp) cc_final: 0.8794 (mmp) REVERT: B 53 GLN cc_start: 0.9224 (OUTLIER) cc_final: 0.8805 (tt0) REVERT: B 285 TYR cc_start: 0.9383 (OUTLIER) cc_final: 0.8615 (m-80) REVERT: C 285 TYR cc_start: 0.9331 (OUTLIER) cc_final: 0.6820 (m-80) REVERT: C 405 GLU cc_start: 0.8838 (tt0) cc_final: 0.8319 (pm20) REVERT: E 349 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8238 (mp0) REVERT: E 369 ASN cc_start: 0.7697 (t0) cc_final: 0.7334 (t0) REVERT: E 441 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8481 (mt0) REVERT: E 470 TRP cc_start: 0.8967 (t-100) cc_final: 0.8656 (t-100) REVERT: G 28 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8249 (mt-10) REVERT: G 423 PHE cc_start: 0.8747 (p90) cc_final: 0.8441 (p90) REVERT: G 474 LYS cc_start: 0.8543 (mmpt) cc_final: 0.8109 (tmtm) REVERT: H 88 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8558 (mt-10) REVERT: H 221 ARG cc_start: 0.8244 (tmm160) cc_final: 0.7522 (tmm160) REVERT: H 228 MET cc_start: 0.7363 (tpp) cc_final: 0.6928 (tpt) REVERT: H 383 MET cc_start: 0.8795 (mmm) cc_final: 0.8238 (mmt) REVERT: H 423 PHE cc_start: 0.8785 (p90) cc_final: 0.8463 (p90) REVERT: I 232 LYS cc_start: 0.8089 (mmmt) cc_final: 0.7027 (mppt) REVERT: I 364 GLN cc_start: 0.8733 (pp30) cc_final: 0.8502 (pp30) REVERT: I 404 ASP cc_start: 0.8247 (t0) cc_final: 0.7703 (t0) REVERT: J 11 ASP cc_start: 0.7963 (t70) cc_final: 0.7509 (t0) REVERT: J 228 MET cc_start: 0.6015 (OUTLIER) cc_final: 0.5612 (tpt) REVERT: J 277 ASP cc_start: 0.8350 (m-30) cc_final: 0.8111 (m-30) REVERT: J 285 TYR cc_start: 0.9343 (OUTLIER) cc_final: 0.9031 (m-80) REVERT: J 412 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8305 (mm-30) REVERT: J 441 GLN cc_start: 0.8711 (OUTLIER) cc_final: 0.7570 (mp10) REVERT: K 232 LYS cc_start: 0.8983 (OUTLIER) cc_final: 0.8602 (mmmm) REVERT: X 212 MET cc_start: 0.3170 (mmt) cc_final: 0.2488 (mpp) REVERT: Y 137 ASP cc_start: 0.5762 (p0) cc_final: 0.5555 (OUTLIER) REVERT: Y 338 LYS cc_start: 0.2476 (OUTLIER) cc_final: 0.1088 (mptt) REVERT: Y 377 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2111 (mmm) outliers start: 68 outliers final: 25 residues processed: 440 average time/residue: 1.4703 time to fit residues: 802.5728 Evaluate side-chains 407 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 373 time to evaluate : 4.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 53 GLN Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 441 GLN Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain X residue 82 GLU Chi-restraints excluded: chain X residue 288 MET Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 114 ASN Chi-restraints excluded: chain Y residue 190 SER Chi-restraints excluded: chain Y residue 289 MET Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain Y residue 448 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 536 optimal weight: 0.7980 chunk 365 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 479 optimal weight: 0.9980 chunk 265 optimal weight: 3.9990 chunk 549 optimal weight: 0.0270 chunk 444 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 328 optimal weight: 7.9990 chunk 577 optimal weight: 7.9990 chunk 162 optimal weight: 3.9990 overall best weight: 0.9640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN F 377 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 54296 Z= 0.176 Angle : 0.602 16.307 73858 Z= 0.299 Chirality : 0.043 0.299 8366 Planarity : 0.005 0.062 9280 Dihedral : 12.103 179.114 7973 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.93 % Allowed : 9.54 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.10), residues: 6688 helix: 2.19 (0.13), residues: 1968 sheet: 0.72 (0.14), residues: 1236 loop : -1.98 (0.10), residues: 3484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP B 470 HIS 0.004 0.001 HIS H 79 PHE 0.018 0.001 PHE G 264 TYR 0.021 0.001 TYR Y 336 ARG 0.012 0.000 ARG E 221 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 387 time to evaluate : 4.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8696 (t0) cc_final: 0.8449 (t0) REVERT: A 354 ASP cc_start: 0.8660 (m-30) cc_final: 0.8423 (m-30) REVERT: B 285 TYR cc_start: 0.9315 (OUTLIER) cc_final: 0.8315 (m-80) REVERT: B 383 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7682 (mmm) REVERT: C 285 TYR cc_start: 0.9221 (OUTLIER) cc_final: 0.6804 (m-80) REVERT: C 405 GLU cc_start: 0.8822 (tt0) cc_final: 0.8325 (pm20) REVERT: D 285 TYR cc_start: 0.8932 (OUTLIER) cc_final: 0.6859 (m-80) REVERT: E 285 TYR cc_start: 0.9319 (OUTLIER) cc_final: 0.8852 (m-80) REVERT: E 349 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8215 (mp0) REVERT: E 353 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 369 ASN cc_start: 0.7693 (t0) cc_final: 0.7320 (t0) REVERT: E 470 TRP cc_start: 0.8955 (t-100) cc_final: 0.8662 (t-100) REVERT: G 28 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8339 (mt-10) REVERT: G 84 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8635 (mpt) REVERT: G 423 PHE cc_start: 0.8779 (p90) cc_final: 0.8444 (p90) REVERT: G 474 LYS cc_start: 0.8530 (mmpt) cc_final: 0.8090 (tmtm) REVERT: H 26 GLU cc_start: 0.7448 (pm20) cc_final: 0.7122 (pm20) REVERT: H 88 GLU cc_start: 0.8773 (mt-10) cc_final: 0.8543 (mt-10) REVERT: H 221 ARG cc_start: 0.8203 (tmm160) cc_final: 0.7521 (tmm160) REVERT: H 228 MET cc_start: 0.7325 (tpp) cc_final: 0.6987 (tpt) REVERT: H 423 PHE cc_start: 0.8781 (p90) cc_final: 0.8444 (p90) REVERT: I 54 GLU cc_start: 0.8869 (pt0) cc_final: 0.8654 (pp20) REVERT: I 364 GLN cc_start: 0.8763 (pp30) cc_final: 0.8501 (pp30) REVERT: I 404 ASP cc_start: 0.8206 (t0) cc_final: 0.7655 (t0) REVERT: J 11 ASP cc_start: 0.7932 (t70) cc_final: 0.7494 (t0) REVERT: J 228 MET cc_start: 0.6053 (OUTLIER) cc_final: 0.5608 (tpt) REVERT: J 285 TYR cc_start: 0.9305 (OUTLIER) cc_final: 0.8612 (m-80) REVERT: J 412 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8280 (mm-30) REVERT: J 470 TRP cc_start: 0.9150 (t60) cc_final: 0.8741 (t-100) REVERT: K 221 ARG cc_start: 0.8025 (mtp-110) cc_final: 0.7797 (mtp-110) REVERT: K 232 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8588 (mmmm) REVERT: L 221 ARG cc_start: 0.7061 (OUTLIER) cc_final: 0.6763 (ptm160) REVERT: X 212 MET cc_start: 0.3108 (mmt) cc_final: 0.2498 (mpp) REVERT: Y 137 ASP cc_start: 0.5682 (p0) cc_final: 0.5459 (OUTLIER) REVERT: Y 338 LYS cc_start: 0.2539 (OUTLIER) cc_final: 0.1120 (mptt) REVERT: Y 377 MET cc_start: 0.3152 (OUTLIER) cc_final: 0.2225 (mmm) outliers start: 53 outliers final: 17 residues processed: 419 average time/residue: 1.4703 time to fit residues: 771.4385 Evaluate side-chains 400 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 371 time to evaluate : 4.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 383 MET Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 289 MET Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 216 optimal weight: 2.9990 chunk 579 optimal weight: 9.9990 chunk 127 optimal weight: 0.2980 chunk 377 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 644 optimal weight: 40.0000 chunk 534 optimal weight: 8.9990 chunk 298 optimal weight: 0.8980 chunk 53 optimal weight: 6.9990 chunk 213 optimal weight: 0.7980 chunk 338 optimal weight: 10.0000 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN C 209 ASN F 377 ASN Y 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 54296 Z= 0.264 Angle : 0.632 16.967 73858 Z= 0.317 Chirality : 0.044 0.332 8366 Planarity : 0.005 0.062 9280 Dihedral : 12.012 179.988 7973 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 1.00 % Allowed : 9.91 % Favored : 89.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 6688 helix: 2.23 (0.13), residues: 1965 sheet: 0.71 (0.15), residues: 1198 loop : -2.02 (0.09), residues: 3525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 470 HIS 0.005 0.001 HIS C 259 PHE 0.017 0.001 PHE E 423 TYR 0.019 0.001 TYR Y 336 ARG 0.005 0.000 ARG A 221 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 384 time to evaluate : 4.560 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8736 (t0) cc_final: 0.8489 (t0) REVERT: A 84 MET cc_start: 0.9204 (mmp) cc_final: 0.8858 (mmp) REVERT: B 285 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8399 (m-80) REVERT: C 285 TYR cc_start: 0.9286 (OUTLIER) cc_final: 0.6764 (m-80) REVERT: C 405 GLU cc_start: 0.8861 (tt0) cc_final: 0.8293 (pm20) REVERT: D 55 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8090 (tt) REVERT: D 285 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.6934 (m-80) REVERT: E 285 TYR cc_start: 0.9373 (OUTLIER) cc_final: 0.8863 (m-80) REVERT: E 349 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8177 (mp0) REVERT: E 353 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: E 369 ASN cc_start: 0.7700 (t0) cc_final: 0.7325 (t0) REVERT: E 470 TRP cc_start: 0.8960 (t-100) cc_final: 0.8672 (t-100) REVERT: F 9 ASP cc_start: 0.8978 (t70) cc_final: 0.8728 (t0) REVERT: G 28 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8300 (mt-10) REVERT: G 84 MET cc_start: 0.9010 (OUTLIER) cc_final: 0.8590 (mpt) REVERT: G 423 PHE cc_start: 0.8797 (p90) cc_final: 0.8496 (p90) REVERT: G 474 LYS cc_start: 0.8539 (mmpt) cc_final: 0.8082 (tmtm) REVERT: H 26 GLU cc_start: 0.7423 (pm20) cc_final: 0.7122 (pm20) REVERT: H 88 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8526 (mt-10) REVERT: H 221 ARG cc_start: 0.8181 (tmm160) cc_final: 0.7529 (tmm160) REVERT: H 228 MET cc_start: 0.7391 (tpp) cc_final: 0.6952 (tpt) REVERT: H 423 PHE cc_start: 0.8782 (p90) cc_final: 0.8441 (p90) REVERT: I 54 GLU cc_start: 0.8889 (pt0) cc_final: 0.8674 (pp20) REVERT: I 232 LYS cc_start: 0.7931 (mmmt) cc_final: 0.6849 (mppt) REVERT: I 364 GLN cc_start: 0.8791 (pp30) cc_final: 0.8530 (pp30) REVERT: I 404 ASP cc_start: 0.8222 (t0) cc_final: 0.7658 (t0) REVERT: J 11 ASP cc_start: 0.7945 (t70) cc_final: 0.7489 (t0) REVERT: J 228 MET cc_start: 0.6110 (OUTLIER) cc_final: 0.5679 (tpt) REVERT: J 285 TYR cc_start: 0.9351 (OUTLIER) cc_final: 0.8902 (m-80) REVERT: J 412 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8465 (mm-30) REVERT: J 441 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: J 470 TRP cc_start: 0.9142 (t60) cc_final: 0.8695 (t-100) REVERT: K 232 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8576 (mmmm) REVERT: X 212 MET cc_start: 0.3110 (mmt) cc_final: 0.2501 (mpp) REVERT: Y 338 LYS cc_start: 0.2532 (OUTLIER) cc_final: 0.1130 (mptt) REVERT: Y 377 MET cc_start: 0.3210 (OUTLIER) cc_final: 0.2237 (mmm) outliers start: 57 outliers final: 21 residues processed: 427 average time/residue: 1.4430 time to fit residues: 767.3929 Evaluate side-chains 409 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 375 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 84 MET Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain X residue 82 GLU Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 137 ASP Chi-restraints excluded: chain Y residue 190 SER Chi-restraints excluded: chain Y residue 289 MET Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 621 optimal weight: 4.9990 chunk 72 optimal weight: 3.9990 chunk 367 optimal weight: 2.9990 chunk 470 optimal weight: 0.9990 chunk 364 optimal weight: 5.9990 chunk 542 optimal weight: 3.9990 chunk 359 optimal weight: 3.9990 chunk 641 optimal weight: 9.9990 chunk 401 optimal weight: 3.9990 chunk 391 optimal weight: 0.9990 chunk 296 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN F 377 ASN G 377 ASN Y 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 54296 Z= 0.325 Angle : 0.661 17.390 73858 Z= 0.333 Chirality : 0.046 0.351 8366 Planarity : 0.005 0.062 9280 Dihedral : 12.014 178.750 7973 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.47 % Favored : 94.47 % Rotamer: Outliers : 1.04 % Allowed : 10.31 % Favored : 88.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 6688 helix: 2.17 (0.13), residues: 1967 sheet: 0.73 (0.15), residues: 1149 loop : -2.08 (0.09), residues: 3572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 470 HIS 0.006 0.001 HIS F 429 PHE 0.019 0.002 PHE E 450 TYR 0.019 0.002 TYR Y 336 ARG 0.012 0.000 ARG K 221 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 374 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8747 (t0) cc_final: 0.8496 (t0) REVERT: B 285 TYR cc_start: 0.9364 (OUTLIER) cc_final: 0.8538 (m-80) REVERT: C 285 TYR cc_start: 0.9281 (OUTLIER) cc_final: 0.6647 (m-80) REVERT: C 405 GLU cc_start: 0.8880 (tt0) cc_final: 0.8242 (pm20) REVERT: D 55 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8132 (tt) REVERT: D 285 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.6943 (m-80) REVERT: E 285 TYR cc_start: 0.9395 (OUTLIER) cc_final: 0.8841 (m-80) REVERT: E 349 GLU cc_start: 0.8401 (mt-10) cc_final: 0.8175 (mp0) REVERT: E 353 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: E 369 ASN cc_start: 0.7647 (t0) cc_final: 0.7273 (t0) REVERT: E 470 TRP cc_start: 0.8977 (t-100) cc_final: 0.8661 (t-100) REVERT: F 9 ASP cc_start: 0.8991 (t70) cc_final: 0.8739 (t0) REVERT: G 423 PHE cc_start: 0.8774 (p90) cc_final: 0.8484 (p90) REVERT: G 474 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8179 (tmtm) REVERT: H 26 GLU cc_start: 0.7511 (pm20) cc_final: 0.7191 (pm20) REVERT: H 88 GLU cc_start: 0.8769 (mt-10) cc_final: 0.8483 (mt-10) REVERT: H 221 ARG cc_start: 0.8192 (tmm160) cc_final: 0.7533 (tmm160) REVERT: H 228 MET cc_start: 0.7373 (tpp) cc_final: 0.6904 (tpt) REVERT: H 423 PHE cc_start: 0.8771 (p90) cc_final: 0.8467 (p90) REVERT: I 364 GLN cc_start: 0.8847 (pp30) cc_final: 0.8603 (pp30) REVERT: I 404 ASP cc_start: 0.8195 (t0) cc_final: 0.7564 (t0) REVERT: J 11 ASP cc_start: 0.7947 (t70) cc_final: 0.7478 (t0) REVERT: J 221 ARG cc_start: 0.7432 (ptp-170) cc_final: 0.7021 (ptt-90) REVERT: J 228 MET cc_start: 0.6150 (OUTLIER) cc_final: 0.5678 (tpt) REVERT: J 285 TYR cc_start: 0.9349 (OUTLIER) cc_final: 0.8922 (m-80) REVERT: J 441 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.7527 (mp10) REVERT: K 232 LYS cc_start: 0.8967 (OUTLIER) cc_final: 0.8582 (mmmm) REVERT: L 221 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.7441 (ptm160) REVERT: X 212 MET cc_start: 0.2977 (mmt) cc_final: 0.2418 (mpp) REVERT: Y 338 LYS cc_start: 0.2478 (OUTLIER) cc_final: 0.1610 (ttpt) REVERT: Y 377 MET cc_start: 0.3183 (OUTLIER) cc_final: 0.2172 (mmm) outliers start: 59 outliers final: 28 residues processed: 413 average time/residue: 1.4563 time to fit residues: 749.5308 Evaluate side-chains 411 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 370 time to evaluate : 4.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 55 ILE Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain I residue 471 LEU Chi-restraints excluded: chain J residue 30 ARG Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 82 GLU Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 288 MET Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 369 GLU Chi-restraints excluded: chain X residue 371 ASP Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 190 SER Chi-restraints excluded: chain Y residue 289 MET Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain Y residue 448 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 397 optimal weight: 3.9990 chunk 256 optimal weight: 6.9990 chunk 383 optimal weight: 3.9990 chunk 193 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 408 optimal weight: 5.9990 chunk 437 optimal weight: 0.8980 chunk 317 optimal weight: 4.9990 chunk 59 optimal weight: 7.9990 chunk 504 optimal weight: 0.4980 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 HIS B 375 ASN F 377 ASN Y 47 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 54296 Z= 0.313 Angle : 0.657 17.312 73858 Z= 0.331 Chirality : 0.045 0.346 8366 Planarity : 0.005 0.063 9280 Dihedral : 11.944 179.367 7973 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.68 % Favored : 94.24 % Rotamer: Outliers : 0.95 % Allowed : 10.61 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 6688 helix: 2.17 (0.13), residues: 1967 sheet: 0.70 (0.15), residues: 1154 loop : -2.11 (0.09), residues: 3567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 470 HIS 0.005 0.001 HIS F 429 PHE 0.015 0.002 PHE H 264 TYR 0.020 0.002 TYR Y 336 ARG 0.011 0.000 ARG K 221 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 380 time to evaluate : 4.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8746 (t0) cc_final: 0.8495 (t0) REVERT: B 285 TYR cc_start: 0.9363 (OUTLIER) cc_final: 0.8543 (m-80) REVERT: B 354 ASP cc_start: 0.8983 (m-30) cc_final: 0.8758 (m-30) REVERT: C 285 TYR cc_start: 0.9280 (OUTLIER) cc_final: 0.6659 (m-80) REVERT: C 405 GLU cc_start: 0.8846 (tt0) cc_final: 0.8244 (pm20) REVERT: D 285 TYR cc_start: 0.9048 (OUTLIER) cc_final: 0.6923 (m-80) REVERT: D 421 TRP cc_start: 0.4444 (p-90) cc_final: 0.4111 (p-90) REVERT: E 285 TYR cc_start: 0.9385 (OUTLIER) cc_final: 0.8836 (m-80) REVERT: E 349 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8175 (mp0) REVERT: E 353 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7812 (mp0) REVERT: E 369 ASN cc_start: 0.7676 (t0) cc_final: 0.7294 (t0) REVERT: E 470 TRP cc_start: 0.8974 (t-100) cc_final: 0.8682 (t-100) REVERT: F 9 ASP cc_start: 0.8991 (t70) cc_final: 0.8749 (t0) REVERT: G 423 PHE cc_start: 0.8759 (p90) cc_final: 0.8437 (p90) REVERT: G 474 LYS cc_start: 0.8569 (mmpt) cc_final: 0.8169 (tmtm) REVERT: H 26 GLU cc_start: 0.7561 (pm20) cc_final: 0.7257 (pm20) REVERT: H 88 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8479 (mt-10) REVERT: H 221 ARG cc_start: 0.8198 (tmm160) cc_final: 0.7532 (tmm160) REVERT: H 228 MET cc_start: 0.7364 (tpp) cc_final: 0.6901 (tpt) REVERT: H 319 ASP cc_start: 0.8577 (t0) cc_final: 0.8362 (t0) REVERT: H 423 PHE cc_start: 0.8764 (p90) cc_final: 0.8449 (p90) REVERT: I 364 GLN cc_start: 0.8893 (pp30) cc_final: 0.8638 (pp30) REVERT: I 404 ASP cc_start: 0.8191 (t0) cc_final: 0.7582 (t0) REVERT: J 11 ASP cc_start: 0.7939 (t70) cc_final: 0.7478 (t0) REVERT: J 228 MET cc_start: 0.6095 (OUTLIER) cc_final: 0.5667 (tpt) REVERT: J 285 TYR cc_start: 0.9347 (OUTLIER) cc_final: 0.8861 (m-80) REVERT: J 441 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.7539 (mp10) REVERT: K 232 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8581 (mmmm) REVERT: L 221 ARG cc_start: 0.7628 (OUTLIER) cc_final: 0.7322 (ptm160) REVERT: X 212 MET cc_start: 0.2966 (mmt) cc_final: 0.2418 (mpp) REVERT: X 487 MET cc_start: 0.6203 (pmm) cc_final: 0.5774 (pmm) REVERT: Y 338 LYS cc_start: 0.2407 (OUTLIER) cc_final: 0.1512 (ttpt) REVERT: Y 377 MET cc_start: 0.3232 (OUTLIER) cc_final: 0.2270 (mmm) outliers start: 54 outliers final: 26 residues processed: 418 average time/residue: 1.4802 time to fit residues: 771.5090 Evaluate side-chains 407 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 369 time to evaluate : 4.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain A residue 393 LYS Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 350 VAL Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain X residue 82 GLU Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 369 GLU Chi-restraints excluded: chain X residue 371 ASP Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 137 ASP Chi-restraints excluded: chain Y residue 190 SER Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain Y residue 410 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 583 optimal weight: 10.0000 chunk 614 optimal weight: 1.9990 chunk 561 optimal weight: 4.9990 chunk 598 optimal weight: 2.9990 chunk 360 optimal weight: 0.7980 chunk 260 optimal weight: 4.9990 chunk 469 optimal weight: 0.0040 chunk 183 optimal weight: 1.9990 chunk 540 optimal weight: 0.8980 chunk 565 optimal weight: 6.9990 chunk 596 optimal weight: 20.0000 overall best weight: 1.1396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS B 375 ASN F 377 ASN Y 47 GLN Y 306 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 54296 Z= 0.191 Angle : 0.614 16.420 73858 Z= 0.305 Chirality : 0.043 0.302 8366 Planarity : 0.005 0.062 9280 Dihedral : 11.675 179.470 7973 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.21 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.62 % Favored : 95.31 % Rotamer: Outliers : 0.79 % Allowed : 10.84 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.10), residues: 6688 helix: 2.27 (0.13), residues: 1966 sheet: 0.67 (0.15), residues: 1193 loop : -2.00 (0.09), residues: 3529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 470 HIS 0.004 0.001 HIS H 79 PHE 0.020 0.001 PHE D 447 TYR 0.021 0.001 TYR Y 336 ARG 0.011 0.000 ARG K 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 382 time to evaluate : 4.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8698 (t0) cc_final: 0.8436 (t0) REVERT: B 285 TYR cc_start: 0.9318 (OUTLIER) cc_final: 0.8385 (m-80) REVERT: B 354 ASP cc_start: 0.8986 (m-30) cc_final: 0.8751 (m-30) REVERT: C 285 TYR cc_start: 0.9245 (OUTLIER) cc_final: 0.6751 (m-80) REVERT: C 405 GLU cc_start: 0.8858 (tt0) cc_final: 0.8242 (pm20) REVERT: D 285 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.6848 (m-80) REVERT: E 285 TYR cc_start: 0.9342 (OUTLIER) cc_final: 0.8764 (m-80) REVERT: E 349 GLU cc_start: 0.8359 (mt-10) cc_final: 0.8131 (mp0) REVERT: E 353 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7807 (mp0) REVERT: E 369 ASN cc_start: 0.7697 (t0) cc_final: 0.7337 (t0) REVERT: E 470 TRP cc_start: 0.8989 (t-100) cc_final: 0.8707 (t-100) REVERT: F 9 ASP cc_start: 0.8967 (t70) cc_final: 0.8724 (t0) REVERT: G 28 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8342 (mt-10) REVERT: G 423 PHE cc_start: 0.8790 (p90) cc_final: 0.8479 (p90) REVERT: G 474 LYS cc_start: 0.8576 (mmpt) cc_final: 0.8180 (tmtm) REVERT: H 26 GLU cc_start: 0.7508 (pm20) cc_final: 0.7203 (pm20) REVERT: H 88 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8482 (mt-10) REVERT: H 221 ARG cc_start: 0.8172 (tmm160) cc_final: 0.7515 (tmm160) REVERT: H 228 MET cc_start: 0.7374 (tpp) cc_final: 0.6908 (tpt) REVERT: H 423 PHE cc_start: 0.8769 (p90) cc_final: 0.8417 (p90) REVERT: I 364 GLN cc_start: 0.8891 (pp30) cc_final: 0.8637 (pp30) REVERT: I 404 ASP cc_start: 0.8147 (t0) cc_final: 0.7601 (t0) REVERT: J 11 ASP cc_start: 0.7932 (t70) cc_final: 0.7475 (t0) REVERT: J 228 MET cc_start: 0.6260 (OUTLIER) cc_final: 0.5710 (tpt) REVERT: J 285 TYR cc_start: 0.9299 (OUTLIER) cc_final: 0.8570 (m-80) REVERT: J 441 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: J 470 TRP cc_start: 0.9148 (t60) cc_final: 0.8715 (t-100) REVERT: K 232 LYS cc_start: 0.8945 (OUTLIER) cc_final: 0.8569 (mmmm) REVERT: L 11 ASP cc_start: 0.9237 (m-30) cc_final: 0.9020 (m-30) REVERT: L 221 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7151 (ptt90) REVERT: X 204 LYS cc_start: 0.7773 (pptt) cc_final: 0.7554 (ptmm) REVERT: X 212 MET cc_start: 0.2956 (mmt) cc_final: 0.2412 (mpp) REVERT: X 487 MET cc_start: 0.6224 (pmm) cc_final: 0.5835 (pmm) REVERT: Y 338 LYS cc_start: 0.2485 (OUTLIER) cc_final: 0.2062 (tttm) REVERT: Y 377 MET cc_start: 0.3202 (OUTLIER) cc_final: 0.2285 (mmm) outliers start: 45 outliers final: 21 residues processed: 414 average time/residue: 1.4687 time to fit residues: 761.4107 Evaluate side-chains 406 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 373 time to evaluate : 4.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 285 TYR Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 358 LEU Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 285 TYR Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain E residue 285 TYR Chi-restraints excluded: chain E residue 353 GLU Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain G residue 285 TYR Chi-restraints excluded: chain H residue 123 MET Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 228 MET Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain J residue 441 GLN Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 288 MET Chi-restraints excluded: chain X residue 296 VAL Chi-restraints excluded: chain X residue 300 THR Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 190 SER Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain Y residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 392 optimal weight: 0.6980 chunk 632 optimal weight: 0.0980 chunk 386 optimal weight: 0.8980 chunk 300 optimal weight: 0.8980 chunk 439 optimal weight: 0.8980 chunk 663 optimal weight: 0.0970 chunk 610 optimal weight: 10.0000 chunk 528 optimal weight: 5.9990 chunk 54 optimal weight: 0.9990 chunk 408 optimal weight: 0.0770 chunk 323 optimal weight: 2.9990 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN F 377 ASN L 265 HIS Y 47 GLN Y 442 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.080 54296 Z= 0.152 Angle : 0.588 15.855 73858 Z= 0.288 Chirality : 0.042 0.278 8366 Planarity : 0.005 0.061 9280 Dihedral : 11.260 178.149 7973 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.31 % Favored : 95.61 % Rotamer: Outliers : 0.53 % Allowed : 11.19 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.11), residues: 6688 helix: 2.36 (0.13), residues: 1969 sheet: 0.79 (0.15), residues: 1218 loop : -1.90 (0.10), residues: 3501 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP B 470 HIS 0.009 0.000 HIS Y 306 PHE 0.035 0.001 PHE D 447 TYR 0.022 0.001 TYR K 382 ARG 0.011 0.000 ARG K 221 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13376 Ramachandran restraints generated. 6688 Oldfield, 0 Emsley, 6688 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 392 time to evaluate : 4.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 ASP cc_start: 0.8641 (t0) cc_final: 0.8389 (t0) REVERT: A 84 MET cc_start: 0.9114 (mmp) cc_final: 0.8817 (mmp) REVERT: A 228 MET cc_start: 0.5137 (tpt) cc_final: 0.4215 (ppp) REVERT: A 354 ASP cc_start: 0.8621 (m-30) cc_final: 0.8407 (m-30) REVERT: B 285 TYR cc_start: 0.9268 (OUTLIER) cc_final: 0.8219 (m-80) REVERT: B 354 ASP cc_start: 0.9011 (m-30) cc_final: 0.8798 (m-30) REVERT: C 285 TYR cc_start: 0.9145 (OUTLIER) cc_final: 0.6634 (m-80) REVERT: C 405 GLU cc_start: 0.8858 (tt0) cc_final: 0.8269 (pm20) REVERT: D 436 ASP cc_start: 0.8782 (t0) cc_final: 0.8354 (t0) REVERT: E 349 GLU cc_start: 0.8335 (mt-10) cc_final: 0.8128 (mp0) REVERT: E 369 ASN cc_start: 0.7741 (t0) cc_final: 0.7421 (t0) REVERT: E 470 TRP cc_start: 0.8969 (t-100) cc_final: 0.8684 (t-100) REVERT: G 84 MET cc_start: 0.8982 (mpt) cc_final: 0.8604 (mpt) REVERT: G 423 PHE cc_start: 0.8808 (p90) cc_final: 0.8516 (p90) REVERT: G 474 LYS cc_start: 0.8561 (mmpt) cc_final: 0.8179 (tmtm) REVERT: H 26 GLU cc_start: 0.7427 (pm20) cc_final: 0.7148 (pm20) REVERT: H 88 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8474 (mt-10) REVERT: H 228 MET cc_start: 0.7407 (tpp) cc_final: 0.6985 (tpt) REVERT: H 319 ASP cc_start: 0.8521 (t0) cc_final: 0.8231 (t0) REVERT: H 423 PHE cc_start: 0.8783 (p90) cc_final: 0.8462 (p90) REVERT: I 364 GLN cc_start: 0.8833 (pp30) cc_final: 0.8583 (pp30) REVERT: I 404 ASP cc_start: 0.8094 (t0) cc_final: 0.7517 (t0) REVERT: J 11 ASP cc_start: 0.7928 (t70) cc_final: 0.7512 (t0) REVERT: J 285 TYR cc_start: 0.9248 (OUTLIER) cc_final: 0.8542 (m-80) REVERT: J 470 TRP cc_start: 0.9169 (t60) cc_final: 0.8763 (t-100) REVERT: K 232 LYS cc_start: 0.8957 (OUTLIER) cc_final: 0.8578 (mmmm) REVERT: L 221 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.6708 (ptt90) REVERT: L 340 ASP cc_start: 0.8654 (m-30) cc_final: 0.8443 (m-30) REVERT: X 212 MET cc_start: 0.2875 (mmt) cc_final: 0.2389 (mpp) REVERT: X 487 MET cc_start: 0.6241 (pmm) cc_final: 0.5875 (pmm) REVERT: Y 338 LYS cc_start: 0.2459 (OUTLIER) cc_final: 0.1749 (pptt) REVERT: Y 377 MET cc_start: 0.3342 (OUTLIER) cc_final: 0.2509 (mmm) REVERT: Y 424 LYS cc_start: 0.5345 (pptt) cc_final: 0.4796 (mmtm) outliers start: 30 outliers final: 13 residues processed: 413 average time/residue: 1.4847 time to fit residues: 770.9667 Evaluate side-chains 398 residues out of total 5776 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 378 time to evaluate : 4.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 285 TYR Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain C residue 285 TYR Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain D residue 450 PHE Chi-restraints excluded: chain F residue 285 TYR Chi-restraints excluded: chain I residue 285 TYR Chi-restraints excluded: chain J residue 285 TYR Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain L residue 221 ARG Chi-restraints excluded: chain L residue 285 TYR Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 91 ASP Chi-restraints excluded: chain X residue 478 LEU Chi-restraints excluded: chain Y residue 115 THR Chi-restraints excluded: chain Y residue 190 SER Chi-restraints excluded: chain Y residue 338 LYS Chi-restraints excluded: chain Y residue 377 MET Chi-restraints excluded: chain Y residue 410 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 666 random chunks: chunk 419 optimal weight: 0.0370 chunk 562 optimal weight: 6.9990 chunk 161 optimal weight: 0.4980 chunk 487 optimal weight: 0.0870 chunk 78 optimal weight: 5.9990 chunk 146 optimal weight: 2.9990 chunk 529 optimal weight: 5.9990 chunk 221 optimal weight: 0.2980 chunk 543 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 overall best weight: 0.7838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 375 ASN F 377 ASN G 377 ASN H 389 GLN Y 47 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.114172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.071029 restraints weight = 240772.471| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 4.66 r_work: 0.2679 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2681 r_free = 0.2681 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 54296 Z= 0.166 Angle : 0.597 16.097 73858 Z= 0.292 Chirality : 0.042 0.293 8366 Planarity : 0.005 0.062 9280 Dihedral : 11.091 177.805 7973 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.27 % Favored : 95.66 % Rotamer: Outliers : 0.67 % Allowed : 11.42 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.11), residues: 6688 helix: 2.41 (0.13), residues: 1971 sheet: 0.81 (0.15), residues: 1207 loop : -1.87 (0.10), residues: 3510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 470 HIS 0.005 0.001 HIS Y 130 PHE 0.016 0.001 PHE E 450 TYR 0.026 0.001 TYR K 382 ARG 0.011 0.000 ARG K 221 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13836.03 seconds wall clock time: 241 minutes 34.77 seconds (14494.77 seconds total)