Starting phenix.real_space_refine on Mon Apr 15 02:54:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8uu8_42571/04_2024/8uu8_42571_updated.pdb" } resolution = 3.1 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= 0.002 sd= 1.124 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 4617 5.49 5 Mg 423 5.21 5 S 112 5.16 5 C 70502 2.51 5 N 26254 2.21 5 O 40119 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "d ASP 95": "OD1" <-> "OD2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "e GLU 117": "OE1" <-> "OE2" Residue "f TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 28": "OD1" <-> "OD2" Residue "f TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o ASP 19": "OD1" <-> "OD2" Residue "t ASP 48": "OD1" <-> "OD2" Residue "v GLU 38": "OE1" <-> "OE2" Residue "v ASP 93": "OD1" <-> "OD2" Residue "v GLU 153": "OE1" <-> "OE2" Residue "v PHE 232": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v TYR 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v GLU 353": "OE1" <-> "OE2" Residue "C GLU 30": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 121": "OE1" <-> "OE2" Residue "C ASP 134": "OD1" <-> "OD2" Residue "C TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 55": "OD1" <-> "OD2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "D PHE 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 10": "OD1" <-> "OD2" Residue "E GLU 56": "OE1" <-> "OE2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 203": "OE1" <-> "OE2" Residue "G TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 12": "OD1" <-> "OD2" Residue "N ASP 114": "OD1" <-> "OD2" Residue "O TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 111": "OE1" <-> "OE2" Residue "P ASP 100": "OD1" <-> "OD2" Residue "Q ASP 95": "OD1" <-> "OD2" Residue "R TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 49": "OD1" <-> "OD2" Residue "S ASP 97": "OD1" <-> "OD2" Residue "T ASP 36": "OD1" <-> "OD2" Residue "U ASP 27": "OD1" <-> "OD2" Residue "U ASP 82": "OD1" <-> "OD2" Residue "V ASP 21": "OD1" <-> "OD2" Residue "V PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 43": "OE1" <-> "OE2" Residue "V TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 7": "OD1" <-> "OD2" Residue "Y ASP 23": "OD1" <-> "OD2" Residue "Z GLU 4": "OE1" <-> "OE2" Residue "1 GLU 23": "OE1" <-> "OE2" Residue "2 ASP 39": "OD1" <-> "OD2" Residue "4 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 12": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 142031 Number of models: 1 Model: "" Number of chains: 95 Chain: "a" Number of atoms: 32515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1516, 32515 Classifications: {'RNA': 1516} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 90, 'rna3p_pur': 742, 'rna3p_pyr': 566} Link IDs: {'rna2p': 208, 'rna3p': 1307} Chain breaks: 3 Chain: "b" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1396 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'PTRANS': 7, 'TRANS': 201} Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 367 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'ASN:plan1': 5, 'ASP:plan': 10, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 172 Chain: "c" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1003 Classifications: {'peptide': 204} Incomplete info: {'truncation_to_alanine': 165} Link IDs: {'PTRANS': 3, 'TRANS': 200} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 647 Unresolved non-hydrogen angles: 824 Unresolved non-hydrogen dihedrals: 538 Unresolved non-hydrogen chiralities: 55 Planarities with less than four sites: {'GLN:plan1': 7, 'HIS:plan': 6, 'TYR:plan': 7, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 13, 'PHE:plan': 2, 'GLU:plan': 15, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 377 Chain: "d" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1562 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 7, 'TRANS': 191} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "e" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1057 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 145} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "f" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 785 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "g" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 650 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 104} Link IDs: {'PTRANS': 3, 'TRANS': 126} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 389 Unresolved non-hydrogen angles: 484 Unresolved non-hydrogen dihedrals: 319 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 211 Chain: "h" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1022 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 635 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 7, 'TRANS': 119} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 381 Unresolved non-hydrogen angles: 485 Unresolved non-hydrogen dihedrals: 317 Unresolved non-hydrogen chiralities: 33 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'ARG%COO:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 14} Unresolved non-hydrogen planarities: 212 Chain: "j" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 477 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 88} Link IDs: {'PTRANS': 6, 'TRANS': 89} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 307 Unresolved non-hydrogen angles: 387 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 31 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 7, 'TYR:plan': 3, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 147 Chain: "k" Number of atoms: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 748 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 107} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 38 Chain: "l" Number of atoms: 993 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 993 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 8, 'TRANS': 126} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 Chain: "m" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 529 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 92} Link IDs: {'PTRANS': 2, 'TRANS': 105} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 342 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 268 Unresolved non-hydrogen chiralities: 35 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 5, 'GLU:plan': 11, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 188 Chain: "n" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 260 Classifications: {'peptide': 50} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 142 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 84 Chain: "o" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 695 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "p" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 661 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 82} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 23 Chain: "q" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 650 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "r" Number of atoms: 494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 494 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 2, 'TRANS': 61} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "s" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 365 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 4, 'TRANS': 69} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 4, 'TYR:plan': 2, 'TRP:plan': 1, 'HIS:plan': 3, 'PHE:plan': 4, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 126 Chain: "t" Number of atoms: 583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 583 Classifications: {'peptide': 81} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'TRANS': 80} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "x" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1591 Classifications: {'RNA': 74} Modifications used: {'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 1 Chain: "w" Number of atoms: 190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 190 Classifications: {'RNA': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "v" Number of atoms: 3282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3282 Classifications: {'peptide': 417} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 406} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 40 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'ASP:plan': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 47 Chain: "A" Number of atoms: 62318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2901, 62318 Classifications: {'RNA': 2901} Modifications used: {'rna2p_pur': 308, 'rna2p_pyr': 150, 'rna3p_pur': 1395, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 458, 'rna3p': 2442} Chain breaks: 3 Chain: "B" Number of atoms: 2428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 2428 Classifications: {'RNA': 114} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 13, 'rna3p_pur': 54, 'rna3p_pyr': 45} Link IDs: {'rna2p': 15, 'rna3p': 98} Chain: "C" Number of atoms: 2084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2084 Classifications: {'peptide': 274} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 259} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 1544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1544 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 9, 'TRANS': 196} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 30 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "E" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1536 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 196} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 7, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "F" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1173 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 58} Link IDs: {'PTRANS': 7, 'TRANS': 167} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 197 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 20 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 7, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 1305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1305 Classifications: {'peptide': 171} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 160} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 636 Classifications: {'peptide': 129} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 2, 'TRANS': 126} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 346 Unresolved non-hydrogen angles: 437 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 39 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 6, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 169 Chain: "H" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 673 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 102} Link IDs: {'PTRANS': 10, 'TRANS': 124} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 329 Unresolved non-hydrogen angles: 412 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 40 Planarities with less than four sites: {'GLN:plan1': 5, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 5, 'GLU:plan': 9, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 133 Chain: "L" Number of atoms: 1112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1112 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 135} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 893 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 4, 'TRANS': 117} Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 13 Chain: "N" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1071 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 141} Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 1062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1062 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 7, 'TRANS': 127} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "P" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 982 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain breaks: 1 Chain: "Q" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 884 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 885 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 107} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "S" Number of atoms: 949 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 949 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 117} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "T" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 774 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 97} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "U" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 106} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "V" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 726 Classifications: {'peptide': 92} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 90} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "W" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 760 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 95} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "Y" Number of atoms: 567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 567 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 73} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "Z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 444 Classifications: {'peptide': 59} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 1, 'TRANS': 57} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "1" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 477 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "2" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 3, 'TRANS': 52} Chain: "3" Number of atoms: 523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 523 Classifications: {'peptide': 73} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 68} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "4" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 417 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 49} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "5" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 394 Classifications: {'peptide': 48} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "6" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 365 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "7" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 520 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "8" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 280 Classifications: {'peptide': 36} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 32} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "a" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 151 Unusual residues: {' MG': 151} Classifications: {'undetermined': 151} Link IDs: {None: 150} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "n" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 2, ' ZN': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 34 Unusual residues: {' MG': 2, 'GCP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 249 Unusual residues: {' MG': 249} Classifications: {'undetermined': 249} Link IDs: {None: 248} Chain: "B" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "5" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 94 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 94 Classifications: {'water': 94} Link IDs: {None: 93} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "p" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "t" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "v" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 235 Classifications: {'water': 235} Link IDs: {None: 234} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 43509 SG CYS n 27 136.400 181.049 66.789 1.00 59.38 S ATOM 43574 SG CYS n 40 139.172 183.110 65.359 1.00 58.22 S ATOM 43590 SG CYS n 43 138.808 179.693 64.147 1.00 56.96 S ATOM A0UGF SG CYS 4 30 105.057 42.238 193.785 1.00 81.70 S ATOM A0UGV SG CYS 4 33 107.326 42.824 196.670 1.00 84.95 S ATOM A0UJ6 SG CYS 4 43 108.382 43.999 193.242 1.00 77.83 S ATOM A0UJO SG CYS 4 46 108.835 40.687 193.635 1.00 84.47 S ATOM A0UND SG CYS 5 9 157.304 188.357 182.972 1.00 80.98 S ATOM A0UNV SG CYS 5 12 158.735 187.388 186.453 1.00 83.12 S ATOM A0UTC SG CYS 5 36 154.992 187.080 185.744 1.00 76.17 S ATOM A0VN9 SG CYS 8 11 65.647 132.943 133.010 1.00 78.92 S ATOM A0VNT SG CYS 8 14 67.039 131.481 136.354 1.00 77.40 S ATOM A0VQH SG CYS 8 27 65.023 129.326 133.948 1.00 78.80 S Time building chain proxies: 54.47, per 1000 atoms: 0.38 Number of scatterers: 142031 At special positions: 0 Unit cell: (243.95, 250.75, 279.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 112 16.00 P 4617 15.00 Mg 423 11.99 O 40119 8.00 N 26254 7.00 C 70502 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 55.16 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 46 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 43 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 33 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 30 " pdb=" ZN 5 101 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 36 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 12 " pdb="ZN ZN 5 101 " - pdb=" SG CYS 5 9 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 32 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " pdb=" ZN n 103 " pdb="ZN ZN n 103 " - pdb=" SG CYS n 40 " pdb="ZN ZN n 103 " - pdb=" SG CYS n 27 " pdb="ZN ZN n 103 " - pdb=" SG CYS n 43 " Number of angles added : 9 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10904 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 178 helices and 73 sheets defined 38.2% alpha, 18.8% beta 1547 base pairs and 2466 stacking pairs defined. Time for finding SS restraints: 71.75 Creating SS restraints... Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.346A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N LYS b 29 " --> pdb=" O PRO b 25 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N TYR b 30 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ILE b 31 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N PHE b 32 " --> pdb=" O LYS b 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 24 through 32' Processing helix chain 'b' and resid 42 through 61 removed outlier: 4.076A pdb=" N THR b 46 " --> pdb=" O ASP b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 Processing helix chain 'b' and resid 103 through 123 Processing helix chain 'b' and resid 135 through 149 removed outlier: 5.224A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLN b 141 " --> pdb=" O LEU b 137 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 3.796A pdb=" N MET b 154 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LYS b 155 " --> pdb=" O ILE b 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 150 through 155' Processing helix chain 'b' and resid 165 through 170 removed outlier: 3.700A pdb=" N ARG b 170 " --> pdb=" O PRO b 166 " (cutoff:3.500A) Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 226 removed outlier: 3.642A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) Processing helix chain 'c' and resid 27 through 45 removed outlier: 4.457A pdb=" N LEU c 32 " --> pdb=" O TYR c 28 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N HIS c 33 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLU c 34 " --> pdb=" O ASP c 30 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL c 42 " --> pdb=" O ILE c 38 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA c 43 " --> pdb=" O ARG c 39 " (cutoff:3.500A) Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.940A pdb=" N GLY c 77 " --> pdb=" O GLY c 73 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 95 removed outlier: 3.624A pdb=" N ALA c 85 " --> pdb=" O SER c 81 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU c 86 " --> pdb=" O GLU c 82 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LYS c 88 " --> pdb=" O GLU c 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU c 93 " --> pdb=" O ASN c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 111 through 126 removed outlier: 3.709A pdb=" N ARG c 126 " --> pdb=" O GLN c 122 " (cutoff:3.500A) Processing helix chain 'c' and resid 128 through 144 removed outlier: 4.070A pdb=" N MET c 141 " --> pdb=" O ILE c 137 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA c 143 " --> pdb=" O ARG c 139 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY c 144 " --> pdb=" O THR c 140 " (cutoff:3.500A) Processing helix chain 'c' and resid 11 through 16 removed outlier: 3.807A pdb=" N ARG c 16 " --> pdb=" O ARG c 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 11 through 16' Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.584A pdb=" N VAL d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N SER d 12 " --> pdb=" O SER d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.593A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 78 removed outlier: 3.982A pdb=" N LYS d 77 " --> pdb=" O ASN d 73 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N LEU d 78 " --> pdb=" O LYS d 74 " (cutoff:3.500A) Processing helix chain 'd' and resid 81 through 93 removed outlier: 4.621A pdb=" N ASN d 85 " --> pdb=" O LYS d 81 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG d 93 " --> pdb=" O LEU d 89 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 102 Processing helix chain 'd' and resid 106 through 117 removed outlier: 3.551A pdb=" N ALA d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLN d 112 " --> pdb=" O ARG d 108 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLY d 117 " --> pdb=" O LEU d 113 " (cutoff:3.500A) Processing helix chain 'd' and resid 142 through 147 removed outlier: 6.473A pdb=" N ALA d 146 " --> pdb=" O ARG d 142 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LYS d 147 " --> pdb=" O GLU d 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 142 through 147' Processing helix chain 'd' and resid 148 through 158 removed outlier: 3.756A pdb=" N GLU d 156 " --> pdb=" O ALA d 152 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER d 158 " --> pdb=" O SER d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 181 through 186 removed outlier: 4.092A pdb=" N LEU d 185 " --> pdb=" O GLU d 181 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ALA d 186 " --> pdb=" O ARG d 182 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 181 through 186' Processing helix chain 'd' and resid 190 through 200 removed outlier: 4.289A pdb=" N ILE d 194 " --> pdb=" O ASN d 190 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU d 196 " --> pdb=" O ALA d 192 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG d 200 " --> pdb=" O GLU d 196 " (cutoff:3.500A) Processing helix chain 'e' and resid 56 through 72 removed outlier: 3.516A pdb=" N LYS e 69 " --> pdb=" O VAL e 65 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS e 70 " --> pdb=" O GLU e 66 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ASN e 71 " --> pdb=" O ASP e 67 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N MET e 72 " --> pdb=" O ALA e 68 " (cutoff:3.500A) Processing helix chain 'e' and resid 109 through 120 removed outlier: 3.510A pdb=" N GLY e 120 " --> pdb=" O LEU e 116 " (cutoff:3.500A) Processing helix chain 'e' and resid 133 through 148 removed outlier: 3.691A pdb=" N LEU e 148 " --> pdb=" O GLY e 144 " (cutoff:3.500A) Processing helix chain 'f' and resid 17 through 34 removed outlier: 5.019A pdb=" N ASN f 34 " --> pdb=" O ILE f 30 " (cutoff:3.500A) Processing helix chain 'f' and resid 71 through 84 removed outlier: 6.295A pdb=" N ASN f 75 " --> pdb=" O ALA f 71 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU f 76 " --> pdb=" O ASP f 72 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE f 83 " --> pdb=" O ARG f 79 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N SER f 84 " --> pdb=" O LEU f 80 " (cutoff:3.500A) Processing helix chain 'g' and resid 21 through 26 Processing helix chain 'g' and resid 27 through 32 removed outlier: 4.132A pdb=" N VAL g 32 " --> pdb=" O ASN g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 4.660A pdb=" N SER g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 69 removed outlier: 3.710A pdb=" N VAL g 61 " --> pdb=" O ASP g 57 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLU g 63 " --> pdb=" O MET g 59 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N ALA g 65 " --> pdb=" O VAL g 61 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET g 66 " --> pdb=" O PHE g 62 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N LYS g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASN g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N ILE g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.920A pdb=" N SER g 97 " --> pdb=" O ALA g 93 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ARG g 111 " --> pdb=" O TYR g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 134 through 149 removed outlier: 3.923A pdb=" N ARG g 138 " --> pdb=" O SER g 134 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N GLU g 139 " --> pdb=" O VAL g 135 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASP g 140 " --> pdb=" O LYS g 136 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR g 141 " --> pdb=" O LYS g 137 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N HIS g 142 " --> pdb=" O ARG g 138 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N MET g 144 " --> pdb=" O ASP g 140 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 removed outlier: 3.606A pdb=" N ASP h 9 " --> pdb=" O ASP h 5 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE h 10 " --> pdb=" O PRO h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.655A pdb=" N GLU h 38 " --> pdb=" O LYS h 34 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE h 39 " --> pdb=" O GLU h 35 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LEU h 40 " --> pdb=" O ILE h 36 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ARG h 42 " --> pdb=" O GLU h 38 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU h 43 " --> pdb=" O ILE h 39 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY h 44 " --> pdb=" O LEU h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 114 through 122 removed outlier: 3.886A pdb=" N ALA h 120 " --> pdb=" O LYS h 116 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LYS h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 34 through 40 removed outlier: 3.639A pdb=" N TYR i 38 " --> pdb=" O ASP i 34 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE i 39 " --> pdb=" O TRP i 35 " (cutoff:3.500A) Proline residue: i 40 - end of helix No H-bonds generated for 'chain 'i' and resid 34 through 40' Processing helix chain 'i' and resid 42 through 54 removed outlier: 4.339A pdb=" N GLU i 46 " --> pdb=" O ALA i 42 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL i 47 " --> pdb=" O ALA i 43 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE i 48 " --> pdb=" O LEU i 44 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Proline residue: i 51 - end of helix Processing helix chain 'i' and resid 71 through 91 removed outlier: 3.609A pdb=" N ALA i 76 " --> pdb=" O TYR i 72 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG i 80 " --> pdb=" O ALA i 76 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ARG i 85 " --> pdb=" O HIS i 81 " (cutoff:3.500A) Processing helix chain 'i' and resid 92 through 102 Proline residue: i 96 - end of helix removed outlier: 3.731A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 removed outlier: 4.570A pdb=" N LEU j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP j 19 " --> pdb=" O HIS j 15 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N SER j 21 " --> pdb=" O ILE j 17 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 87 removed outlier: 4.013A pdb=" N ASP j 85 " --> pdb=" O PRO j 81 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N SER j 86 " --> pdb=" O GLN j 82 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.743A pdb=" N LEU k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 46 through 51' Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.591A pdb=" N SER k 73 " --> pdb=" O SER k 69 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLU k 76 " --> pdb=" O LYS k 72 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N HIS k 77 " --> pdb=" O SER k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 4.052A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLY k 104 " --> pdb=" O LEU k 100 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 21 through 26 removed outlier: 3.753A pdb=" N ASN l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS l 26 " --> pdb=" O PRO l 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 21 through 26' Processing helix chain 'l' and resid 126 through 131 removed outlier: 5.050A pdb=" N TYR l 130 " --> pdb=" O SER l 126 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLY l 131 " --> pdb=" O ARG l 127 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 126 through 131' Processing helix chain 'm' and resid 14 through 21 removed outlier: 3.828A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.936A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 27 through 38 removed outlier: 4.352A pdb=" N LYS m 31 " --> pdb=" O LYS m 27 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.735A pdb=" N LEU m 48 " --> pdb=" O ARG m 44 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N THR m 49 " --> pdb=" O THR m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 62 removed outlier: 5.059A pdb=" N ARG m 62 " --> pdb=" O GLU m 58 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.965A pdb=" N ARG m 70 " --> pdb=" O GLU m 66 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG m 71 " --> pdb=" O GLY m 67 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU m 72 " --> pdb=" O ASP m 68 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL m 73 " --> pdb=" O LEU m 69 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ASN m 76 " --> pdb=" O GLU m 72 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 removed outlier: 4.659A pdb=" N LYS m 110 " --> pdb=" O ALA m 106 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 11 removed outlier: 4.692A pdb=" N MET n 6 " --> pdb=" O ALA n 2 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N ILE n 7 " --> pdb=" O LYS n 3 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ALA n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LYS n 9 " --> pdb=" O SER n 5 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N GLN n 10 " --> pdb=" O MET n 6 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS n 11 " --> pdb=" O ILE n 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 2 through 11' Processing helix chain 'n' and resid 41 through 51 removed outlier: 5.555A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA n 48 " --> pdb=" O PHE n 44 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N TYR n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LYS n 50 " --> pdb=" O GLU n 46 " (cutoff:3.500A) Processing helix chain 'o' and resid 4 through 16 removed outlier: 3.696A pdb=" N LYS o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 47 removed outlier: 3.708A pdb=" N LYS o 47 " --> pdb=" O VAL o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 Processing helix chain 'o' and resid 75 through 86 removed outlier: 3.616A pdb=" N LEU o 85 " --> pdb=" O LEU o 81 " (cutoff:3.500A) Processing helix chain 'p' and resid 52 through 63 removed outlier: 3.792A pdb=" N LEU p 57 " --> pdb=" O GLU p 53 " (cutoff:3.500A) Processing helix chain 'p' and resid 78 through 89 Processing helix chain 'p' and resid 70 through 75 removed outlier: 6.073A pdb=" N SER p 75 " --> pdb=" O VAL p 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 70 through 75' Processing helix chain 'r' and resid 15 through 21 removed outlier: 3.857A pdb=" N GLY r 21 " --> pdb=" O PHE r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 29 through 37 removed outlier: 4.325A pdb=" N LYS r 35 " --> pdb=" O GLU r 31 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N PHE r 36 " --> pdb=" O LEU r 32 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N VAL r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 45 through 50 removed outlier: 3.658A pdb=" N THR r 49 " --> pdb=" O PRO r 45 " (cutoff:3.500A) Processing helix chain 'r' and resid 52 through 70 removed outlier: 3.527A pdb=" N GLN r 56 " --> pdb=" O SER r 52 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA r 70 " --> pdb=" O SER r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 17 removed outlier: 3.838A pdb=" N MET s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) Processing helix chain 's' and resid 18 through 23 removed outlier: 5.793A pdb=" N ALA s 23 " --> pdb=" O LYS s 18 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 18 through 23' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.762A pdb=" N ILE t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) Processing helix chain 't' and resid 43 through 64 removed outlier: 4.169A pdb=" N LYS t 47 " --> pdb=" O ALA t 43 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N GLU t 52 " --> pdb=" O ASP t 48 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA t 53 " --> pdb=" O LEU t 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER t 54 " --> pdb=" O TYR t 50 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N LYS t 55 " --> pdb=" O VAL t 51 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N LYS t 56 " --> pdb=" O GLU t 52 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU t 57 " --> pdb=" O ALA t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 67 through 82 removed outlier: 3.641A pdb=" N ALA t 80 " --> pdb=" O SER t 76 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS t 81 " --> pdb=" O ARG t 77 " (cutoff:3.500A) Processing helix chain 'v' and resid 16 through 32 removed outlier: 4.100A pdb=" N ASN v 32 " --> pdb=" O ALA v 28 " (cutoff:3.500A) Processing helix chain 'v' and resid 53 through 68 removed outlier: 4.587A pdb=" N ASP v 58 " --> pdb=" O LYS v 54 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLU v 59 " --> pdb=" O GLY v 55 " (cutoff:3.500A) Processing helix chain 'v' and resid 79 through 91 Processing helix chain 'v' and resid 96 through 109 Processing helix chain 'v' and resid 111 through 128 Proline residue: v 128 - end of helix Processing helix chain 'v' and resid 129 through 141 removed outlier: 4.658A pdb=" N ASP v 136 " --> pdb=" O GLY v 132 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N MET v 137 " --> pdb=" O GLN v 133 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLN v 140 " --> pdb=" O ASP v 136 " (cutoff:3.500A) Processing helix chain 'v' and resid 154 through 192 removed outlier: 3.896A pdb=" N HIS v 169 " --> pdb=" O HIS v 165 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU v 170 " --> pdb=" O GLN v 166 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLU v 182 " --> pdb=" O VAL v 178 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N VAL v 183 " --> pdb=" O ASP v 179 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG v 184 " --> pdb=" O ASP v 180 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ARG v 185 " --> pdb=" O ARG v 181 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS v 187 " --> pdb=" O VAL v 183 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG v 188 " --> pdb=" O ARG v 184 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N GLU v 192 " --> pdb=" O ARG v 188 " (cutoff:3.500A) Processing helix chain 'v' and resid 205 through 217 Processing helix chain 'v' and resid 263 through 274 removed outlier: 3.567A pdb=" N ALA v 269 " --> pdb=" O GLN v 265 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N SER v 272 " --> pdb=" O LYS v 268 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N THR v 273 " --> pdb=" O ALA v 269 " (cutoff:3.500A) Processing helix chain 'v' and resid 275 through 280 removed outlier: 4.057A pdb=" N ALA v 280 " --> pdb=" O GLU v 276 " (cutoff:3.500A) Processing helix chain 'v' and resid 293 through 309 Processing helix chain 'v' and resid 321 through 326 removed outlier: 4.032A pdb=" N LEU v 325 " --> pdb=" O LYS v 321 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N GLU v 326 " --> pdb=" O ALA v 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 321 through 326' Processing helix chain 'v' and resid 344 through 360 removed outlier: 3.588A pdb=" N LEU v 348 " --> pdb=" O GLU v 344 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N GLU v 349 " --> pdb=" O GLU v 345 " (cutoff:3.500A) Processing helix chain 'v' and resid 375 through 385 removed outlier: 6.445A pdb=" N ALA v 379 " --> pdb=" O GLY v 375 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR v 380 " --> pdb=" O GLN v 376 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ALA v 385 " --> pdb=" O LEU v 381 " (cutoff:3.500A) Processing helix chain 'v' and resid 404 through 412 removed outlier: 3.798A pdb=" N GLN v 409 " --> pdb=" O PRO v 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.642A pdb=" N HIS C 15 " --> pdb=" O ASN C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 removed outlier: 3.718A pdb=" N ILE C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Proline residue: C 136 - end of helix No H-bonds generated for 'chain 'C' and resid 131 through 136' Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.868A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N MET C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY C 215 " --> pdb=" O SER C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.693A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 266 through 271 removed outlier: 3.881A pdb=" N ILE C 270 " --> pdb=" O SER C 266 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N VAL C 271 " --> pdb=" O ASP C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 271' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.433A pdb=" N GLU C 201 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 62 removed outlier: 5.064A pdb=" N ASN D 62 " --> pdb=" O ALA D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.607A pdb=" N GLY D 67 " --> pdb=" O LYS D 63 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N HIS D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'E' and resid 29 through 45 removed outlier: 4.162A pdb=" N ASP E 35 " --> pdb=" O LYS E 31 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N LEU E 44 " --> pdb=" O GLN E 40 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 removed outlier: 3.596A pdb=" N LEU E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS E 117 " --> pdb=" O ILE E 113 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL E 118 " --> pdb=" O LEU E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 135 through 147 removed outlier: 4.474A pdb=" N SER E 147 " --> pdb=" O LEU E 143 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 169 removed outlier: 3.805A pdb=" N ALA E 167 " --> pdb=" O VAL E 163 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N ARG E 168 " --> pdb=" O GLU E 164 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N ASN E 169 " --> pdb=" O LEU E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 190 removed outlier: 5.176A pdb=" N ASP E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 removed outlier: 4.063A pdb=" N GLU E 200 " --> pdb=" O LYS E 196 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LYS E 201 " --> pdb=" O ALA E 197 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU E 206 " --> pdb=" O VAL E 202 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 20 removed outlier: 3.654A pdb=" N GLN F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ILE F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 5.319A pdb=" N VAL F 13 " --> pdb=" O LEU F 9 " (cutoff:3.500A) Proline residue: F 14 - end of helix removed outlier: 4.262A pdb=" N SER F 18 " --> pdb=" O PRO F 14 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS F 19 " --> pdb=" O ALA F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 4.172A pdb=" N VAL F 28 " --> pdb=" O SER F 24 " (cutoff:3.500A) Proline residue: F 29 - end of helix No H-bonds generated for 'chain 'F' and resid 24 through 29' Processing helix chain 'F' and resid 46 through 62 removed outlier: 3.905A pdb=" N ASP F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA F 53 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU F 56 " --> pdb=" O SER F 52 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE F 60 " --> pdb=" O GLU F 56 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR F 61 " --> pdb=" O LEU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 94 through 105 removed outlier: 3.895A pdb=" N ASP F 98 " --> pdb=" O GLU F 94 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N LEU F 100 " --> pdb=" O MET F 96 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N ASP F 101 " --> pdb=" O TYR F 97 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS F 102 " --> pdb=" O ASP F 98 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU F 103 " --> pdb=" O PHE F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 111 Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.556A pdb=" N LEU F 170 " --> pdb=" O SER F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.993A pdb=" N ALA F 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR F 44 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 3.784A pdb=" N ALA G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU G 64 " --> pdb=" O ASN G 60 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY G 66 " --> pdb=" O ARG G 62 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG G 69 " --> pdb=" O HIS G 65 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER G 80 " --> pdb=" O VAL G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.796A pdb=" N VAL G 151 " --> pdb=" O ASN G 147 " (cutoff:3.500A) removed outlier: 4.920A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Proline residue: G 153 - end of helix Processing helix chain 'I' and resid 1 through 22 removed outlier: 3.618A pdb=" N ILE I 15 " --> pdb=" O ALA I 11 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LYS I 16 " --> pdb=" O VAL I 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 47 removed outlier: 3.829A pdb=" N ILE I 38 " --> pdb=" O ASN I 34 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR I 39 " --> pdb=" O VAL I 35 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) Processing helix chain 'I' and resid 56 through 68 removed outlier: 3.535A pdb=" N ALA I 63 " --> pdb=" O LEU I 59 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL I 64 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ALA I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N GLY I 68 " --> pdb=" O VAL I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 103 Proline residue: I 92 - end of helix removed outlier: 3.640A pdb=" N ASN I 97 " --> pdb=" O ALA I 93 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 129 removed outlier: 3.753A pdb=" N LYS I 124 " --> pdb=" O LEU I 120 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ALA I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 75 removed outlier: 5.471A pdb=" N GLU I 73 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLY I 74 " --> pdb=" O GLY I 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 23 through 28 removed outlier: 5.323A pdb=" N ALA H 27 " --> pdb=" O PRO H 23 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N LEU H 28 " --> pdb=" O VAL H 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 23 through 28' Processing helix chain 'H' and resid 34 through 47 removed outlier: 5.094A pdb=" N GLU H 41 " --> pdb=" O GLY H 37 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N PHE H 42 " --> pdb=" O PHE H 38 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 84 removed outlier: 3.524A pdb=" N LYS H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 117 removed outlier: 3.703A pdb=" N GLN H 106 " --> pdb=" O ARG H 102 " (cutoff:3.500A) Proline residue: H 114 - end of helix removed outlier: 5.067A pdb=" N ASN H 117 " --> pdb=" O MET H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 120 through 136 removed outlier: 3.705A pdb=" N VAL H 128 " --> pdb=" O ALA H 124 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLU H 129 " --> pdb=" O MET H 125 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY H 130 " --> pdb=" O LEU H 126 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLY H 136 " --> pdb=" O ALA H 132 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 39 removed outlier: 3.825A pdb=" N GLU L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER L 35 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG L 38 " --> pdb=" O ALA L 34 " (cutoff:3.500A) Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 98 through 111 removed outlier: 3.548A pdb=" N LEU L 102 " --> pdb=" O PRO L 98 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY L 108 " --> pdb=" O LEU L 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N MET L 109 " --> pdb=" O SER L 105 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU L 110 " --> pdb=" O ILE L 106 " (cutoff:3.500A) Proline residue: L 111 - end of helix Processing helix chain 'L' and resid 113 through 123 removed outlier: 3.631A pdb=" N GLN L 118 " --> pdb=" O SER L 114 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS L 122 " --> pdb=" O GLN L 118 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LEU L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 110 removed outlier: 4.065A pdb=" N GLU M 108 " --> pdb=" O ARG M 104 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ASN M 109 " --> pdb=" O GLU M 105 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN M 110 " --> pdb=" O LEU M 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 110' Processing helix chain 'M' and resid 111 through 118 Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.808A pdb=" N ARG N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Proline residue: N 62 - end of helix No H-bonds generated for 'chain 'N' and resid 56 through 62' Processing helix chain 'N' and resid 78 through 84 removed outlier: 4.338A pdb=" N LEU N 82 " --> pdb=" O ASN N 78 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASN N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N ARG N 84 " --> pdb=" O ASP N 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 84' Processing helix chain 'N' and resid 92 through 100 removed outlier: 4.296A pdb=" N GLU N 98 " --> pdb=" O GLU N 94 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N THR N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLY N 100 " --> pdb=" O LEU N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 129 through 140 removed outlier: 3.595A pdb=" N GLU N 134 " --> pdb=" O ALA N 130 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLY N 140 " --> pdb=" O ILE N 136 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 59 removed outlier: 3.894A pdb=" N MET O 54 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N TYR O 57 " --> pdb=" O ALA O 53 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N MET O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 110 through 126 removed outlier: 3.617A pdb=" N HIS O 123 " --> pdb=" O ARG O 119 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LYS O 124 " --> pdb=" O LEU O 120 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU O 125 " --> pdb=" O ALA O 121 " (cutoff:3.500A) Proline residue: O 126 - end of helix Processing helix chain 'P' and resid 9 through 28 removed outlier: 3.740A pdb=" N ASP P 19 " --> pdb=" O ALA P 15 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE P 25 " --> pdb=" O ALA P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 34 through 54 removed outlier: 4.342A pdb=" N GLU P 39 " --> pdb=" O ALA P 35 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG P 41 " --> pdb=" O ALA P 37 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LYS P 42 " --> pdb=" O LYS P 38 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL P 43 " --> pdb=" O GLU P 39 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU P 45 " --> pdb=" O ARG P 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU P 47 " --> pdb=" O VAL P 43 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER P 50 " --> pdb=" O LYS P 46 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N GLY P 51 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY P 54 " --> pdb=" O SER P 50 " (cutoff:3.500A) Processing helix chain 'P' and resid 55 through 66 removed outlier: 3.745A pdb=" N ALA P 64 " --> pdb=" O ARG P 60 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N PHE P 65 " --> pdb=" O GLN P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 93 through 107 removed outlier: 3.856A pdb=" N VAL P 102 " --> pdb=" O LEU P 98 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ALA P 103 " --> pdb=" O PHE P 99 " (cutoff:3.500A) Proline residue: P 104 - end of helix removed outlier: 3.915A pdb=" N ALA P 107 " --> pdb=" O ALA P 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 20 removed outlier: 3.586A pdb=" N ARG Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL Q 18 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 69 through 88 removed outlier: 4.386A pdb=" N ALA Q 73 " --> pdb=" O LYS Q 69 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N SER Q 74 " --> pdb=" O VAL Q 70 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA Q 81 " --> pdb=" O GLY Q 77 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LYS Q 82 " --> pdb=" O GLU Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 116 removed outlier: 4.321A pdb=" N GLY Q 116 " --> pdb=" O ALA Q 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 10 removed outlier: 3.635A pdb=" N ASP R 6 " --> pdb=" O ASN R 2 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU R 7 " --> pdb=" O LYS R 3 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ILE R 8 " --> pdb=" O LEU R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 104 removed outlier: 4.996A pdb=" N ASN R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LEU R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ARG R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 98 through 104' Processing helix chain 'S' and resid 7 through 22 removed outlier: 6.776A pdb=" N ARG S 11 " --> pdb=" O GLY S 7 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LYS S 12 " --> pdb=" O THR S 8 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LYS S 16 " --> pdb=" O LYS S 12 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA S 21 " --> pdb=" O ILE S 17 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS S 22 " --> pdb=" O VAL S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 4.498A pdb=" N LEU S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.591A pdb=" N GLN S 37 " --> pdb=" O LYS S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 4.187A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N MET S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N GLN S 72 " --> pdb=" O ALA S 68 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ASP S 73 " --> pdb=" O ALA S 69 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 removed outlier: 3.507A pdb=" N HIS S 81 " --> pdb=" O SER S 77 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY S 82 " --> pdb=" O LYS S 78 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS S 84 " --> pdb=" O MET S 80 " (cutoff:3.500A) Processing helix chain 'S' and resid 91 through 101 Processing helix chain 'S' and resid 102 through 119 removed outlier: 3.605A pdb=" N PHE S 106 " --> pdb=" O ASP S 102 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N THR S 108 " --> pdb=" O ALA S 104 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 30 removed outlier: 3.772A pdb=" N ILE U 24 " --> pdb=" O ARG U 20 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N VAL U 25 " --> pdb=" O LYS U 21 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP U 27 " --> pdb=" O ARG U 23 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N LEU U 28 " --> pdb=" O ILE U 24 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ILE U 29 " --> pdb=" O VAL U 25 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ARG U 30 " --> pdb=" O ILE U 26 " (cutoff:3.500A) Processing helix chain 'U' and resid 33 through 45 removed outlier: 3.790A pdb=" N ALA U 39 " --> pdb=" O GLY U 35 " (cutoff:3.500A) Proline residue: U 45 - end of helix Processing helix chain 'U' and resid 46 through 66 Proline residue: U 50 - end of helix removed outlier: 3.621A pdb=" N SER U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 8 removed outlier: 3.502A pdb=" N ILE V 7 " --> pdb=" O ALA V 3 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N LYS V 8 " --> pdb=" O ARG V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 21 removed outlier: 3.601A pdb=" N ILE V 19 " --> pdb=" O GLU V 15 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ASP V 21 " --> pdb=" O THR V 17 " (cutoff:3.500A) Processing helix chain 'V' and resid 34 through 46 removed outlier: 3.622A pdb=" N GLU V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 64 through 69 removed outlier: 4.308A pdb=" N VAL W 68 " --> pdb=" O HIS W 64 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N MET W 69 " --> pdb=" O VAL W 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 64 through 69' Processing helix chain 'Z' and resid 50 through 56 removed outlier: 4.959A pdb=" N SER Z 56 " --> pdb=" O ARG Z 52 " (cutoff:3.500A) Processing helix chain '1' and resid 3 through 9 removed outlier: 4.080A pdb=" N ASP 1 8 " --> pdb=" O ASN 1 4 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU 1 9 " --> pdb=" O ASP 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 35 removed outlier: 5.861A pdb=" N ILE 1 14 " --> pdb=" O SER 1 10 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N GLN 1 15 " --> pdb=" O THR 1 11 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 62 removed outlier: 4.719A pdb=" N ILE 1 43 " --> pdb=" O ASN 1 39 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ARG 1 44 " --> pdb=" O THR 1 40 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU 1 45 " --> pdb=" O ALA 1 41 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA 1 51 " --> pdb=" O ARG 1 47 " (cutoff:3.500A) Processing helix chain '2' and resid 16 through 27 removed outlier: 3.592A pdb=" N GLN 2 24 " --> pdb=" O ARG 2 20 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY 2 27 " --> pdb=" O VAL 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 40 through 51 removed outlier: 3.591A pdb=" N MET 2 46 " --> pdb=" O ALA 2 42 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 2 47 " --> pdb=" O ILE 2 43 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N THR 2 48 " --> pdb=" O ARG 2 44 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LYS 2 49 " --> pdb=" O GLY 2 45 " (cutoff:3.500A) Processing helix chain '3' and resid 69 through 80 removed outlier: 4.622A pdb=" N ARG 3 73 " --> pdb=" O GLY 3 69 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE 3 74 " --> pdb=" O ARG 3 70 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS 3 76 " --> pdb=" O ASP 3 72 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 3.992A pdb=" N ARG 4 17 " --> pdb=" O LYS 4 13 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N THR 4 18 " --> pdb=" O ARG 4 14 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N HIS 4 19 " --> pdb=" O LYS 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 removed outlier: 3.689A pdb=" N VAL 6 15 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 17 through 24 removed outlier: 3.560A pdb=" N ARG 6 21 " --> pdb=" O GLY 6 17 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N THR 6 24 " --> pdb=" O THR 6 20 " (cutoff:3.500A) Processing helix chain '6' and resid 25 through 38 removed outlier: 3.619A pdb=" N ARG 6 29 " --> pdb=" O LYS 6 25 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYS 6 37 " --> pdb=" O SER 6 33 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 14 removed outlier: 4.093A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.037A pdb=" N LYS 7 36 " --> pdb=" O MET 7 32 " (cutoff:3.500A) removed outlier: 5.731A pdb=" N SER 7 37 " --> pdb=" O PHE 7 33 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 32 through 37' Processing helix chain '7' and resid 38 through 46 removed outlier: 3.638A pdb=" N LYS 7 43 " --> pdb=" O LYS 7 39 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 7 44 " --> pdb=" O GLN 7 40 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG 7 45 " --> pdb=" O LYS 7 41 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS 7 46 " --> pdb=" O ARG 7 42 " (cutoff:3.500A) Processing helix chain '7' and resid 51 through 63 removed outlier: 3.652A pdb=" N ARG 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLN 7 60 " --> pdb=" O LYS 7 56 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N MET 7 61 " --> pdb=" O ARG 7 57 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N VAL 7 62 " --> pdb=" O ILE 7 58 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'b' and resid 90 through 93 removed outlier: 3.936A pdb=" N TYR b 90 " --> pdb=" O ILE b 67 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'c' and resid 19 through 22 removed outlier: 4.408A pdb=" N ARG c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU c 57 " --> pdb=" O ASN c 64 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN c 64 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG c 97 " --> pdb=" O ASN c 61 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL c 63 " --> pdb=" O ARG c 97 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N HIS c 99 " --> pdb=" O VAL c 63 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE c 67 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N THR c 69 " --> pdb=" O VAL c 103 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.540A pdb=" N VAL c 152 " --> pdb=" O GLU c 165 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY c 147 " --> pdb=" O TYR c 202 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLN c 151 " --> pdb=" O LYS c 198 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LYS c 198 " --> pdb=" O GLN c 151 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'd' and resid 164 through 169 removed outlier: 7.772A pdb=" N TYR d 164 " --> pdb=" O ASN d 177 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR d 166 " --> pdb=" O SER d 175 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'e' and resid 12 through 17 removed outlier: 3.944A pdb=" N GLY e 41 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N LEU e 37 " --> pdb=" O VAL e 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 84 through 89 removed outlier: 8.023A pdb=" N HIS e 84 " --> pdb=" O PRO e 99 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N GLU e 94 " --> pdb=" O LEU e 129 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N ALA e 100 " --> pdb=" O ASP e 123 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ASP e 123 " --> pdb=" O ALA e 100 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 34 through 42 removed outlier: 3.786A pdb=" N VAL e 38 " --> pdb=" O GLY e 50 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N HIS e 46 " --> pdb=" O ASP e 42 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'f' and resid 41 through 48 removed outlier: 6.610A pdb=" N LYS f 4 " --> pdb=" O GLU f 95 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N MET f 8 " --> pdb=" O MET f 91 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'g' and resid 74 through 79 removed outlier: 4.615A pdb=" N ILE g 89 " --> pdb=" O GLU g 74 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LYS g 76 " --> pdb=" O VAL g 87 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N VAL g 87 " --> pdb=" O LYS g 76 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'h' and resid 23 through 28 removed outlier: 5.993A pdb=" N ASP h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU h 64 " --> pdb=" O ASP h 23 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU h 25 " --> pdb=" O VAL h 62 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL h 62 " --> pdb=" O LEU h 25 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'h' and resid 76 through 79 removed outlier: 4.433A pdb=" N GLY h 76 " --> pdb=" O TRP h 132 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N ILE h 105 " --> pdb=" O LEU h 128 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'i' and resid 5 through 11 removed outlier: 4.436A pdb=" N VAL i 16 " --> pdb=" O HIS i 68 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N HIS i 68 " --> pdb=" O VAL i 16 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN i 66 " --> pdb=" O ARG i 18 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'j' and resid 5 through 13 removed outlier: 3.904A pdb=" N ILE j 6 " --> pdb=" O ILE j 76 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ILE j 76 " --> pdb=" O ILE j 6 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ILE j 8 " --> pdb=" O ILE j 74 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE j 74 " --> pdb=" O ILE j 8 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N PHE j 65 " --> pdb=" O TYR j 49 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N MET j 67 " --> pdb=" O SER j 47 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N SER j 47 " --> pdb=" O MET j 67 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'k' and resid 20 through 25 removed outlier: 3.571A pdb=" N ALA k 43 " --> pdb=" O ILE k 34 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'l' and resid 27 through 30 removed outlier: 3.804A pdb=" N GLY l 27 " --> pdb=" O THR l 36 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLU l 34 " --> pdb=" O ASN l 29 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'l' and resid 42 through 45 removed outlier: 5.086A pdb=" N LEU l 94 " --> pdb=" O VAL l 111 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'l' and resid 49 through 54 removed outlier: 3.745A pdb=" N ARG l 49 " --> pdb=" O ARG l 67 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY l 51 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG l 63 " --> pdb=" O MET l 53 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N LYS l 64 " --> pdb=" O ILE l 80 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE l 80 " --> pdb=" O LYS l 64 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA l 66 " --> pdb=" O ALA l 78 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'p' and resid 5 through 11 removed outlier: 4.683A pdb=" N LYS p 8 " --> pdb=" O ARG p 19 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY p 38 " --> pdb=" O ILE p 20 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'q' and resid 9 through 13 removed outlier: 7.006A pdb=" N ARG q 62 " --> pdb=" O LEU q 78 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'q' and resid 21 through 33 No H-bonds generated for sheet with id= 20 Processing sheet with id= 21, first strand: chain 's' and resid 48 through 52 removed outlier: 3.822A pdb=" N ILE s 49 " --> pdb=" O VAL s 60 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'v' and resid 33 through 36 removed outlier: 7.002A pdb=" N ILE v 7 " --> pdb=" O VAL v 36 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLY v 37 " --> pdb=" O VAL v 5 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'v' and resid 237 through 244 removed outlier: 3.589A pdb=" N SER v 238 " --> pdb=" O ASP v 254 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS v 248 " --> pdb=" O LEU v 244 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU v 282 " --> pdb=" O VAL v 195 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ASN v 336 " --> pdb=" O VAL v 315 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'v' and resid 365 through 371 removed outlier: 3.788A pdb=" N ALA v 401 " --> pdb=" O ALA v 366 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY v 396 " --> pdb=" O LEU v 393 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'v' and resid 4 through 9 removed outlier: 3.694A pdb=" N LEU v 71 " --> pdb=" O LYS v 4 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 2 through 5 removed outlier: 6.437A pdb=" N ALA C 2 " --> pdb=" O ASP C 20 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 20 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.750A pdb=" N THR C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE C 91 " --> pdb=" O GLU C 82 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLN C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'C' and resid 137 through 142 removed outlier: 7.696A pdb=" N VAL C 137 " --> pdb=" O GLY C 166 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLY C 166 " --> pdb=" O VAL C 137 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N THR C 139 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N VAL C 164 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N ARG C 175 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY C 166 " --> pdb=" O LEU C 173 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N TYR C 171 " --> pdb=" O GLU C 168 " (cutoff:3.500A) removed outlier: 8.308A pdb=" N LYS C 170 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.312A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.301A pdb=" N LYS D 3 " --> pdb=" O THR D 204 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N GLU D 167 " --> pdb=" O SER D 114 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N GLY D 116 " --> pdb=" O GLY D 165 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY D 165 " --> pdb=" O GLY D 116 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N GLY D 118 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ARG D 163 " --> pdb=" O GLY D 118 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 11 through 17 removed outlier: 3.989A pdb=" N GLY D 11 " --> pdb=" O VAL D 27 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N GLU D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LYS D 178 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'D' and resid 79 through 84 removed outlier: 6.506A pdb=" N PHE D 79 " --> pdb=" O PHE D 53 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN D 50 " --> pdb=" O LEU D 36 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ASN D 33 " --> pdb=" O VAL D 97 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ALA D 95 " --> pdb=" O VAL D 35 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 2 through 6 removed outlier: 3.778A pdb=" N GLY E 15 " --> pdb=" O LEU E 6 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'E' and resid 122 through 125 removed outlier: 3.841A pdb=" N LEU E 153 " --> pdb=" O LYS E 191 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N THR E 174 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'F' and resid 65 through 69 removed outlier: 4.082A pdb=" N GLY F 86 " --> pdb=" O THR F 68 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ALA F 87 " --> pdb=" O THR F 38 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N THR F 38 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL F 89 " --> pdb=" O ILE F 36 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N MET F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N VAL F 132 " --> pdb=" O MET F 152 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'F' and resid 72 through 75 removed outlier: 7.309A pdb=" N ASN F 72 " --> pdb=" O GLU F 81 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU F 81 " --> pdb=" O ASN F 72 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 39, first strand: chain 'G' and resid 41 through 45 removed outlier: 4.852A pdb=" N THR G 42 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER G 53 " --> pdb=" O THR G 42 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.266A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.541A pdb=" N ASN G 106 " --> pdb=" O ARG G 95 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N VAL G 104 " --> pdb=" O GLN G 97 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'I' and resid 82 through 86 removed outlier: 6.096A pdb=" N THR I 25 " --> pdb=" O GLY I 111 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY I 111 " --> pdb=" O THR I 25 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N ILE I 27 " --> pdb=" O LYS I 109 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'H' and resid 7 through 12 removed outlier: 3.961A pdb=" N VAL H 9 " --> pdb=" O ILE H 58 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ILE H 58 " --> pdb=" O VAL H 9 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU H 11 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL H 56 " --> pdb=" O LEU H 11 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N THR H 59 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR H 67 " --> pdb=" O THR H 59 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'L' and resid 53 through 58 removed outlier: 5.172A pdb=" N ASP L 20 " --> pdb=" O TYR L 141 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'L' and resid 75 through 79 removed outlier: 7.257A pdb=" N GLY L 84 " --> pdb=" O SER L 79 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'M' and resid 17 through 21 removed outlier: 6.383A pdb=" N ARG M 17 " --> pdb=" O VAL M 10 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N VAL M 19 " --> pdb=" O MET M 8 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER M 6 " --> pdb=" O THR M 21 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASN M 82 " --> pdb=" O ARG M 7 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'N' and resid 73 through 77 removed outlier: 4.661A pdb=" N GLY N 108 " --> pdb=" O GLU N 73 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'O' and resid 38 through 41 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'O' and resid 63 through 66 removed outlier: 4.112A pdb=" N PHE O 104 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LEU O 34 " --> pdb=" O PHE O 104 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU O 34 " --> pdb=" O MET O 103 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS O 101 " --> pdb=" O ALA O 36 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'O' and resid 31 through 37 removed outlier: 7.574A pdb=" N GLU O 31 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N LYS O 128 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'P' and resid 29 through 33 removed outlier: 3.509A pdb=" N ILE P 30 " --> pdb=" O ILE P 132 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE P 132 " --> pdb=" O ILE P 30 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR P 32 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ARG P 122 " --> pdb=" O GLY P 126 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N GLY P 120 " --> pdb=" O PRO P 128 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL P 130 " --> pdb=" O LYS P 118 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LYS P 118 " --> pdb=" O VAL P 130 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILE P 132 " --> pdb=" O ILE P 116 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ILE P 116 " --> pdb=" O ILE P 132 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU P 134 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N THR P 114 " --> pdb=" O LEU P 134 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'P' and resid 72 through 76 removed outlier: 3.715A pdb=" N GLU P 72 " --> pdb=" O VAL P 92 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N LYS P 88 " --> pdb=" O VAL P 76 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'Q' and resid 29 through 35 removed outlier: 3.984A pdb=" N ALA Q 54 " --> pdb=" O VAL Q 44 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 38 through 45 removed outlier: 6.916A pdb=" N THR R 25 " --> pdb=" O ILE R 87 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS R 83 " --> pdb=" O HIS R 29 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'R' and resid 49 through 53 removed outlier: 3.959A pdb=" N LYS R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ALA R 53 " --> pdb=" O SER R 56 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER R 56 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLU R 57 " --> pdb=" O VAL R 76 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.685A pdb=" N TYR T 2 " --> pdb=" O GLY T 42 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE T 40 " --> pdb=" O ILE T 4 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL T 41 " --> pdb=" O ALA T 46 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N ALA T 46 " --> pdb=" O VAL T 41 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N GLY T 43 " --> pdb=" O ASP T 44 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'T' and resid 18 through 23 removed outlier: 4.630A pdb=" N GLN T 18 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LYS T 94 " --> pdb=" O GLU T 63 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N THR T 59 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N ASP T 31 " --> pdb=" O VAL T 62 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 64 through 67 removed outlier: 3.902A pdb=" N LYS T 64 " --> pdb=" O LYS T 94 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 70 through 77 removed outlier: 3.711A pdb=" N HIS T 88 " --> pdb=" O LEU T 71 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR T 82 " --> pdb=" O LYS T 77 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'U' and resid 7 through 13 removed outlier: 4.916A pdb=" N THR U 105 " --> pdb=" O GLY U 84 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLY U 84 " --> pdb=" O THR U 105 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU U 78 " --> pdb=" O VAL U 111 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 86 through 93 removed outlier: 4.279A pdb=" N ARG U 97 " --> pdb=" O ARG U 93 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'V' and resid 23 through 28 removed outlier: 6.360A pdb=" N LYS V 23 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS V 61 " --> pdb=" O THR V 72 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS V 74 " --> pdb=" O LYS V 59 " (cutoff:3.500A) removed outlier: 7.170A pdb=" N LYS V 59 " --> pdb=" O LYS V 74 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG V 76 " --> pdb=" O ASN V 57 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN V 57 " --> pdb=" O ARG V 76 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ALA V 78 " --> pdb=" O VAL V 55 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL V 55 " --> pdb=" O ALA V 78 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VAL V 80 " --> pdb=" O VAL V 53 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N VAL V 53 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'W' and resid 25 through 28 removed outlier: 3.620A pdb=" N ALA W 25 " --> pdb=" O LEU W 34 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'W' and resid 39 through 44 removed outlier: 5.454A pdb=" N ASN W 39 " --> pdb=" O ALA W 61 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Y' and resid 37 through 40 removed outlier: 4.350A pdb=" N GLN Y 37 " --> pdb=" O VAL Y 75 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Z' and resid 11 through 19 No H-bonds generated for sheet with id= 66 Processing sheet with id= 67, first strand: chain '2' and resid 32 through 38 removed outlier: 4.135A pdb=" N SER 2 33 " --> pdb=" O LEU 2 8 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N LEU 2 53 " --> pdb=" O LYS 2 9 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 22 through 25 removed outlier: 4.634A pdb=" N GLU 3 33 " --> pdb=" O LEU 3 45 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '4' and resid 27 through 30 removed outlier: 4.204A pdb=" N GLU 4 35 " --> pdb=" O CYS 4 30 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '5' and resid 2 through 7 removed outlier: 3.755A pdb=" N TYR 5 17 " --> pdb=" O LEU 5 7 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '5' and resid 30 through 34 removed outlier: 6.137A pdb=" N ILE 5 30 " --> pdb=" O GLU 5 47 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain '8' and resid 1 through 4 removed outlier: 6.174A pdb=" N HIS 8 32 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 32 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N VAL 8 23 " --> pdb=" O GLN 8 36 " (cutoff:3.500A) 1618 hydrogen bonds defined for protein. 4782 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3890 hydrogen bonds 6232 hydrogen bond angles 0 basepair planarities 1547 basepair parallelities 2466 stacking parallelities Total time for adding SS restraints: 298.07 Time building geometry restraints manager: 60.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 18422 1.33 - 1.45: 68561 1.45 - 1.58: 57221 1.58 - 1.70: 9225 1.70 - 1.83: 204 Bond restraints: 153633 Sorted by residual: bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.58e+02 bond pdb=" N1 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.635 1.338 0.297 2.00e-02 2.50e+03 2.21e+02 bond pdb=" C2' GCP v 503 " pdb=" C3' GCP v 503 " ideal model delta sigma weight residual 1.241 1.511 -0.270 2.00e-02 2.50e+03 1.82e+02 bond pdb=" C5 5MU x 54 " pdb=" C6 5MU x 54 " ideal model delta sigma weight residual 1.155 1.384 -0.229 2.00e-02 2.50e+03 1.31e+02 bond pdb=" C13 MIA x 37 " pdb=" C14 MIA x 37 " ideal model delta sigma weight residual 1.317 1.523 -0.206 2.00e-02 2.50e+03 1.07e+02 ... (remaining 153628 not shown) Histogram of bond angle deviations from ideal: 96.65 - 105.21: 21596 105.21 - 113.78: 100794 113.78 - 122.35: 77469 122.35 - 130.91: 29407 130.91 - 139.48: 1443 Bond angle restraints: 230709 Sorted by residual: angle pdb=" CA PRO b 130 " pdb=" N PRO b 130 " pdb=" CD PRO b 130 " ideal model delta sigma weight residual 112.00 100.75 11.25 1.40e+00 5.10e-01 6.46e+01 angle pdb=" O3' A a 756 " pdb=" C3' A a 756 " pdb=" C2' A a 756 " ideal model delta sigma weight residual 109.50 121.41 -11.91 1.50e+00 4.44e-01 6.30e+01 angle pdb=" C1' GCP v 503 " pdb=" N9 GCP v 503 " pdb=" C4 GCP v 503 " ideal model delta sigma weight residual 108.44 125.48 -17.04 3.00e+00 1.11e-01 3.23e+01 angle pdb=" C6 5MU x 54 " pdb=" C5 5MU x 54 " pdb=" C5M 5MU x 54 " ideal model delta sigma weight residual 106.09 120.69 -14.60 3.00e+00 1.11e-01 2.37e+01 angle pdb=" C3' 4SU x 8 " pdb=" C2' 4SU x 8 " pdb=" C1' 4SU x 8 " ideal model delta sigma weight residual 101.30 105.93 -4.63 1.00e+00 1.00e+00 2.14e+01 ... (remaining 230704 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 86930 35.93 - 71.86: 9674 71.86 - 107.80: 1152 107.80 - 143.73: 32 143.73 - 179.66: 34 Dihedral angle restraints: 97822 sinusoidal: 80914 harmonic: 16908 Sorted by residual: dihedral pdb=" O4' U A2339 " pdb=" C1' U A2339 " pdb=" N1 U A2339 " pdb=" C2 U A2339 " ideal model delta sinusoidal sigma weight residual -160.00 16.94 -176.94 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a 929 " pdb=" C1' U a 929 " pdb=" N1 U a 929 " pdb=" C2 U a 929 " ideal model delta sinusoidal sigma weight residual 200.00 37.39 162.61 1 1.50e+01 4.44e-03 8.34e+01 dihedral pdb=" O4' C A1904 " pdb=" C1' C A1904 " pdb=" N1 C A1904 " pdb=" C2 C A1904 " ideal model delta sinusoidal sigma weight residual -160.00 -16.30 -143.70 1 1.50e+01 4.44e-03 7.71e+01 ... (remaining 97819 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 28424 0.087 - 0.173: 1289 0.173 - 0.260: 80 0.260 - 0.346: 7 0.346 - 0.433: 2 Chirality restraints: 29802 Sorted by residual: chirality pdb=" C3' A a 756 " pdb=" C4' A a 756 " pdb=" O3' A a 756 " pdb=" C2' A a 756 " both_signs ideal model delta sigma weight residual False -2.74 -2.31 -0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" C1' G a1012 " pdb=" O4' G a1012 " pdb=" C2' G a1012 " pdb=" N9 G a1012 " both_signs ideal model delta sigma weight residual False 2.46 2.07 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" C3' A A2472 " pdb=" C4' A A2472 " pdb=" O3' A A2472 " pdb=" C2' A A2472 " both_signs ideal model delta sigma weight residual False -2.74 -2.40 -0.35 2.00e-01 2.50e+01 3.00e+00 ... (remaining 29799 not shown) Planarity restraints: 12169 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU x 54 " 0.031 2.00e-02 2.50e+03 5.67e-01 7.22e+03 pdb=" C4' 5MU x 54 " 0.434 2.00e-02 2.50e+03 pdb=" O4' 5MU x 54 " 0.624 2.00e-02 2.50e+03 pdb=" C3' 5MU x 54 " -0.588 2.00e-02 2.50e+03 pdb=" O3' 5MU x 54 " -0.563 2.00e-02 2.50e+03 pdb=" C2' 5MU x 54 " -0.213 2.00e-02 2.50e+03 pdb=" O2' 5MU x 54 " 0.902 2.00e-02 2.50e+03 pdb=" C1' 5MU x 54 " 0.230 2.00e-02 2.50e+03 pdb=" N1 5MU x 54 " -0.857 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GCP v 503 " 0.365 2.00e-02 2.50e+03 4.09e-01 3.76e+03 pdb=" C2' GCP v 503 " -0.448 2.00e-02 2.50e+03 pdb=" C3' GCP v 503 " -0.445 2.00e-02 2.50e+03 pdb=" C4' GCP v 503 " 0.364 2.00e-02 2.50e+03 pdb=" C5' GCP v 503 " -0.420 2.00e-02 2.50e+03 pdb=" N9 GCP v 503 " -0.423 2.00e-02 2.50e+03 pdb=" O2' GCP v 503 " 0.182 2.00e-02 2.50e+03 pdb=" O3' GCP v 503 " 0.174 2.00e-02 2.50e+03 pdb=" O4' GCP v 503 " 0.649 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 MIA x 37 " -0.091 2.00e-02 2.50e+03 1.94e-01 4.73e+02 pdb=" C13 MIA x 37 " 0.235 2.00e-02 2.50e+03 pdb=" C14 MIA x 37 " -0.323 2.00e-02 2.50e+03 pdb=" C15 MIA x 37 " 0.040 2.00e-02 2.50e+03 pdb=" C16 MIA x 37 " 0.140 2.00e-02 2.50e+03 ... (remaining 12166 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 685 2.42 - 3.04: 76141 3.04 - 3.66: 241711 3.66 - 4.28: 385419 4.28 - 4.90: 539466 Nonbonded interactions: 1243422 Sorted by model distance: nonbonded pdb=" OP2 A A 621 " pdb="MG MG A3218 " model vdw 1.798 2.170 nonbonded pdb=" OP1 G a 392 " pdb="MG MG a3121 " model vdw 1.853 2.170 nonbonded pdb=" OP1 C A1389 " pdb="MG MG A3243 " model vdw 1.856 2.170 nonbonded pdb=" OG SER v 207 " pdb="MG MG v 502 " model vdw 1.862 2.170 nonbonded pdb=" N7 G A2535 " pdb="MG MG A3234 " model vdw 1.895 2.250 ... (remaining 1243417 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 30.770 Check model and map are aligned: 1.520 Set scattering table: 0.930 Process input model: 597.340 Find NCS groups from input model: 2.880 Set up NCS constraints: 0.380 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: 0.030 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 645.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 153633 Z= 0.325 Angle : 0.616 17.045 230709 Z= 0.324 Chirality : 0.038 0.433 29802 Planarity : 0.008 0.567 12169 Dihedral : 22.811 179.661 86918 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.03 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.80 (0.11), residues: 5827 helix: -0.41 (0.13), residues: 1727 sheet: -1.20 (0.15), residues: 1134 loop : -1.64 (0.11), residues: 2966 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.002 TRP b 23 HIS 0.011 0.001 HIS k 118 PHE 0.015 0.001 PHE O 13 TYR 0.023 0.002 TYR b 198 ARG 0.010 0.001 ARG r 46 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 954 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 954 time to evaluate : 5.891 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 111 ILE cc_start: 0.8407 (pt) cc_final: 0.8033 (mm) REVERT: k 38 HIS cc_start: 0.6818 (p90) cc_final: 0.6528 (p-80) REVERT: k 127 ARG cc_start: 0.8638 (mtm180) cc_final: 0.8421 (mtm180) REVERT: v 66 MET cc_start: 0.8460 (ppp) cc_final: 0.8228 (tmm) REVERT: F 92 ARG cc_start: 0.7969 (ttm-80) cc_final: 0.7423 (ttm110) REVERT: F 152 MET cc_start: 0.7133 (mmm) cc_final: 0.6905 (mmm) REVERT: G 144 LEU cc_start: 0.8753 (tp) cc_final: 0.8520 (tp) REVERT: L 97 ASN cc_start: 0.8572 (m110) cc_final: 0.8280 (m-40) REVERT: O 16 ASN cc_start: 0.8950 (p0) cc_final: 0.8633 (p0) REVERT: Q 9 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8591 (mmtm) REVERT: R 66 ASN cc_start: 0.9065 (m110) cc_final: 0.8814 (m110) REVERT: S 102 ASP cc_start: 0.8722 (t70) cc_final: 0.8447 (t0) REVERT: V 21 ASP cc_start: 0.7957 (p0) cc_final: 0.7677 (p0) REVERT: Y 61 ARG cc_start: 0.8363 (ptm160) cc_final: 0.7907 (ttt180) REVERT: 1 44 ARG cc_start: 0.8462 (ttm-80) cc_final: 0.8257 (ttm-80) REVERT: 2 55 ASP cc_start: 0.7451 (m-30) cc_final: 0.7213 (m-30) outliers start: 0 outliers final: 0 residues processed: 954 average time/residue: 1.2801 time to fit residues: 2089.5061 Evaluate side-chains 824 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 824 time to evaluate : 5.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 869 optimal weight: 4.9990 chunk 780 optimal weight: 6.9990 chunk 433 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 526 optimal weight: 40.0000 chunk 417 optimal weight: 10.0000 chunk 807 optimal weight: 5.9990 chunk 312 optimal weight: 7.9990 chunk 490 optimal weight: 10.0000 chunk 600 optimal weight: 20.0000 chunk 935 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: d 70 ASN d 79 GLN d 85 ASN d 112 GLN ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 177 ASN e 84 HIS e 132 ASN f 14 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 126 GLN k 75 GLN l 25 ASN l 59 ASN o 9 ASN o 18 HIS o 40 ASN o 65 ASN r 24 HIS r 56 GLN t 24 GLN v 82 GLN v 117 GLN v 224 GLN v 264 HIS v 382 ASN C 114 GLN D 32 GLN ** D 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 152 ASN E 46 GLN E 119 ASN E 171 GLN F 172 GLN G 99 GLN G 147 ASN N 27 ASN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Q 58 ASN Q 102 HIS R 2 ASN S 37 GLN S 81 HIS T 81 ASN W 67 ASN Y 20 ASN Y 58 ASN Z 16 ASN Z 23 ASN 2 19 GLN 2 40 ASN 7 26 HIS 7 35 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.123 153633 Z= 0.463 Angle : 0.812 26.072 230709 Z= 0.413 Chirality : 0.046 0.448 29802 Planarity : 0.006 0.126 12169 Dihedral : 23.214 179.896 78091 Min Nonbonded Distance : 1.638 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.88 % Favored : 91.97 % Rotamer: Outliers : 2.62 % Allowed : 13.16 % Favored : 84.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -2.02 (0.10), residues: 5827 helix: -0.47 (0.12), residues: 1816 sheet: -1.33 (0.15), residues: 1110 loop : -1.90 (0.11), residues: 2901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP b 23 HIS 0.015 0.002 HIS k 118 PHE 0.021 0.002 PHE f 27 TYR 0.024 0.002 TYR r 55 ARG 0.009 0.001 ARG v 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 848 time to evaluate : 5.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 139 LYS cc_start: 0.7953 (ttmt) cc_final: 0.7733 (ttmt) REVERT: h 34 LYS cc_start: 0.8599 (mttt) cc_final: 0.8310 (mttm) REVERT: l 107 ARG cc_start: 0.7626 (ptm160) cc_final: 0.7310 (ptm160) REVERT: o 16 ARG cc_start: 0.8408 (ptp90) cc_final: 0.7864 (ptp90) REVERT: o 44 ARG cc_start: 0.7510 (mtm180) cc_final: 0.7253 (mtm110) REVERT: o 59 MET cc_start: 0.8548 (mtm) cc_final: 0.8124 (ttm) REVERT: t 25 ARG cc_start: 0.8894 (mtm110) cc_final: 0.8683 (ttm110) REVERT: v 66 MET cc_start: 0.8525 (ppp) cc_final: 0.8132 (tmm) REVERT: F 88 LYS cc_start: 0.8155 (mmtt) cc_final: 0.7952 (mmtp) REVERT: F 92 ARG cc_start: 0.7965 (ttm-80) cc_final: 0.7584 (ttm110) REVERT: F 133 ARG cc_start: 0.6277 (mmp-170) cc_final: 0.5888 (mmp-170) REVERT: F 134 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5921 (tm-30) REVERT: F 136 LEU cc_start: 0.6485 (OUTLIER) cc_final: 0.5992 (mt) REVERT: G 62 ARG cc_start: 0.8177 (mtm-85) cc_final: 0.7971 (mtm-85) REVERT: L 97 ASN cc_start: 0.8563 (m110) cc_final: 0.8273 (m-40) REVERT: O 16 ASN cc_start: 0.8985 (p0) cc_final: 0.8741 (p0) REVERT: P 131 ILE cc_start: 0.9033 (mm) cc_final: 0.8817 (mm) REVERT: Q 9 LYS cc_start: 0.8877 (mmtp) cc_final: 0.8534 (mmtm) REVERT: R 66 ASN cc_start: 0.9070 (m110) cc_final: 0.8717 (m110) REVERT: S 49 ASP cc_start: 0.8846 (m-30) cc_final: 0.8532 (m-30) REVERT: S 102 ASP cc_start: 0.8305 (t70) cc_final: 0.7901 (t70) REVERT: U 42 LYS cc_start: 0.9294 (tttt) cc_final: 0.9076 (tttt) REVERT: 1 44 ARG cc_start: 0.8163 (ttm-80) cc_final: 0.7909 (ttm-80) outliers start: 98 outliers final: 58 residues processed: 901 average time/residue: 1.3007 time to fit residues: 2003.1293 Evaluate side-chains 854 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 795 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 85 ILE Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 51 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 64 SER Chi-restraints excluded: chain r residue 24 HIS Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 136 LEU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain S residue 108 THR Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 22 ASP Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 519 optimal weight: 10.0000 chunk 290 optimal weight: 40.0000 chunk 778 optimal weight: 0.0030 chunk 636 optimal weight: 10.0000 chunk 258 optimal weight: 3.9990 chunk 937 optimal weight: 5.9990 chunk 1012 optimal weight: 8.9990 chunk 834 optimal weight: 9.9990 chunk 929 optimal weight: 0.8980 chunk 319 optimal weight: 10.0000 chunk 751 optimal weight: 4.9990 overall best weight: 3.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 177 ASN h 16 ASN ** k 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 70 ASN D 33 ASN E 171 GLN F 172 GLN G 99 GLN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN ** 4 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 153633 Z= 0.210 Angle : 0.595 17.320 230709 Z= 0.310 Chirality : 0.037 0.359 29802 Planarity : 0.005 0.121 12169 Dihedral : 23.063 179.773 78091 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.30 % Favored : 93.55 % Rotamer: Outliers : 2.86 % Allowed : 16.82 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.51 (0.11), residues: 5827 helix: 0.19 (0.12), residues: 1813 sheet: -1.11 (0.15), residues: 1123 loop : -1.73 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 23 HIS 0.010 0.001 HIS k 118 PHE 0.025 0.001 PHE d 160 TYR 0.017 0.001 TYR r 55 ARG 0.007 0.000 ARG 1 58 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 925 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 818 time to evaluate : 5.847 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 32 PHE cc_start: 0.8176 (t80) cc_final: 0.7969 (t80) REVERT: b 139 LYS cc_start: 0.7973 (ttmt) cc_final: 0.7719 (ttmt) REVERT: b 167 ARG cc_start: 0.8422 (ttt-90) cc_final: 0.7985 (ttt-90) REVERT: e 146 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8137 (mtmm) REVERT: h 25 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8490 (mp) REVERT: k 65 MET cc_start: 0.8671 (mpp) cc_final: 0.8416 (mpp) REVERT: l 63 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.6955 (mtt90) REVERT: l 107 ARG cc_start: 0.7628 (ptm160) cc_final: 0.7426 (ptm160) REVERT: o 16 ARG cc_start: 0.8259 (ptp90) cc_final: 0.7791 (ptp90) REVERT: o 59 MET cc_start: 0.8396 (mtm) cc_final: 0.8047 (ttm) REVERT: t 25 ARG cc_start: 0.8859 (mtm110) cc_final: 0.8639 (ttm110) REVERT: v 66 MET cc_start: 0.8504 (ppp) cc_final: 0.8153 (tmm) REVERT: C 247 MET cc_start: 0.8520 (mmm) cc_final: 0.8256 (mmt) REVERT: E 200 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7433 (mp0) REVERT: F 88 LYS cc_start: 0.8144 (mmtt) cc_final: 0.7807 (mmtt) REVERT: F 92 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7373 (ttm110) REVERT: F 133 ARG cc_start: 0.6276 (mmp-170) cc_final: 0.5962 (mmp-170) REVERT: F 165 GLU cc_start: 0.8201 (pm20) cc_final: 0.7920 (pm20) REVERT: L 97 ASN cc_start: 0.8550 (m110) cc_final: 0.8332 (m-40) REVERT: O 16 ASN cc_start: 0.8957 (p0) cc_final: 0.8699 (p0) REVERT: Q 9 LYS cc_start: 0.8889 (mmtp) cc_final: 0.8586 (mmtm) REVERT: R 66 ASN cc_start: 0.9061 (m110) cc_final: 0.8785 (m110) REVERT: S 49 ASP cc_start: 0.8698 (m-30) cc_final: 0.8403 (m-30) REVERT: S 102 ASP cc_start: 0.8299 (t70) cc_final: 0.7932 (t70) REVERT: U 42 LYS cc_start: 0.9321 (tttt) cc_final: 0.9101 (tttt) REVERT: 1 44 ARG cc_start: 0.8150 (ttm-80) cc_final: 0.7889 (ttm-80) REVERT: 2 10 ARG cc_start: 0.8105 (mmm160) cc_final: 0.7845 (mmt180) REVERT: 8 35 LYS cc_start: 0.8682 (ttmm) cc_final: 0.8277 (ttpt) outliers start: 107 outliers final: 62 residues processed: 876 average time/residue: 1.2566 time to fit residues: 1898.5328 Evaluate side-chains 860 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 794 time to evaluate : 5.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 85 ILE Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 198 TYR Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain q residue 9 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 64 SER Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 79 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain O residue 106 ILE Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 925 optimal weight: 4.9990 chunk 704 optimal weight: 20.0000 chunk 486 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 447 optimal weight: 10.0000 chunk 629 optimal weight: 50.0000 chunk 940 optimal weight: 2.9990 chunk 995 optimal weight: 6.9990 chunk 491 optimal weight: 10.0000 chunk 891 optimal weight: 8.9990 chunk 268 optimal weight: 0.0670 overall best weight: 4.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS k 38 HIS l 5 ASN o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 171 GLN F 172 GLN ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 153633 Z= 0.310 Angle : 0.665 17.429 230709 Z= 0.344 Chirality : 0.040 0.362 29802 Planarity : 0.005 0.116 12169 Dihedral : 23.090 179.601 78091 Min Nonbonded Distance : 1.722 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.00 % Favored : 91.85 % Rotamer: Outliers : 3.66 % Allowed : 18.80 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.49 (0.11), residues: 5827 helix: 0.28 (0.12), residues: 1799 sheet: -1.06 (0.15), residues: 1098 loop : -1.78 (0.11), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP b 23 HIS 0.015 0.001 HIS e 89 PHE 0.026 0.002 PHE d 160 TYR 0.025 0.002 TYR v 125 ARG 0.009 0.001 ARG h 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 944 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 807 time to evaluate : 6.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 32 PHE cc_start: 0.8204 (t80) cc_final: 0.7982 (t80) REVERT: b 120 MET cc_start: 0.6903 (ptp) cc_final: 0.6631 (ptp) REVERT: e 146 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8100 (mtmm) REVERT: f 40 GLU cc_start: 0.5893 (OUTLIER) cc_final: 0.5588 (pm20) REVERT: k 119 ASN cc_start: 0.7116 (m110) cc_final: 0.6886 (m110) REVERT: l 63 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7299 (mtt90) REVERT: l 107 ARG cc_start: 0.7637 (ptm160) cc_final: 0.7343 (ptm160) REVERT: o 59 MET cc_start: 0.8409 (mtm) cc_final: 0.8100 (ttm) REVERT: q 17 ASP cc_start: 0.7667 (t0) cc_final: 0.7391 (t0) REVERT: v 66 MET cc_start: 0.8526 (ppp) cc_final: 0.8137 (tmm) REVERT: E 82 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8475 (pt0) REVERT: E 126 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8156 (tt) REVERT: E 200 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7397 (mp0) REVERT: F 67 ILE cc_start: 0.8718 (mp) cc_final: 0.8491 (mm) REVERT: F 78 ARG cc_start: 0.7513 (pmt-80) cc_final: 0.7038 (pmt-80) REVERT: F 88 LYS cc_start: 0.8402 (mmtt) cc_final: 0.8014 (mttt) REVERT: F 92 ARG cc_start: 0.7940 (ttm-80) cc_final: 0.7519 (ttm110) REVERT: F 117 VAL cc_start: 0.7186 (m) cc_final: 0.6912 (p) REVERT: L 109 MET cc_start: 0.8770 (mtt) cc_final: 0.8308 (mtt) REVERT: N 105 GLU cc_start: 0.7680 (tm-30) cc_final: 0.7430 (tm-30) REVERT: O 16 ASN cc_start: 0.8977 (p0) cc_final: 0.8760 (p0) REVERT: Q 9 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8600 (mmtm) REVERT: R 66 ASN cc_start: 0.9059 (m110) cc_final: 0.8771 (m110) REVERT: S 49 ASP cc_start: 0.8755 (m-30) cc_final: 0.8443 (m-30) REVERT: S 102 ASP cc_start: 0.8425 (t70) cc_final: 0.8079 (t70) REVERT: W 40 MET cc_start: 0.9253 (mmm) cc_final: 0.9048 (mmm) REVERT: 1 44 ARG cc_start: 0.8239 (ttm-80) cc_final: 0.7979 (ttm-80) outliers start: 137 outliers final: 98 residues processed: 879 average time/residue: 1.2247 time to fit residues: 1848.8902 Evaluate side-chains 887 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 783 time to evaluate : 5.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 171 THR Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain v residue 191 ASN Chi-restraints excluded: chain v residue 300 THR Chi-restraints excluded: chain v residue 337 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain P residue 31 GLU Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 22 ASP Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 4 residue 22 LEU Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 8 GLU Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 829 optimal weight: 30.0000 chunk 565 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 741 optimal weight: 7.9990 chunk 410 optimal weight: 7.9990 chunk 849 optimal weight: 4.9990 chunk 688 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 508 optimal weight: 10.0000 chunk 893 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 62 HIS i 126 GLN l 5 ASN o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 153633 Z= 0.420 Angle : 0.728 16.671 230709 Z= 0.374 Chirality : 0.044 0.390 29802 Planarity : 0.006 0.119 12169 Dihedral : 23.156 179.904 78091 Min Nonbonded Distance : 1.712 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.98 % Favored : 91.87 % Rotamer: Outliers : 4.59 % Allowed : 20.16 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.70 (0.11), residues: 5827 helix: 0.07 (0.12), residues: 1807 sheet: -1.09 (0.16), residues: 1102 loop : -1.94 (0.11), residues: 2918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP b 96 HIS 0.019 0.002 HIS e 89 PHE 0.030 0.002 PHE d 160 TYR 0.028 0.002 TYR v 125 ARG 0.012 0.001 ARG v 70 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 966 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 794 time to evaluate : 5.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 167 ARG cc_start: 0.8618 (ttt-90) cc_final: 0.8127 (ttt-90) REVERT: d 127 ASP cc_start: 0.7235 (m-30) cc_final: 0.6969 (t0) REVERT: e 146 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8091 (mtmm) REVERT: f 40 GLU cc_start: 0.5839 (OUTLIER) cc_final: 0.5363 (pm20) REVERT: h 25 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8564 (mp) REVERT: l 21 SER cc_start: 0.8202 (OUTLIER) cc_final: 0.7752 (p) REVERT: l 63 ARG cc_start: 0.8316 (OUTLIER) cc_final: 0.6831 (mtt90) REVERT: l 107 ARG cc_start: 0.7708 (ptm160) cc_final: 0.7459 (ptm160) REVERT: o 16 ARG cc_start: 0.8386 (ptp90) cc_final: 0.7871 (ptp90) REVERT: o 72 LYS cc_start: 0.8234 (tptp) cc_final: 0.7853 (mtpt) REVERT: q 17 ASP cc_start: 0.7683 (t0) cc_final: 0.7427 (t0) REVERT: t 25 ARG cc_start: 0.8920 (mtm110) cc_final: 0.8702 (ttm110) REVERT: v 66 MET cc_start: 0.8541 (ppp) cc_final: 0.8003 (tmm) REVERT: v 289 TYR cc_start: 0.7875 (OUTLIER) cc_final: 0.7455 (t80) REVERT: C 247 MET cc_start: 0.8536 (mmm) cc_final: 0.8249 (mmt) REVERT: E 82 GLN cc_start: 0.9405 (OUTLIER) cc_final: 0.8418 (pt0) REVERT: F 92 ARG cc_start: 0.7832 (ttm-80) cc_final: 0.7377 (ttm110) REVERT: F 133 ARG cc_start: 0.6439 (mmp-170) cc_final: 0.5781 (mmp-170) REVERT: F 165 GLU cc_start: 0.8234 (pm20) cc_final: 0.7930 (pm20) REVERT: O 16 ASN cc_start: 0.8967 (p0) cc_final: 0.8764 (p0) REVERT: Q 9 LYS cc_start: 0.8923 (mmtp) cc_final: 0.8616 (mmtm) REVERT: R 66 ASN cc_start: 0.9077 (m110) cc_final: 0.8759 (m110) REVERT: R 103 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8608 (mp) REVERT: S 102 ASP cc_start: 0.8407 (t70) cc_final: 0.7997 (t70) REVERT: W 40 MET cc_start: 0.9127 (mmm) cc_final: 0.8562 (mmm) REVERT: 1 9 LEU cc_start: 0.8685 (mt) cc_final: 0.8470 (mp) REVERT: 1 44 ARG cc_start: 0.8304 (ttm-80) cc_final: 0.8002 (ttm-80) REVERT: 7 21 LYS cc_start: 0.8743 (mtpt) cc_final: 0.8521 (mtpt) outliers start: 172 outliers final: 134 residues processed: 895 average time/residue: 1.2588 time to fit residues: 1944.1881 Evaluate side-chains 927 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 785 time to evaluate : 5.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 85 ILE Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 89 HIS Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain e residue 146 LYS Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 62 ASN Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 20 ASP Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 64 SER Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 149 ARG Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 235 LEU Chi-restraints excluded: chain v residue 289 TYR Chi-restraints excluded: chain v residue 298 MET Chi-restraints excluded: chain v residue 300 THR Chi-restraints excluded: chain v residue 337 THR Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 27 ASP Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 22 ASP Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 8 GLU Chi-restraints excluded: chain 5 residue 12 CYS Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 334 optimal weight: 5.9990 chunk 896 optimal weight: 2.9990 chunk 196 optimal weight: 2.9990 chunk 584 optimal weight: 10.0000 chunk 245 optimal weight: 40.0000 chunk 996 optimal weight: 3.9990 chunk 827 optimal weight: 7.9990 chunk 461 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 329 optimal weight: 3.9990 chunk 523 optimal weight: 40.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN o 18 HIS r 24 HIS t 24 GLN v 166 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 ASN P 75 GLN P 89 ASN 4 23 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 153633 Z= 0.257 Angle : 0.613 16.815 230709 Z= 0.319 Chirality : 0.038 0.351 29802 Planarity : 0.005 0.117 12169 Dihedral : 23.063 179.923 78091 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.33 % Favored : 92.52 % Rotamer: Outliers : 4.09 % Allowed : 21.39 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.44 (0.11), residues: 5827 helix: 0.37 (0.12), residues: 1826 sheet: -1.04 (0.15), residues: 1110 loop : -1.82 (0.11), residues: 2891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 132 HIS 0.034 0.001 HIS e 89 PHE 0.032 0.001 PHE e 90 TYR 0.021 0.001 TYR v 125 ARG 0.010 0.000 ARG r 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 965 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 812 time to evaluate : 5.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 127 ASP cc_start: 0.7207 (m-30) cc_final: 0.6971 (t0) REVERT: f 4 LYS cc_start: 0.8322 (mmmm) cc_final: 0.7936 (mmmm) REVERT: f 30 ILE cc_start: 0.8528 (mp) cc_final: 0.8321 (mp) REVERT: f 40 GLU cc_start: 0.5649 (OUTLIER) cc_final: 0.5338 (pm20) REVERT: h 25 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8536 (mp) REVERT: l 21 SER cc_start: 0.8200 (OUTLIER) cc_final: 0.7757 (p) REVERT: l 63 ARG cc_start: 0.8264 (OUTLIER) cc_final: 0.7151 (mtt90) REVERT: l 107 ARG cc_start: 0.7696 (ptm160) cc_final: 0.7452 (ptm160) REVERT: o 16 ARG cc_start: 0.8302 (ptp90) cc_final: 0.7792 (ptp90) REVERT: q 17 ASP cc_start: 0.7744 (t0) cc_final: 0.7448 (t0) REVERT: t 25 ARG cc_start: 0.8893 (mtm110) cc_final: 0.8664 (ttm110) REVERT: v 66 MET cc_start: 0.8510 (ppp) cc_final: 0.8038 (tmm) REVERT: v 149 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7094 (mtm180) REVERT: v 289 TYR cc_start: 0.7779 (OUTLIER) cc_final: 0.7323 (t80) REVERT: C 247 MET cc_start: 0.8556 (mmm) cc_final: 0.8254 (mmt) REVERT: E 82 GLN cc_start: 0.9369 (OUTLIER) cc_final: 0.8416 (pt0) REVERT: F 92 ARG cc_start: 0.7836 (ttm-80) cc_final: 0.7367 (ttm110) REVERT: F 133 ARG cc_start: 0.6375 (mmp-170) cc_final: 0.5746 (mmp-170) REVERT: F 165 GLU cc_start: 0.8210 (pm20) cc_final: 0.7888 (pm20) REVERT: L 109 MET cc_start: 0.8746 (mtt) cc_final: 0.8326 (mtt) REVERT: O 16 ASN cc_start: 0.8928 (p0) cc_final: 0.8726 (p0) REVERT: Q 9 LYS cc_start: 0.8916 (mmtp) cc_final: 0.8655 (mmtm) REVERT: R 103 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8600 (mp) REVERT: S 102 ASP cc_start: 0.8366 (t70) cc_final: 0.7974 (t70) REVERT: W 40 MET cc_start: 0.9202 (mmm) cc_final: 0.8898 (mmm) REVERT: 1 44 ARG cc_start: 0.8187 (ttm-80) cc_final: 0.7918 (ttm-80) REVERT: 5 31 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7954 (mt-10) REVERT: 5 46 ARG cc_start: 0.8348 (ptp90) cc_final: 0.8100 (ptp-110) outliers start: 153 outliers final: 118 residues processed: 894 average time/residue: 1.2673 time to fit residues: 1955.6789 Evaluate side-chains 924 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 797 time to evaluate : 5.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 85 ILE Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 38 HIS Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 9 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 24 HIS Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 149 ARG Chi-restraints excluded: chain v residue 191 ASN Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 235 LEU Chi-restraints excluded: chain v residue 278 ARG Chi-restraints excluded: chain v residue 289 TYR Chi-restraints excluded: chain v residue 298 MET Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 123 ILE Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 960 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 567 optimal weight: 10.0000 chunk 727 optimal weight: 0.0040 chunk 563 optimal weight: 10.0000 chunk 838 optimal weight: 50.0000 chunk 556 optimal weight: 20.0000 chunk 992 optimal weight: 3.9990 chunk 621 optimal weight: 10.0000 chunk 605 optimal weight: 20.0000 chunk 458 optimal weight: 10.0000 overall best weight: 5.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 89 HIS ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN o 18 HIS r 24 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 2 ASN F 172 GLN 4 23 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 153633 Z= 0.324 Angle : 0.656 16.693 230709 Z= 0.340 Chirality : 0.040 0.365 29802 Planarity : 0.005 0.117 12169 Dihedral : 23.076 179.834 78091 Min Nonbonded Distance : 1.756 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.93 % Favored : 91.90 % Rotamer: Outliers : 4.97 % Allowed : 21.20 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.47 (0.11), residues: 5827 helix: 0.36 (0.12), residues: 1812 sheet: -0.97 (0.15), residues: 1114 loop : -1.87 (0.11), residues: 2901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 132 HIS 0.042 0.002 HIS r 24 PHE 0.031 0.002 PHE d 160 TYR 0.023 0.002 TYR v 125 ARG 0.012 0.001 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 983 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 797 time to evaluate : 5.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 127 ASP cc_start: 0.7191 (m-30) cc_final: 0.6953 (t0) REVERT: f 4 LYS cc_start: 0.8361 (mmmm) cc_final: 0.7985 (mmmm) REVERT: f 30 ILE cc_start: 0.8550 (mp) cc_final: 0.8334 (mp) REVERT: f 40 GLU cc_start: 0.5753 (OUTLIER) cc_final: 0.5354 (pm20) REVERT: h 25 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8551 (mp) REVERT: l 21 SER cc_start: 0.8213 (OUTLIER) cc_final: 0.7757 (p) REVERT: l 63 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.6695 (mtt90) REVERT: l 107 ARG cc_start: 0.7702 (ptm160) cc_final: 0.7463 (ptm160) REVERT: o 16 ARG cc_start: 0.8310 (ptp90) cc_final: 0.7785 (ptp90) REVERT: o 72 LYS cc_start: 0.8248 (tptp) cc_final: 0.7833 (mtmt) REVERT: q 17 ASP cc_start: 0.7733 (t0) cc_final: 0.7441 (t0) REVERT: t 25 ARG cc_start: 0.8913 (mtm110) cc_final: 0.8684 (ttm110) REVERT: v 18 ASP cc_start: 0.8205 (OUTLIER) cc_final: 0.7526 (p0) REVERT: v 66 MET cc_start: 0.8499 (ppp) cc_final: 0.7993 (tmm) REVERT: v 149 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7178 (mtm180) REVERT: v 289 TYR cc_start: 0.7838 (OUTLIER) cc_final: 0.7365 (t80) REVERT: C 247 MET cc_start: 0.8570 (mmm) cc_final: 0.8265 (mmt) REVERT: E 82 GLN cc_start: 0.9391 (OUTLIER) cc_final: 0.8420 (pt0) REVERT: F 92 ARG cc_start: 0.7813 (ttm-80) cc_final: 0.7342 (ttm110) REVERT: F 133 ARG cc_start: 0.6347 (mmp-170) cc_final: 0.5797 (mmp-170) REVERT: F 165 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7879 (pm20) REVERT: L 109 MET cc_start: 0.8797 (mtt) cc_final: 0.8458 (mtt) REVERT: Q 9 LYS cc_start: 0.8920 (mmtp) cc_final: 0.8665 (mmtm) REVERT: R 103 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8578 (mp) REVERT: S 102 ASP cc_start: 0.8376 (t70) cc_final: 0.7994 (t70) REVERT: W 40 MET cc_start: 0.9195 (mmm) cc_final: 0.8753 (mmm) REVERT: 1 44 ARG cc_start: 0.8259 (ttm-80) cc_final: 0.7985 (ttm-80) REVERT: 5 31 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7923 (mt-10) REVERT: 5 46 ARG cc_start: 0.8325 (ptp90) cc_final: 0.8069 (ptp-110) outliers start: 186 outliers final: 158 residues processed: 902 average time/residue: 1.3705 time to fit residues: 2150.7314 Evaluate side-chains 958 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 789 time to evaluate : 5.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 111 ILE Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 89 HIS Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 78 ASP Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 25 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 38 HIS Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 9 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 43 ILE Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 149 ARG Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 176 MET Chi-restraints excluded: chain v residue 191 ASN Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 235 LEU Chi-restraints excluded: chain v residue 278 ARG Chi-restraints excluded: chain v residue 289 TYR Chi-restraints excluded: chain v residue 298 MET Chi-restraints excluded: chain v residue 300 THR Chi-restraints excluded: chain v residue 337 THR Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain v residue 351 LEU Chi-restraints excluded: chain v residue 403 VAL Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain F residue 172 GLN Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 27 ASP Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 8 GLU Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 614 optimal weight: 8.9990 chunk 396 optimal weight: 0.9980 chunk 592 optimal weight: 8.9990 chunk 299 optimal weight: 3.9990 chunk 195 optimal weight: 2.9990 chunk 192 optimal weight: 10.0000 chunk 631 optimal weight: 50.0000 chunk 676 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 780 optimal weight: 7.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 177 ASN e 89 HIS ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 172 GLN 4 23 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 153633 Z= 0.308 Angle : 0.638 16.681 230709 Z= 0.331 Chirality : 0.040 0.363 29802 Planarity : 0.005 0.117 12169 Dihedral : 23.055 179.982 78091 Min Nonbonded Distance : 1.767 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.59 % Favored : 92.28 % Rotamer: Outliers : 5.05 % Allowed : 21.52 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.42 (0.11), residues: 5827 helix: 0.42 (0.12), residues: 1815 sheet: -0.99 (0.16), residues: 1103 loop : -1.83 (0.11), residues: 2909 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 132 HIS 0.038 0.001 HIS e 89 PHE 0.031 0.002 PHE e 90 TYR 0.020 0.002 TYR v 125 ARG 0.012 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 989 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 800 time to evaluate : 5.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 125 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7307 (ptm160) REVERT: d 127 ASP cc_start: 0.7203 (m-30) cc_final: 0.6930 (t0) REVERT: d 191 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.7515 (pp20) REVERT: f 4 LYS cc_start: 0.8335 (mmmm) cc_final: 0.7982 (mmmm) REVERT: f 25 GLU cc_start: 0.7697 (OUTLIER) cc_final: 0.7406 (mp0) REVERT: f 30 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8444 (mp) REVERT: f 40 GLU cc_start: 0.5719 (OUTLIER) cc_final: 0.5331 (pm20) REVERT: h 25 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8543 (mp) REVERT: l 21 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7789 (p) REVERT: l 28 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8580 (tp) REVERT: l 63 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7304 (mtt90) REVERT: l 107 ARG cc_start: 0.7699 (ptm160) cc_final: 0.7468 (ptm160) REVERT: o 16 ARG cc_start: 0.8294 (ptp90) cc_final: 0.7936 (ptp90) REVERT: q 17 ASP cc_start: 0.7739 (t0) cc_final: 0.7435 (t0) REVERT: q 74 HIS cc_start: 0.8631 (OUTLIER) cc_final: 0.8120 (m-70) REVERT: t 25 ARG cc_start: 0.8903 (mtm110) cc_final: 0.8674 (ttm110) REVERT: v 66 MET cc_start: 0.8506 (ppp) cc_final: 0.7994 (tmm) REVERT: v 289 TYR cc_start: 0.7829 (OUTLIER) cc_final: 0.7350 (t80) REVERT: C 247 MET cc_start: 0.8568 (mmm) cc_final: 0.8265 (mmt) REVERT: E 74 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.7406 (ptp-170) REVERT: E 82 GLN cc_start: 0.9378 (OUTLIER) cc_final: 0.8413 (pt0) REVERT: F 92 ARG cc_start: 0.7825 (ttm-80) cc_final: 0.7355 (ttm110) REVERT: F 133 ARG cc_start: 0.6290 (mmp-170) cc_final: 0.5536 (mmp-170) REVERT: F 165 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: L 109 MET cc_start: 0.8815 (mtt) cc_final: 0.8457 (mtt) REVERT: Q 9 LYS cc_start: 0.8907 (mmtp) cc_final: 0.8654 (mmtm) REVERT: R 103 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8578 (mp) REVERT: S 102 ASP cc_start: 0.8382 (t70) cc_final: 0.7978 (t70) REVERT: W 40 MET cc_start: 0.9186 (mmm) cc_final: 0.8749 (mmm) REVERT: 1 29 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8220 (mmt180) REVERT: 1 44 ARG cc_start: 0.8226 (ttm-80) cc_final: 0.7953 (ttm-80) REVERT: 5 31 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7916 (mt-10) REVERT: 5 46 ARG cc_start: 0.8312 (ptp90) cc_final: 0.8053 (ptp-110) outliers start: 189 outliers final: 154 residues processed: 912 average time/residue: 1.3432 time to fit residues: 2135.3131 Evaluate side-chains 975 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 804 time to evaluate : 5.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 125 ARG Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 58 ASP Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 46 ILE Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 38 HIS Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 28 LEU Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain v residue 33 MET Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 176 MET Chi-restraints excluded: chain v residue 191 ASN Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 235 LEU Chi-restraints excluded: chain v residue 278 ARG Chi-restraints excluded: chain v residue 289 TYR Chi-restraints excluded: chain v residue 298 MET Chi-restraints excluded: chain v residue 300 THR Chi-restraints excluded: chain v residue 337 THR Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain v residue 403 VAL Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 17 THR Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain D residue 191 ASN Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 17 MET Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain T residue 59 THR Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Chi-restraints excluded: chain 7 residue 56 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 903 optimal weight: 0.9980 chunk 951 optimal weight: 0.0270 chunk 867 optimal weight: 8.9990 chunk 925 optimal weight: 7.9990 chunk 950 optimal weight: 0.8980 chunk 556 optimal weight: 20.0000 chunk 403 optimal weight: 3.9990 chunk 726 optimal weight: 7.9990 chunk 283 optimal weight: 8.9990 chunk 835 optimal weight: 10.0000 chunk 874 optimal weight: 10.0000 overall best weight: 2.7842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN 4 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.2907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 153633 Z= 0.186 Angle : 0.589 16.690 230709 Z= 0.309 Chirality : 0.036 0.362 29802 Planarity : 0.005 0.116 12169 Dihedral : 23.079 179.925 78091 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.33 % Favored : 92.53 % Rotamer: Outliers : 4.35 % Allowed : 22.38 % Favored : 73.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.31 (0.11), residues: 5827 helix: 0.52 (0.12), residues: 1828 sheet: -0.93 (0.16), residues: 1094 loop : -1.77 (0.11), residues: 2905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP h 132 HIS 0.008 0.001 HIS e 89 PHE 0.032 0.001 PHE d 160 TYR 0.021 0.001 TYR v 125 ARG 0.015 0.000 ARG F 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 804 time to evaluate : 5.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 191 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7491 (pp20) REVERT: f 25 GLU cc_start: 0.7775 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: f 30 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8404 (mp) REVERT: f 40 GLU cc_start: 0.5664 (OUTLIER) cc_final: 0.5309 (pm20) REVERT: h 25 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8540 (mp) REVERT: l 63 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7104 (mtt90) REVERT: l 107 ARG cc_start: 0.7685 (ptm160) cc_final: 0.7433 (ptm160) REVERT: o 16 ARG cc_start: 0.8253 (ptp90) cc_final: 0.7910 (ptp90) REVERT: o 72 LYS cc_start: 0.8132 (tptp) cc_final: 0.7741 (mtmt) REVERT: q 17 ASP cc_start: 0.7726 (t0) cc_final: 0.7420 (t0) REVERT: q 74 HIS cc_start: 0.8579 (OUTLIER) cc_final: 0.8171 (m-70) REVERT: v 18 ASP cc_start: 0.8133 (OUTLIER) cc_final: 0.7437 (p0) REVERT: v 66 MET cc_start: 0.8512 (ppp) cc_final: 0.8105 (tmm) REVERT: v 289 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7320 (t80) REVERT: C 247 MET cc_start: 0.8545 (mmm) cc_final: 0.8251 (mmt) REVERT: E 74 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.7375 (ptp-170) REVERT: E 82 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8441 (pt0) REVERT: F 92 ARG cc_start: 0.7864 (ttm-80) cc_final: 0.7393 (ttm110) REVERT: F 133 ARG cc_start: 0.6247 (mmp-170) cc_final: 0.5747 (mmp-170) REVERT: F 165 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7923 (pm20) REVERT: L 109 MET cc_start: 0.8814 (mtt) cc_final: 0.8469 (mtt) REVERT: Q 9 LYS cc_start: 0.8901 (mmtp) cc_final: 0.8651 (mmtm) REVERT: R 103 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8609 (mp) REVERT: S 102 ASP cc_start: 0.8331 (t70) cc_final: 0.7953 (t70) REVERT: W 40 MET cc_start: 0.9165 (mmm) cc_final: 0.8756 (mmm) REVERT: 1 44 ARG cc_start: 0.8201 (ttm-80) cc_final: 0.7937 (ttm-80) REVERT: 5 31 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7920 (mt-10) REVERT: 5 46 ARG cc_start: 0.8298 (ptp90) cc_final: 0.8016 (ptp-110) outliers start: 163 outliers final: 137 residues processed: 895 average time/residue: 1.2276 time to fit residues: 1896.3535 Evaluate side-chains 947 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 796 time to evaluate : 5.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 25 GLU Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 38 HIS Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 5 ASN Chi-restraints excluded: chain q residue 9 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 6 LEU Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 235 LEU Chi-restraints excluded: chain v residue 289 TYR Chi-restraints excluded: chain v residue 298 MET Chi-restraints excluded: chain v residue 337 THR Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain v residue 403 VAL Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 21 ASP Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain G residue 125 VAL Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 27 ASP Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 1 residue 6 ILE Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 19 THR Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 921 optimal weight: 8.9990 chunk 607 optimal weight: 10.0000 chunk 978 optimal weight: 8.9990 chunk 597 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 chunk 680 optimal weight: 10.0000 chunk 1026 optimal weight: 10.0000 chunk 944 optimal weight: 0.3980 chunk 817 optimal weight: 50.0000 chunk 84 optimal weight: 10.0000 chunk 631 optimal weight: 50.0000 overall best weight: 7.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 5 ASN o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 153633 Z= 0.468 Angle : 0.751 16.823 230709 Z= 0.383 Chirality : 0.045 0.396 29802 Planarity : 0.006 0.118 12169 Dihedral : 23.132 179.813 78091 Min Nonbonded Distance : 1.686 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.14 % Allowed : 9.08 % Favored : 90.78 % Rotamer: Outliers : 4.65 % Allowed : 22.00 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.95 % 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: -1.59 (0.11), residues: 5827 helix: 0.25 (0.12), residues: 1800 sheet: -1.04 (0.15), residues: 1123 loop : -1.93 (0.11), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP b 23 HIS 0.009 0.001 HIS k 118 PHE 0.031 0.002 PHE d 160 TYR 0.027 0.002 TYR r 55 ARG 0.014 0.001 ARG F 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11654 Ramachandran restraints generated. 5827 Oldfield, 0 Emsley, 5827 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 967 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 793 time to evaluate : 5.938 Fit side-chains revert: symmetry clash REVERT: b 116 LYS cc_start: 0.7241 (mmmt) cc_final: 0.7021 (mmmt) REVERT: d 125 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: d 191 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: f 30 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8513 (mp) REVERT: f 40 GLU cc_start: 0.5904 (OUTLIER) cc_final: 0.5406 (pm20) REVERT: h 25 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8582 (mp) REVERT: l 21 SER cc_start: 0.8251 (OUTLIER) cc_final: 0.7831 (p) REVERT: l 63 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.6822 (mtt90) REVERT: l 107 ARG cc_start: 0.7719 (ptm160) cc_final: 0.7500 (ptm160) REVERT: o 16 ARG cc_start: 0.8409 (ptp90) cc_final: 0.8032 (ptp90) REVERT: o 72 LYS cc_start: 0.8306 (tptp) cc_final: 0.7851 (mtmt) REVERT: q 17 ASP cc_start: 0.7863 (t0) cc_final: 0.7551 (t0) REVERT: q 74 HIS cc_start: 0.8686 (OUTLIER) cc_final: 0.8226 (m-70) REVERT: t 25 ARG cc_start: 0.8918 (mtm110) cc_final: 0.8703 (ttm110) REVERT: v 18 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7524 (p0) REVERT: v 66 MET cc_start: 0.8578 (ppp) cc_final: 0.8027 (tmm) REVERT: v 149 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7240 (mtm180) REVERT: v 289 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7465 (t80) REVERT: C 247 MET cc_start: 0.8587 (mmm) cc_final: 0.8271 (mmt) REVERT: E 74 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.7469 (ptp-170) REVERT: E 82 GLN cc_start: 0.9410 (OUTLIER) cc_final: 0.8477 (pt0) REVERT: E 200 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7365 (mp0) REVERT: F 92 ARG cc_start: 0.7844 (ttm-80) cc_final: 0.7406 (ttm110) REVERT: F 165 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7903 (pm20) REVERT: Q 9 LYS cc_start: 0.8925 (mmtp) cc_final: 0.8649 (mmtm) REVERT: R 103 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8600 (mp) REVERT: S 102 ASP cc_start: 0.8435 (t70) cc_final: 0.8063 (t70) REVERT: T 63 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7658 (mt-10) REVERT: W 40 MET cc_start: 0.9200 (mmm) cc_final: 0.8668 (mmm) REVERT: 1 29 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8269 (mmt180) REVERT: 1 44 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.7998 (ttm-80) REVERT: 5 31 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7957 (mt-10) REVERT: 5 46 ARG cc_start: 0.8328 (ptp90) cc_final: 0.8075 (ptp-110) outliers start: 174 outliers final: 144 residues processed: 898 average time/residue: 1.2689 time to fit residues: 1963.1250 Evaluate side-chains 950 residues out of total 4986 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 788 time to evaluate : 5.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 20 THR Chi-restraints excluded: chain b residue 46 THR Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 92 VAL Chi-restraints excluded: chain b residue 101 LEU Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 173 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 125 ARG Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain d residue 191 GLU Chi-restraints excluded: chain e residue 12 LEU Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 71 ASN Chi-restraints excluded: chain e residue 85 THR Chi-restraints excluded: chain e residue 96 LEU Chi-restraints excluded: chain e residue 115 VAL Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 128 SER Chi-restraints excluded: chain f residue 30 ILE Chi-restraints excluded: chain f residue 40 GLU Chi-restraints excluded: chain f residue 63 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 88 VAL Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 30 SER Chi-restraints excluded: chain h residue 50 GLU Chi-restraints excluded: chain h residue 71 GLU Chi-restraints excluded: chain h residue 87 VAL Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 105 ILE Chi-restraints excluded: chain h residue 131 VAL Chi-restraints excluded: chain k residue 20 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 37 THR Chi-restraints excluded: chain k residue 38 HIS Chi-restraints excluded: chain k residue 50 LEU Chi-restraints excluded: chain l residue 21 SER Chi-restraints excluded: chain l residue 39 ASN Chi-restraints excluded: chain l residue 63 ARG Chi-restraints excluded: chain l residue 95 ILE Chi-restraints excluded: chain l residue 110 ILE Chi-restraints excluded: chain l residue 125 GLN Chi-restraints excluded: chain o residue 7 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 4 LYS Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 36 THR Chi-restraints excluded: chain p residue 88 LEU Chi-restraints excluded: chain q residue 9 VAL Chi-restraints excluded: chain q residue 15 VAL Chi-restraints excluded: chain q residue 52 ASN Chi-restraints excluded: chain q residue 65 GLU Chi-restraints excluded: chain q residue 74 HIS Chi-restraints excluded: chain r residue 29 ASP Chi-restraints excluded: chain r residue 71 LEU Chi-restraints excluded: chain t residue 3 ASN Chi-restraints excluded: chain t residue 13 THR Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain v residue 18 ASP Chi-restraints excluded: chain v residue 58 ASP Chi-restraints excluded: chain v residue 68 ASP Chi-restraints excluded: chain v residue 79 SER Chi-restraints excluded: chain v residue 96 ASP Chi-restraints excluded: chain v residue 118 VAL Chi-restraints excluded: chain v residue 125 TYR Chi-restraints excluded: chain v residue 149 ARG Chi-restraints excluded: chain v residue 174 LEU Chi-restraints excluded: chain v residue 191 ASN Chi-restraints excluded: chain v residue 199 VAL Chi-restraints excluded: chain v residue 235 LEU Chi-restraints excluded: chain v residue 289 TYR Chi-restraints excluded: chain v residue 298 MET Chi-restraints excluded: chain v residue 300 THR Chi-restraints excluded: chain v residue 337 THR Chi-restraints excluded: chain v residue 339 ILE Chi-restraints excluded: chain v residue 403 VAL Chi-restraints excluded: chain v residue 408 LEU Chi-restraints excluded: chain C residue 88 SER Chi-restraints excluded: chain C residue 134 ASP Chi-restraints excluded: chain C residue 219 THR Chi-restraints excluded: chain D residue 5 ILE Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 114 SER Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 154 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 181 VAL Chi-restraints excluded: chain E residue 74 ARG Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 174 THR Chi-restraints excluded: chain E residue 181 ILE Chi-restraints excluded: chain E residue 200 GLU Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 153 ASP Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain F residue 169 LEU Chi-restraints excluded: chain G residue 25 THR Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 116 VAL Chi-restraints excluded: chain L residue 20 ASP Chi-restraints excluded: chain L residue 87 SER Chi-restraints excluded: chain L residue 105 SER Chi-restraints excluded: chain L residue 114 SER Chi-restraints excluded: chain M residue 32 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 89 THR Chi-restraints excluded: chain N residue 99 THR Chi-restraints excluded: chain N residue 105 GLU Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 40 SER Chi-restraints excluded: chain O residue 64 VAL Chi-restraints excluded: chain O residue 132 VAL Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain P residue 32 THR Chi-restraints excluded: chain P residue 43 VAL Chi-restraints excluded: chain P residue 66 ILE Chi-restraints excluded: chain P residue 71 VAL Chi-restraints excluded: chain Q residue 5 ILE Chi-restraints excluded: chain Q residue 39 ASN Chi-restraints excluded: chain Q residue 70 VAL Chi-restraints excluded: chain Q residue 90 THR Chi-restraints excluded: chain Q residue 93 THR Chi-restraints excluded: chain R residue 60 THR Chi-restraints excluded: chain R residue 102 ASN Chi-restraints excluded: chain R residue 103 LEU Chi-restraints excluded: chain T residue 1 MET Chi-restraints excluded: chain T residue 41 VAL Chi-restraints excluded: chain U residue 9 LYS Chi-restraints excluded: chain U residue 26 ILE Chi-restraints excluded: chain U residue 27 ASP Chi-restraints excluded: chain U residue 68 ASP Chi-restraints excluded: chain U residue 86 THR Chi-restraints excluded: chain V residue 12 VAL Chi-restraints excluded: chain V residue 62 LEU Chi-restraints excluded: chain V residue 81 THR Chi-restraints excluded: chain W residue 9 VAL Chi-restraints excluded: chain W residue 41 VAL Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain Y residue 39 VAL Chi-restraints excluded: chain Y residue 40 THR Chi-restraints excluded: chain Y residue 65 ASP Chi-restraints excluded: chain Y residue 72 ASP Chi-restraints excluded: chain Y residue 74 VAL Chi-restraints excluded: chain Z residue 24 SER Chi-restraints excluded: chain 1 residue 29 ARG Chi-restraints excluded: chain 2 residue 23 VAL Chi-restraints excluded: chain 5 residue 6 THR Chi-restraints excluded: chain 5 residue 8 GLU Chi-restraints excluded: chain 5 residue 20 THR Chi-restraints excluded: chain 5 residue 31 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1030 random chunks: chunk 501 optimal weight: 8.9990 chunk 649 optimal weight: 8.9990 chunk 870 optimal weight: 0.9980 chunk 250 optimal weight: 5.9990 chunk 753 optimal weight: 0.9990 chunk 120 optimal weight: 10.0000 chunk 227 optimal weight: 6.9990 chunk 818 optimal weight: 40.0000 chunk 342 optimal weight: 0.6980 chunk 840 optimal weight: 0.4980 chunk 103 optimal weight: 9.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 137 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN o 18 HIS t 24 GLN ** v 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 23 GLN ** 4 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.133552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.101519 restraints weight = 271586.815| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.09 r_work: 0.3256 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 153633 Z= 0.146 Angle : 0.566 16.847 230709 Z= 0.294 Chirality : 0.035 0.363 29802 Planarity : 0.004 0.116 12169 Dihedral : 23.013 179.640 78091 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.96 % Favored : 93.91 % Rotamer: Outliers : 2.94 % Allowed : 24.11 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.95 % Cis-general : 0.00 % Twisted Proline : 0.47 % 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: -1.18 (0.11), residues: 5827 helix: 0.68 (0.13), residues: 1821 sheet: -0.88 (0.16), residues: 1104 loop : -1.73 (0.11), residues: 2902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP k 44 HIS 0.004 0.001 HIS 5 45 PHE 0.030 0.001 PHE d 160 TYR 0.019 0.001 TYR 3 43 ARG 0.015 0.000 ARG F 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32570.39 seconds wall clock time: 569 minutes 36.84 seconds (34176.84 seconds total)