Starting phenix.real_space_refine on Thu Mar 21 12:48:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8syl_40882/03_2024/8syl_40882_updated.pdb" } resolution = 2.9 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= -0.001 sd= 0.027 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 2 6.06 5 P 4729 5.49 5 Mg 474 5.21 5 S 142 5.16 5 C 71970 2.51 5 N 26818 2.21 5 O 40456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 165": "OD1" <-> "OD2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c GLU 105": "OE1" <-> "OE2" Residue "c TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 65": "OE1" <-> "OE2" Residue "g PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 48": "OE1" <-> "OE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "h ASP 48": "OD1" <-> "OD2" Residue "l TYR 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "E ASP 116": "OD1" <-> "OD2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "E ASP 145": "OD1" <-> "OD2" Residue "E ASP 154": "OD1" <-> "OD2" Residue "F PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 137": "OD1" <-> "OD2" Residue "L TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L GLU 90": "OE1" <-> "OE2" Residue "L GLU 98": "OE1" <-> "OE2" Residue "M ASP 12": "OD1" <-> "OD2" Residue "M GLU 121": "OE1" <-> "OE2" Residue "O ASP 25": "OD1" <-> "OD2" Residue "O GLU 75": "OE1" <-> "OE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "Q ASP 2": "OD1" <-> "OD2" Residue "Q ASP 93": "OD1" <-> "OD2" Residue "U GLU 52": "OE1" <-> "OE2" Residue "U GLU 78": "OE1" <-> "OE2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "X TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 56": "OD1" <-> "OD2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "4 GLU 36": "OE1" <-> "OE2" Residue "4 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144591 Number of models: 1 Model: "" Number of chains: 76 Chain: "a" Number of atoms: 32803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32803 Classifications: {'RNA': 1528} Modifications used: {'rna2p': 1, 'rna2p_pur': 116, 'rna2p_pyr': 77, 'rna3p': 10, 'rna3p_pur': 750, 'rna3p_pyr': 574} Link IDs: {'rna2p': 194, 'rna3p': 1333} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "b" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1514 Classifications: {'peptide': 224} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 7, 'TRANS': 216} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 243 Unresolved non-hydrogen angles: 295 Unresolved non-hydrogen dihedrals: 196 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'GLN:plan1': 4, 'ASN:plan1': 3, 'ASP:plan': 11, 'PHE:plan': 2, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 132 Chain: "c" Number of atoms: 1613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1613 Classifications: {'peptide': 206} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 198} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "d" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "e" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1117 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 20 Chain: "f" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 778 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 96} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 64 Unresolved non-hydrogen dihedrals: 46 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "g" Number of atoms: 1054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1054 Classifications: {'peptide': 152} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 146} Unresolved non-hydrogen bonds: 138 Unresolved non-hydrogen angles: 165 Unresolved non-hydrogen dihedrals: 114 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 8, 'ARG:plan': 5, 'TYR:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 79 Chain: "h" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 969 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 123} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "i" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 937 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 122} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 66 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 49 Chain: "j" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 673 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 91} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 4, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 63 Chain: "k" Number of atoms: 860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 860 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'IAS:plan-2': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "l" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 924 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 113} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'D2T:plan-1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "m" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 823 Classifications: {'peptide': 113} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 3, 'TRANS': 109} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "o" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 703 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "p" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 613 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 77} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "q" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 630 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 76} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "r" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 441 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "s" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 641 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 76} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "t" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 648 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "u" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 373 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 52} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 64 Chain: "w" Number of atoms: 1591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1591 Classifications: {'RNA': 74} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 31, 'rna3p_pyr': 26} Link IDs: {'rna2p': 10, 'rna3p': 63} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "x" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p': 4, 'rna3p_pur': 33, 'rna3p_pyr': 29} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "y" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 1585 Classifications: {'RNA': 74} Modifications used: {'p5*END': 1, 'rna2p': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p': 6, 'rna3p_pur': 32, 'rna3p_pyr': 26} Link IDs: {'rna2p': 9, 'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'MIA%rna3p:plan-2': 1, 'MIA%rna3p:plan-3': 1} Unresolved non-hydrogen planarities: 7 Chain: "v" Number of atoms: 255 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 255 Classifications: {'RNA': 12} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 4, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 9} Chain: "A" Number of atoms: 61097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2845, 61097 Classifications: {'RNA': 2845} Modifications used: {'rna2p': 7, 'rna2p_pur': 272, 'rna2p_pyr': 142, 'rna3p': 16, 'rna3p_pur': 1362, 'rna3p_pyr': 1045} Link IDs: {'rna2p': 421, 'rna3p': 2423} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "B" Number of atoms: 2572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2572 Classifications: {'RNA': 120} Modifications used: {'p5*END': 1, 'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "C" Number of atoms: 2069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2069 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 253} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1559 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 1, 'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1538 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 195} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1401 Classifications: {'peptide': 177} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 6, 'TRANS': 170} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1299 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 166} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "H" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "L" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "M" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "N" Number of atoms: 1048 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1048 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "O" Number of atoms: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Unusual residues: {'MS6': 1} Classifications: {'peptide': 135, 'undetermined': 1} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 126, None: 2} Not linked: pdbres="4D4 O 81 " pdbres="MS6 O 82 " Not linked: pdbres="MS6 O 82 " pdbres="GLY O 83 " Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 876 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 113} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 913 Classifications: {'peptide': 114} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "T" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} 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: "V" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "W" Number of atoms: 769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 769 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 98} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "X" Number of atoms: 750 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 750 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "Y" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "Z" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "3" Number of atoms: 468 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 468 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "4" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "5" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 138 Unusual residues: {' MG': 98, 'AKN': 1} Classifications: {'undetermined': 99} Link IDs: {None: 98} Chain: "w" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 11 Classifications: {'peptide': 1} Chain: "x" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "v" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 399 Unusual residues: {' MG': 359, 'AKN': 1} Classifications: {'undetermined': 360} Link IDs: {None: 359} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "P" 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: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 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: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "n" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "x" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "N" 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 A0W2Y SG CYS 3 16 111.226 19.481 107.059 1.00107.23 S ATOM A0W3A SG CYS 3 18 113.745 16.740 106.260 1.00109.11 S ATOM A0W78 SG CYS 3 37 114.525 19.291 109.013 1.00104.78 S ATOM A0W7T SG CYS 3 40 114.519 20.333 105.341 1.00105.61 S ATOM A0XQT SG CYS 8 11 180.323 104.097 125.640 1.00 57.07 S ATOM A0XRI SG CYS 8 14 179.754 105.304 129.181 1.00 57.44 S ATOM A0XUD SG CYS 8 27 181.766 107.427 126.711 1.00 59.29 S Time building chain proxies: 55.77, per 1000 atoms: 0.39 Number of scatterers: 144591 At special positions: 0 Unit cell: (231.57, 244.02, 268.09, 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 2 29.99 S 142 16.00 P 4729 15.00 Mg 474 11.99 O 40456 8.00 N 26818 7.00 C 71970 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.16 Conformation dependent library (CDL) restraints added in 7.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 40 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 16 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 18 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 37 " pdb=" ZN 8 101 " pdb="ZN ZN 8 101 " - pdb=" ND1 HIS 8 33 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 11 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 27 " pdb="ZN ZN 8 101 " - pdb=" SG CYS 8 14 " Number of angles added : 9 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10190 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: 172 helices and 72 sheets defined 39.1% alpha, 19.6% beta 1608 base pairs and 2476 stacking pairs defined. Time for finding SS restraints: 73.31 Creating SS restraints... Processing helix chain 'b' and resid 5 through 13 Processing helix chain 'b' and resid 24 through 32 removed outlier: 4.165A pdb=" N LYS b 28 " --> pdb=" O ASN b 24 " (cutoff:3.500A) Proline residue: b 29 - end of helix removed outlier: 5.491A 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 64 Proline residue: b 48 - end of helix removed outlier: 3.926A pdb=" N LYS b 64 " --> pdb=" O ILE b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.739A pdb=" N GLU b 78 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA b 79 " --> pdb=" O ALA b 75 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP b 88 " --> pdb=" O ALA b 84 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 removed outlier: 3.723A pdb=" N GLN b 109 " --> pdb=" O LYS b 105 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER b 110 " --> pdb=" O THR b 106 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY b 124 " --> pdb=" O GLN b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 130 through 148 removed outlier: 6.251A pdb=" N ALA b 134 " --> pdb=" O THR b 130 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU b 135 " --> pdb=" O LYS b 131 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N MET b 136 " --> pdb=" O LYS b 132 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 155 removed outlier: 4.722A pdb=" N MET b 154 " --> pdb=" O GLY b 150 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N GLY 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 Processing helix chain 'b' and resid 171 through 180 Processing helix chain 'b' and resid 206 through 227 Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.020A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.728A pdb=" N ALA c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 3.688A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.225A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.280A pdb=" N ASP c 112 " --> pdb=" O LYS c 108 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N ALA c 113 " --> pdb=" O PRO c 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 108 through 113' Processing helix chain 'c' and resid 114 through 127 Processing helix chain 'c' and resid 129 through 145 removed outlier: 3.730A pdb=" N GLY c 145 " --> pdb=" O ALA c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.519A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER d 12 " --> pdb=" O LYS d 8 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 32 removed outlier: 3.703A pdb=" N LYS d 31 " --> pdb=" O ALA d 27 " (cutoff:3.500A) Processing helix chain 'd' and resid 49 through 66 Processing helix chain 'd' and resid 68 through 83 removed outlier: 5.241A pdb=" N LYS d 83 " --> pdb=" O ALA d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 97 removed outlier: 4.517A pdb=" N ARG d 97 " --> pdb=" O LEU d 93 " (cutoff:3.500A) Processing helix chain 'd' and resid 98 through 106 removed outlier: 3.532A pdb=" N GLY d 106 " --> pdb=" O VAL d 102 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 121 removed outlier: 3.646A pdb=" N LYS d 121 " --> pdb=" O LEU d 117 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 151 removed outlier: 4.633A pdb=" N LYS d 151 " --> pdb=" O GLU d 147 " (cutoff:3.500A) Processing helix chain 'd' and resid 152 through 166 removed outlier: 4.131A pdb=" N GLN d 164 " --> pdb=" O GLU d 160 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N ARG d 165 " --> pdb=" O LEU d 161 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU d 166 " --> pdb=" O ALA d 162 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 192 removed outlier: 5.117A pdb=" N SER d 192 " --> pdb=" O ARG d 188 " (cutoff:3.500A) Processing helix chain 'd' and resid 196 through 206 removed outlier: 3.670A pdb=" N ILE d 200 " --> pdb=" O ASN d 196 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N LYS d 206 " --> pdb=" O GLU d 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 71 removed outlier: 3.645A pdb=" N ARG e 69 " --> pdb=" O GLU e 65 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN e 70 " --> pdb=" O LYS e 66 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N MET e 71 " --> pdb=" O ALA e 67 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 119 Processing helix chain 'e' and resid 132 through 147 Processing helix chain 'e' and resid 149 through 158 Processing helix chain 'e' and resid 160 through 165 Processing helix chain 'f' and resid 11 through 19 removed outlier: 4.824A pdb=" N GLU f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) Proline residue: f 19 - end of helix Processing helix chain 'f' and resid 20 through 33 removed outlier: 4.256A pdb=" N GLY f 31 " --> pdb=" O ALA f 27 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ALA f 32 " --> pdb=" O ALA f 28 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 82 removed outlier: 6.912A pdb=" N ILE f 71 " --> pdb=" O PRO f 67 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASP f 82 " --> pdb=" O PHE f 78 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 31 Processing helix chain 'g' and resid 35 through 55 Processing helix chain 'g' and resid 57 through 70 removed outlier: 4.139A pdb=" N ALA g 61 " --> pdb=" O SER g 57 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N PHE g 62 " --> pdb=" O GLU g 58 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASN g 68 " --> pdb=" O VAL g 64 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N VAL g 69 " --> pdb=" O ALA g 65 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 3.849A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.588A pdb=" N GLU g 129 " --> pdb=" O SER g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 153 removed outlier: 3.950A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N LYS g 149 " --> pdb=" O ALA g 145 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N ALA g 150 " --> pdb=" O GLU g 146 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N PHE g 151 " --> pdb=" O ALA g 147 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA g 152 " --> pdb=" O ASN g 148 " (cutoff:3.500A) removed outlier: 5.552A pdb=" N HIS g 153 " --> pdb=" O LYS g 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 21 Processing helix chain 'h' and resid 30 through 44 removed outlier: 3.638A pdb=" N GLU h 43 " --> pdb=" O VAL h 39 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 120 Processing helix chain 'i' and resid 34 through 40 removed outlier: 4.723A pdb=" N GLY i 40 " --> pdb=" O GLU i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 56 Proline residue: i 51 - end of helix removed outlier: 3.775A pdb=" N VAL i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASP i 56 " --> pdb=" O LEU i 52 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 92 removed outlier: 4.157A pdb=" N GLN i 75 " --> pdb=" O GLY i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 94 through 102 removed outlier: 4.477A pdb=" N LEU i 98 " --> pdb=" O LEU i 94 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA i 101 " --> pdb=" O GLU i 97 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY i 102 " --> pdb=" O LEU i 98 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.650A pdb=" N ARG j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU j 90 " --> pdb=" O ALA j 86 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 4.020A pdb=" N GLY k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 54 through 60 removed outlier: 4.124A pdb=" N SER k 58 " --> pdb=" O GLY k 54 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR k 59 " --> pdb=" O SER k 55 " (cutoff:3.500A) Proline residue: k 60 - end of helix No H-bonds generated for 'chain 'k' and resid 54 through 60' Processing helix chain 'k' and resid 61 through 75 removed outlier: 3.732A pdb=" N ASP k 72 " --> pdb=" O GLU k 68 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LYS k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 104 removed outlier: 4.643A pdb=" N THR k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 11 Proline residue: l 11 - end of helix Processing helix chain 'l' and resid 113 through 118 removed outlier: 3.606A pdb=" N TYR l 117 " --> pdb=" O ALA l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 3.685A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N SER m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N ILE m 22 " --> pdb=" O ALA m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.898A pdb=" N SER m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 4.243A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N SER m 49 " --> pdb=" O ILE 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 64 removed outlier: 3.799A pdb=" N LYS m 62 " --> pdb=" O ASP m 58 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N PHE m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) Processing helix chain 'm' and resid 66 through 84 removed outlier: 4.106A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'm' and resid 106 through 111 Processing helix chain 'n' and resid 3 through 21 Processing helix chain 'n' and resid 22 through 33 Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.671A pdb=" N ARG n 41 " --> pdb=" O SER n 37 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN n 49 " --> pdb=" O VAL n 45 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR n 50 " --> pdb=" O LEU n 46 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 44 removed outlier: 4.355A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N HIS o 42 " --> pdb=" O HIS o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.652A pdb=" N GLY o 55 " --> pdb=" O HIS o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 75 through 86 Processing helix chain 'p' and resid 53 through 64 removed outlier: 3.522A pdb=" N GLY p 64 " --> pdb=" O TRP p 60 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 80 Processing helix chain 'r' and resid 25 through 34 removed outlier: 4.046A pdb=" N ASN r 31 " --> pdb=" O ALA r 27 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ILE r 33 " --> pdb=" O LEU r 29 " (cutoff:3.500A) removed outlier: 5.638A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.615A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 Processing helix chain 's' and resid 70 through 76 removed outlier: 4.135A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALA s 75 " --> pdb=" O LEU s 71 " (cutoff:3.500A) Proline residue: s 76 - end of helix No H-bonds generated for 'chain 's' and resid 70 through 76' Processing helix chain 't' and resid 4 through 42 removed outlier: 3.785A pdb=" N LYS t 8 " --> pdb=" O ILE t 4 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N LYS t 9 " --> pdb=" O LYS t 5 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN t 13 " --> pdb=" O LYS t 9 " (cutoff:3.500A) Processing helix chain 't' and resid 44 through 65 removed outlier: 4.247A pdb=" N GLN t 48 " --> pdb=" O LYS t 44 " (cutoff:3.500A) Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 86 removed outlier: 4.072A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 37 removed outlier: 4.790A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 56 Processing helix chain 'C' and resid 10 through 17 removed outlier: 4.873A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N VAL C 17 " --> pdb=" O ARG C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.993A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ARG C 212 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLY C 215 " --> pdb=" O ALA C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 3.699A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.117A 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 260 through 268 removed outlier: 3.682A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 6.088A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.146A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 40 removed outlier: 3.678A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 removed outlier: 3.926A pdb=" N LEU E 134 " --> pdb=" O LYS E 130 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.616A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.532A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 3.511A pdb=" N VAL F 12 " --> pdb=" O TYR F 8 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ASN F 21 " --> pdb=" O MET F 17 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.503A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.709A pdb=" N ALA F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ILE F 60 " --> pdb=" O ASP F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 3.546A pdb=" N TRP F 97 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ILE F 106 " --> pdb=" O ARG F 102 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 142 through 147 removed outlier: 5.709A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 3.796A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG F 167 " --> pdb=" O ASP F 163 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP F 174 " --> pdb=" O LEU F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.878A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N PHE F 138 " --> pdb=" O GLN F 135 " (cutoff:3.500A) Proline residue: F 139 - end of helix No H-bonds generated for 'chain 'F' and resid 134 through 139' Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.868A pdb=" N GLN G 64 " --> pdb=" O ASP G 60 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA G 70 " --> pdb=" O GLY G 66 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU G 72 " --> pdb=" O ALA G 68 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL G 79 " --> pdb=" O MET G 75 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.993A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 removed outlier: 5.198A pdb=" N GLN H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 38 removed outlier: 4.379A pdb=" N GLU L 31 " --> pdb=" O ARG L 27 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 96 Processing helix chain 'L' and resid 97 through 110 removed outlier: 4.179A pdb=" N ILE L 101 " --> pdb=" O PRO L 97 " (cutoff:3.500A) Proline residue: L 110 - end of helix Processing helix chain 'L' and resid 112 through 123 removed outlier: 4.022A pdb=" N LYS L 121 " --> pdb=" O ALA L 117 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LEU L 122 " --> pdb=" O MET L 118 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N LYS L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) Processing helix chain 'M' and resid 104 through 109 removed outlier: 4.612A pdb=" N ARG M 108 " --> pdb=" O THR M 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER M 109 " --> pdb=" O ARG M 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 104 through 109' Processing helix chain 'M' and resid 112 through 119 Processing helix chain 'N' and resid 37 through 42 removed outlier: 3.839A pdb=" N ARG N 41 " --> pdb=" O GLY N 37 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N SER N 42 " --> pdb=" O GLN N 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 37 through 42' Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.519A pdb=" N LEU N 61 " --> pdb=" O LEU N 57 " (cutoff:3.500A) Proline residue: N 62 - end of helix Processing helix chain 'N' and resid 68 through 75 removed outlier: 3.917A pdb=" N ALA N 72 " --> pdb=" O SER N 68 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE N 73 " --> pdb=" O ARG N 69 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N ALA N 75 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing helix chain 'N' and resid 78 through 85 removed outlier: 3.691A pdb=" N LEU N 82 " --> pdb=" O ARG N 78 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ALA N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N LYS N 84 " --> pdb=" O SER N 80 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N VAL N 85 " --> pdb=" O ASP N 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 78 through 85' Processing helix chain 'N' and resid 91 through 99 removed outlier: 3.530A pdb=" N LYS N 96 " --> pdb=" O LEU N 92 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALA N 98 " --> pdb=" O THR N 94 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN N 99 " --> pdb=" O LEU N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 128 through 139 removed outlier: 3.753A pdb=" N GLY N 139 " --> pdb=" O ILE N 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 58 removed outlier: 3.648A pdb=" N LYS O 58 " --> pdb=" O THR O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 109 through 125 removed outlier: 4.107A pdb=" N LYS O 123 " --> pdb=" O LEU O 119 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU O 124 " --> pdb=" O ALA O 120 " (cutoff:3.500A) Proline residue: O 125 - end of helix Processing helix chain 'P' and resid 13 through 32 Processing helix chain 'P' and resid 37 through 58 removed outlier: 3.580A pdb=" N ARG P 45 " --> pdb=" O ALA P 41 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ARG P 46 " --> pdb=" O LYS P 42 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL P 47 " --> pdb=" O GLU P 43 " (cutoff:3.500A) Proline residue: P 50 - end of helix removed outlier: 4.347A pdb=" N THR P 57 " --> pdb=" O THR P 53 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N ASP P 58 " --> pdb=" O LEU P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 71 removed outlier: 3.618A pdb=" N ARG P 69 " --> pdb=" O LEU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 81 Processing helix chain 'P' and resid 82 through 88 removed outlier: 3.991A pdb=" N PHE P 87 " --> pdb=" O LEU P 83 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 22 removed outlier: 3.606A pdb=" N ALA Q 6 " --> pdb=" O ASP Q 2 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ARG Q 13 " --> pdb=" O ARG Q 9 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ALA Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 55 through 63 removed outlier: 4.359A pdb=" N GLU Q 60 " --> pdb=" O LYS Q 56 " (cutoff:3.500A) removed outlier: 5.825A pdb=" N GLN Q 61 " --> pdb=" O ALA Q 57 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU Q 62 " --> pdb=" O ILE Q 58 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS Q 63 " --> pdb=" O ALA Q 59 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 86 removed outlier: 3.503A pdb=" N LEU Q 83 " --> pdb=" O ALA Q 79 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU Q 84 " --> pdb=" O GLU Q 80 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS Q 85 " --> pdb=" O ARG Q 81 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 114 removed outlier: 3.748A pdb=" N GLY Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 13 removed outlier: 3.950A pdb=" N GLN R 7 " --> pdb=" O ASN R 3 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU R 11 " --> pdb=" O GLN R 7 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLN R 12 " --> pdb=" O LEU R 8 " (cutoff:3.500A) Processing helix chain 'R' and resid 97 through 104 removed outlier: 4.644A pdb=" N ARG R 101 " --> pdb=" O LEU R 97 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N GLU R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG R 103 " --> pdb=" O TYR R 99 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N THR R 104 " --> pdb=" O LEU R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 97 through 104' Processing helix chain 'S' and resid 6 through 22 removed outlier: 3.901A pdb=" N ILE S 17 " --> pdb=" O ARG S 13 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLN S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LYS S 22 " --> pdb=" O LEU S 18 " (cutoff:3.500A) Processing helix chain 'S' and resid 26 through 31 removed outlier: 3.915A pdb=" N ARG S 30 " --> pdb=" O GLY S 26 " (cutoff:3.500A) Processing helix chain 'S' and resid 32 through 37 removed outlier: 3.582A pdb=" N GLN S 37 " --> pdb=" O ARG S 33 " (cutoff:3.500A) Processing helix chain 'S' and resid 39 through 73 removed outlier: 3.767A pdb=" N ARG S 51 " --> pdb=" O TYR S 47 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N ARG S 55 " --> pdb=" O ARG S 51 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 87 Processing helix chain 'S' and resid 91 through 102 removed outlier: 3.814A pdb=" N VAL S 100 " --> pdb=" O ALA S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 118 removed outlier: 3.859A pdb=" N LYS S 112 " --> pdb=" O ALA S 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 25 removed outlier: 3.625A pdb=" N LEU U 19 " --> pdb=" O GLN U 15 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL U 20 " --> pdb=" O LYS U 16 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE U 24 " --> pdb=" O VAL U 20 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG U 25 " --> pdb=" O ALA U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 28 through 39 removed outlier: 3.807A pdb=" N ASP U 34 " --> pdb=" O SER U 30 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE U 35 " --> pdb=" O GLN U 31 " (cutoff:3.500A) Processing helix chain 'U' and resid 41 through 61 removed outlier: 3.698A pdb=" N VAL U 45 " --> pdb=" O LYS U 41 " (cutoff:3.500A) Processing helix chain 'V' and resid 3 through 11 removed outlier: 3.580A pdb=" N LEU V 8 " --> pdb=" O GLU V 4 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS V 9 " --> pdb=" O GLU V 5 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N LEU V 11 " --> pdb=" O LEU V 7 " (cutoff:3.500A) Processing helix chain 'V' and resid 17 through 26 Processing helix chain 'V' and resid 39 through 51 removed outlier: 3.516A pdb=" N LYS V 49 " --> pdb=" O ALA V 45 " (cutoff:3.500A) Processing helix chain 'W' and resid 66 through 71 removed outlier: 4.005A pdb=" N VAL W 70 " --> pdb=" O GLN W 66 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N ALA W 71 " --> pdb=" O VAL W 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 66 through 71' Processing helix chain 'X' and resid 13 through 24 removed outlier: 3.664A pdb=" N ALA X 23 " --> pdb=" O ARG X 19 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ASN X 24 " --> pdb=" O LEU X 20 " (cutoff:3.500A) Processing helix chain 'X' and resid 43 through 53 removed outlier: 3.537A pdb=" N VAL X 47 " --> pdb=" O ASP X 43 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N MET X 50 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA X 52 " --> pdb=" O MET X 48 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS X 53 " --> pdb=" O ASN X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 54 through 59 removed outlier: 4.151A pdb=" N SER X 58 " --> pdb=" O ALA X 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 52 through 63 Processing helix chain 'Z' and resid 64 through 75 Processing helix chain '1' and resid 2 through 8 removed outlier: 4.258A pdb=" N GLU 1 8 " --> pdb=" O LYS 1 4 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 35 removed outlier: 3.546A pdb=" N GLU 1 17 " --> pdb=" O GLU 1 13 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY 1 35 " --> pdb=" O GLN 1 31 " (cutoff:3.500A) Processing helix chain '1' and resid 39 through 62 removed outlier: 4.808A pdb=" N LEU 1 43 " --> pdb=" O GLN 1 39 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS 1 44 " --> pdb=" O SER 1 40 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU 1 56 " --> pdb=" O ARG 1 52 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN 1 58 " --> pdb=" O LYS 1 54 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU 1 59 " --> pdb=" O THR 1 55 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 52 removed outlier: 4.128A pdb=" N MET 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) Processing helix chain '3' and resid 41 through 46 Processing helix chain '3' and resid 55 through 65 removed outlier: 3.649A pdb=" N ASN 3 65 " --> pdb=" O ASN 3 61 " (cutoff:3.500A) Processing helix chain '4' and resid 9 through 19 removed outlier: 4.729A pdb=" N HIS 4 19 " --> pdb=" O MET 4 15 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 25 removed outlier: 4.184A pdb=" N THR 6 24 " --> pdb=" O ALA 6 20 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N LYS 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) Processing helix chain '6' and resid 26 through 38 Processing helix chain '7' and resid 7 through 14 removed outlier: 3.814A pdb=" N ARG 7 13 " --> pdb=" O GLY 7 9 " (cutoff:3.500A) Processing helix chain '7' and resid 32 through 37 removed outlier: 4.878A pdb=" N LYS 7 36 " --> pdb=" O ILE 7 32 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ALA 7 37 " --> pdb=" O LEU 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 Proline residue: 7 46 - end of helix Processing helix chain '7' and resid 51 through 63 removed outlier: 4.566A pdb=" N GLY 7 56 " --> pdb=" O LYS 7 52 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N LEU 7 57 " --> pdb=" O GLY 7 53 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N CYS 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) Proline residue: 7 63 - end of helix Processing sheet with id= 1, first strand: chain 'b' and resid 15 through 18 removed outlier: 5.882A pdb=" N HIS b 15 " --> pdb=" O ILE b 41 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N HIS b 39 " --> pdb=" O GLY b 17 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'b' and resid 89 through 93 removed outlier: 3.591A pdb=" N ILE b 164 " --> pdb=" O VAL b 70 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'c' and resid 54 through 59 Processing sheet with id= 4, first strand: chain 'c' and resid 164 through 169 removed outlier: 6.788A pdb=" N ASP c 181 " --> pdb=" O LYS c 204 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'd' and resid 141 through 144 removed outlier: 3.549A pdb=" N ASP d 141 " --> pdb=" O PHE d 182 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'e' and resid 11 through 16 removed outlier: 6.719A pdb=" N LEU e 36 " --> pdb=" O ILE e 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'e' and resid 84 through 88 removed outlier: 5.427A pdb=" N ASN e 122 " --> pdb=" O ALA e 99 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'e' and resid 33 through 41 removed outlier: 6.313A pdb=" N ARG e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'f' and resid 38 through 41 removed outlier: 3.905A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LEU f 61 " --> pdb=" O GLU f 40 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N VAL f 10 " --> pdb=" O HIS f 58 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 73 through 79 Processing sheet with id= 11, first strand: chain 'h' and resid 23 through 28 removed outlier: 5.884A pdb=" N ALA h 23 " --> pdb=" O LEU h 63 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP h 48 " --> pdb=" O THR h 62 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'h' and resid 74 through 77 removed outlier: 3.729A pdb=" N CYS h 127 " --> pdb=" O VAL h 103 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL h 103 " --> pdb=" O ILE h 126 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N ILE h 85 " --> pdb=" O ILE h 125 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'i' and resid 5 through 11 removed outlier: 4.068A pdb=" N LYS i 27 " --> pdb=" O LEU i 61 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'j' and resid 35 through 38 Processing sheet with id= 15, first strand: chain 'j' and resid 39 through 42 removed outlier: 4.400A pdb=" N LEU j 71 " --> pdb=" O LEU j 42 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'j' and resid 44 through 52 Processing sheet with id= 17, first strand: chain 'k' and resid 30 through 36 removed outlier: 3.960A pdb=" N GLY k 19 " --> pdb=" O ASN k 81 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ILE k 23 " --> pdb=" O MET k 85 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.150A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.915A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'p' and resid 4 through 10 Processing sheet with id= 21, first strand: chain 'q' and resid 7 through 11 removed outlier: 7.302A pdb=" N GLU q 60 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'q' and resid 19 through 30 No H-bonds generated for sheet with id= 22 Processing sheet with id= 23, first strand: chain 's' and resid 30 through 34 removed outlier: 3.656A pdb=" N LEU s 31 " --> pdb=" O THR s 48 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL s 62 " --> pdb=" O LEU s 47 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'C' and resid 33 through 36 No H-bonds generated for sheet with id= 24 Processing sheet with id= 25, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.680A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLY C 127 " --> pdb=" O GLN C 115 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.000A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLN C 163 " --> pdb=" O ARG C 175 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.403A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'D' and resid 3 through 7 removed outlier: 6.998A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.659A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.767A pdb=" N GLN D 36 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA D 47 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.945A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.493A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.041A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'E' and resid 117 through 120 removed outlier: 5.630A pdb=" N ARG E 117 " --> pdb=" O ASP E 184 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.314A pdb=" N THR F 68 " --> pdb=" O GLY F 86 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N CYS F 87 " --> pdb=" O MET F 38 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N MET F 38 " --> pdb=" O CYS F 87 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N VAL F 89 " --> pdb=" O LEU F 36 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASN F 37 " --> pdb=" O ASP F 153 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE F 156 " --> pdb=" O TYR F 128 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N TYR F 128 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'G' and resid 16 through 19 removed outlier: 3.602A pdb=" N LYS G 27 " --> pdb=" O ASP G 16 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 38, first strand: chain 'G' and resid 82 through 89 removed outlier: 6.599A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.503A pdb=" N VAL G 113 " --> pdb=" O LEU G 105 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'H' and resid 18 through 21 removed outlier: 6.680A pdb=" N GLN H 2 " --> pdb=" O ALA H 39 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL H 37 " --> pdb=" O ILE H 4 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'L' and resid 52 through 57 removed outlier: 4.952A pdb=" N ASP L 19 " --> pdb=" O LEU L 140 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'L' and resid 74 through 78 removed outlier: 7.399A pdb=" N GLY L 83 " --> pdb=" O THR L 78 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'M' and resid 18 through 21 removed outlier: 4.074A pdb=" N THR M 6 " --> pdb=" O CYS M 21 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N ASN M 82 " --> pdb=" O MET M 7 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 37 through 40 No H-bonds generated for sheet with id= 44 Processing sheet with id= 45, first strand: chain 'O' and resid 62 through 65 removed outlier: 3.791A pdb=" N TYR O 103 " --> pdb=" O LEU O 33 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N LEU O 33 " --> pdb=" O LEU O 102 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS O 100 " --> pdb=" O ALA O 35 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'O' and resid 30 through 36 removed outlier: 8.464A pdb=" N SER O 30 " --> pdb=" O LYS O 133 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N LYS O 127 " --> pdb=" O VAL O 36 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 33 through 36 removed outlier: 5.435A pdb=" N MET P 110 " --> pdb=" O CYS P 100 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N TYR P 94 " --> pdb=" O VAL P 116 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Q' and resid 49 through 52 removed outlier: 3.845A pdb=" N VAL Q 49 " --> pdb=" O VAL Q 39 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N TYR Q 36 " --> pdb=" O HIS Q 29 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG Q 25 " --> pdb=" O ILE Q 40 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER Q 91 " --> pdb=" O THR Q 24 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU Q 26 " --> pdb=" O SER Q 91 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL Q 28 " --> pdb=" O ASP Q 93 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'R' and resid 38 through 44 removed outlier: 6.406A pdb=" N THR R 25 " --> pdb=" O LYS R 87 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER R 83 " --> pdb=" O LYS R 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'R' and resid 49 through 53 removed outlier: 3.618A pdb=" N ALA R 49 " --> pdb=" O THR R 60 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N ARG R 53 " --> pdb=" O HIS R 56 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N HIS R 56 " --> pdb=" O ARG R 53 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N SER R 57 " --> pdb=" O THR R 76 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'T' and resid 11 through 15 removed outlier: 3.517A pdb=" N MET T 40 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU T 39 " --> pdb=" O GLY T 50 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE T 41 " --> pdb=" O LYS T 48 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N GLU T 46 " --> pdb=" O ASN T 43 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'T' and resid 18 through 23 removed outlier: 4.014A pdb=" N GLN T 18 " --> pdb=" O ILE T 98 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ASP T 95 " --> pdb=" O VAL T 64 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LYS T 60 " --> pdb=" O THR T 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'T' and resid 57 through 60 Processing sheet with id= 54, first strand: chain 'T' and resid 65 through 68 removed outlier: 3.668A pdb=" N GLY T 67 " --> pdb=" O PHE T 93 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'T' and resid 69 through 78 removed outlier: 5.470A pdb=" N GLU T 70 " --> pdb=" O GLN T 91 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLN T 91 " --> pdb=" O GLU T 70 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N TYR T 83 " --> pdb=" O ARG T 78 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'U' and resid 2 through 8 Processing sheet with id= 57, first strand: chain 'V' and resid 28 through 33 removed outlier: 6.588A pdb=" N ASN V 28 " --> pdb=" O LEU V 87 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS V 66 " --> pdb=" O ARG V 77 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASP V 79 " --> pdb=" O LYS V 64 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LYS V 64 " --> pdb=" O ASP V 79 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS V 81 " --> pdb=" O VAL V 62 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL V 62 " --> pdb=" O LYS V 81 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ALA V 83 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N THR V 60 " --> pdb=" O ALA V 83 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL V 85 " --> pdb=" O VAL V 58 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL V 58 " --> pdb=" O VAL V 85 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'W' and resid 11 through 14 removed outlier: 4.425A pdb=" N LYS W 21 " --> pdb=" O VAL W 13 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'W' and resid 40 through 45 removed outlier: 4.841A pdb=" N ASN W 40 " --> pdb=" O ALA W 63 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'W' and resid 83 through 86 Processing sheet with id= 61, first strand: chain 'X' and resid 2 through 5 removed outlier: 3.662A pdb=" N VAL X 72 " --> pdb=" O LEU X 61 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'X' and resid 37 through 42 removed outlier: 3.750A pdb=" N ILE X 89 " --> pdb=" O PRO X 27 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'Y' and resid 29 through 32 removed outlier: 4.737A pdb=" N GLU Y 29 " --> pdb=" O VAL Y 67 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N PHE Y 79 " --> pdb=" O GLU Y 70 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS Y 46 " --> pdb=" O LYS Y 78 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE Y 82 " --> pdb=" O GLY Y 48 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'Y' and resid 50 through 54 removed outlier: 7.035A pdb=" N ASN Y 50 " --> pdb=" O LYS Y 62 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N PHE Y 60 " --> pdb=" O GLY Y 52 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THR Y 58 " --> pdb=" O GLY Y 54 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'Z' and resid 12 through 19 removed outlier: 3.988A pdb=" N THR Z 25 " --> pdb=" O ASN Z 17 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N SER Z 19 " --> pdb=" O ASN Z 23 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ASN Z 23 " --> pdb=" O SER Z 19 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'Z' and resid 35 through 40 removed outlier: 3.513A pdb=" N ARG Z 45 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain '2' and resid 33 through 39 removed outlier: 4.173A pdb=" N HIS 2 34 " --> pdb=" O GLN 2 9 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N MET 2 54 " --> pdb=" O THR 2 10 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain '3' and resid 20 through 25 removed outlier: 4.315A pdb=" N ASN 3 20 " --> pdb=" O CYS 3 16 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain '4' and resid 29 through 32 removed outlier: 4.854A pdb=" N GLU 4 36 " --> pdb=" O ASP 4 31 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain '5' and resid 19 through 24 removed outlier: 6.420A pdb=" N HIS 5 19 " --> pdb=" O SER 5 13 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE 5 48 " --> pdb=" O SER 5 14 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU 5 34 " --> pdb=" O GLU 5 51 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain '7' and resid 22 through 25 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain '8' and resid 1 through 5 removed outlier: 6.659A pdb=" N HIS 8 33 " --> pdb=" O CYS 8 27 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N CYS 8 27 " --> pdb=" O HIS 8 33 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ILE 8 23 " --> pdb=" O GLN 8 37 " (cutoff:3.500A) 1781 hydrogen bonds defined for protein. 5265 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4050 hydrogen bonds 6336 hydrogen bond angles 0 basepair planarities 1608 basepair parallelities 2476 stacking parallelities Total time for adding SS restraints: 285.50 Time building geometry restraints manager: 65.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13287 1.31 - 1.43: 70472 1.43 - 1.56: 63337 1.56 - 1.69: 9451 1.69 - 1.82: 247 Bond restraints: 156794 Sorted by residual: bond pdb=" C4 5MU A 747 " pdb=" C5 5MU A 747 " ideal model delta sigma weight residual 1.802 1.474 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" C4 5MU A1939 " pdb=" C5 5MU A1939 " ideal model delta sigma weight residual 1.802 1.476 0.326 2.00e-02 2.50e+03 2.65e+02 bond pdb=" C4 5MU w 54 " pdb=" C5 5MU w 54 " ideal model delta sigma weight residual 1.802 1.477 0.325 2.00e-02 2.50e+03 2.64e+02 bond pdb=" C4 5MU x 54 " pdb=" C5 5MU x 54 " ideal model delta sigma weight residual 1.802 1.478 0.324 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C4 5MU y 54 " pdb=" C5 5MU y 54 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.58e+02 ... (remaining 156789 not shown) Histogram of bond angle deviations from ideal: 95.94 - 106.18: 26904 106.18 - 116.42: 112969 116.42 - 126.66: 81898 126.66 - 136.90: 13491 136.90 - 147.14: 5 Bond angle restraints: 235267 Sorted by residual: angle pdb=" O3' C w 75 " pdb=" P A w 76 " pdb=" OP1 A w 76 " ideal model delta sigma weight residual 108.00 147.14 -39.14 3.00e+00 1.11e-01 1.70e+02 angle pdb=" C1' 2MA A2503 " pdb=" N9 2MA A2503 " pdb=" C8 2MA A2503 " ideal model delta sigma weight residual 106.32 127.04 -20.72 3.00e+00 1.11e-01 4.77e+01 angle pdb=" N ASN G 30 " pdb=" CA ASN G 30 " pdb=" C ASN G 30 " ideal model delta sigma weight residual 114.56 106.75 7.81 1.27e+00 6.20e-01 3.78e+01 angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C4 OMG A2251 " ideal model delta sigma weight residual 108.29 126.60 -18.31 3.00e+00 1.11e-01 3.72e+01 angle pdb=" C1' OMG A2251 " pdb=" N9 OMG A2251 " pdb=" C8 OMG A2251 " ideal model delta sigma weight residual 142.82 125.09 17.73 3.00e+00 1.11e-01 3.49e+01 ... (remaining 235262 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.94: 88206 35.94 - 71.88: 10825 71.88 - 107.82: 1253 107.82 - 143.75: 23 143.75 - 179.69: 21 Dihedral angle restraints: 100328 sinusoidal: 84532 harmonic: 15796 Sorted by residual: dihedral pdb=" O4' C A 264 " pdb=" C1' C A 264 " pdb=" N1 C A 264 " pdb=" C2 C A 264 " ideal model delta sinusoidal sigma weight residual -160.00 4.77 -164.77 1 1.50e+01 4.44e-03 8.38e+01 dihedral pdb=" O4' U A1779 " pdb=" C1' U A1779 " pdb=" N1 U A1779 " pdb=" C2 U A1779 " ideal model delta sinusoidal sigma weight residual 200.00 45.42 154.58 1 1.50e+01 4.44e-03 8.12e+01 dihedral pdb=" O4' U a 365 " pdb=" C1' U a 365 " pdb=" N1 U a 365 " pdb=" C2 U a 365 " ideal model delta sinusoidal sigma weight residual 200.00 47.51 152.49 1 1.50e+01 4.44e-03 8.05e+01 ... (remaining 100325 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 28753 0.078 - 0.157: 1275 0.157 - 0.235: 81 0.235 - 0.314: 13 0.314 - 0.392: 2 Chirality restraints: 30124 Sorted by residual: chirality pdb=" C1* PSU A2580 " pdb=" O4* PSU A2580 " pdb=" C2* PSU A2580 " pdb=" C5 PSU A2580 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.85e+00 chirality pdb=" C2' 3TD A1915 " pdb=" C3' 3TD A1915 " pdb=" O2' 3TD A1915 " pdb=" C1' 3TD A1915 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" C1' A a 160 " pdb=" O4' A a 160 " pdb=" C2' A a 160 " pdb=" N9 A a 160 " both_signs ideal model delta sigma weight residual False 2.46 2.14 0.31 2.00e-01 2.50e+01 2.45e+00 ... (remaining 30121 not shown) Planarity restraints: 12214 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' OMC A2498 " 0.063 2.00e-02 2.50e+03 5.96e-01 8.01e+03 pdb=" C4' OMC A2498 " 0.440 2.00e-02 2.50e+03 pdb=" O4' OMC A2498 " 0.614 2.00e-02 2.50e+03 pdb=" C3' OMC A2498 " -0.598 2.00e-02 2.50e+03 pdb=" O3' OMC A2498 " -0.642 2.00e-02 2.50e+03 pdb=" C2' OMC A2498 " -0.178 2.00e-02 2.50e+03 pdb=" O2' OMC A2498 " 0.982 2.00e-02 2.50e+03 pdb=" C1' OMC A2498 " 0.221 2.00e-02 2.50e+03 pdb=" N1 OMC A2498 " -0.902 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1516 " -0.055 2.00e-02 2.50e+03 5.94e-01 7.93e+03 pdb=" C4' 2MG a1516 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 2MG a1516 " -0.623 2.00e-02 2.50e+03 pdb=" C3' 2MG a1516 " 0.593 2.00e-02 2.50e+03 pdb=" O3' 2MG a1516 " 0.624 2.00e-02 2.50e+03 pdb=" C2' 2MG a1516 " 0.180 2.00e-02 2.50e+03 pdb=" O2' 2MG a1516 " -0.965 2.00e-02 2.50e+03 pdb=" C1' 2MG a1516 " -0.226 2.00e-02 2.50e+03 pdb=" N9 2MG a1516 " 0.911 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC a1407 " 0.061 2.00e-02 2.50e+03 5.92e-01 7.87e+03 pdb=" C4' 5MC a1407 " 0.440 2.00e-02 2.50e+03 pdb=" O4' 5MC a1407 " 0.599 2.00e-02 2.50e+03 pdb=" C3' 5MC a1407 " -0.592 2.00e-02 2.50e+03 pdb=" O3' 5MC a1407 " -0.638 2.00e-02 2.50e+03 pdb=" C2' 5MC a1407 " -0.176 2.00e-02 2.50e+03 pdb=" O2' 5MC a1407 " 0.973 2.00e-02 2.50e+03 pdb=" C1' 5MC a1407 " 0.229 2.00e-02 2.50e+03 pdb=" N1 5MC a1407 " -0.897 2.00e-02 2.50e+03 ... (remaining 12211 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 155 2.12 - 2.82: 38679 2.82 - 3.51: 197245 3.51 - 4.21: 486897 4.21 - 4.90: 640868 Nonbonded interactions: 1363844 Sorted by model distance: nonbonded pdb=" O3' A w 76 " pdb=" C PHE w 101 " model vdw 1.429 3.270 nonbonded pdb=" OP2 G A1776 " pdb="MG MG A3343 " model vdw 1.865 2.170 nonbonded pdb=" N7 G A2502 " pdb="MG MG A3356 " model vdw 1.894 2.250 nonbonded pdb=" OP1 U A1995 " pdb="MG MG A3319 " model vdw 1.898 2.170 nonbonded pdb=" O6 G A 776 " pdb="MG MG A3159 " model vdw 1.915 2.170 ... (remaining 1363839 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'w' and (resid 1 through 36 or (resid 37 through 38 and (name P or name O \ P1 or name OP2 or name O5' or name C5' or name C4' or name O4' or name C3' or na \ me O3' or name C2' or name O2' or name C1' or name N9 or name C8 or name N7 or n \ ame C5 or name C6 or name N6 or name N1 or name C2 or name N3 or name C4 )) or r \ esid 39 through 76)) selection = (chain 'y' and (resid 1 through 75 or (resid 76 and (name P or name OP1 or name \ O5' or name C5' or name C4' or name O4' or name C3' or name O3' or name C2' or n \ ame O2' or name C1' or name N9 or name C8 or name N7 or name C5 or name C6 or na \ me N6 or name N1 or name C2 or name N3 or name C4 )))) } 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: 6.840 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: 0.130 Extract box with map and model: 30.270 Check model and map are aligned: 1.590 Set scattering table: 0.980 Process input model: 601.890 Find NCS groups from input model: 2.800 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 659.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 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 : 0.007 0.328 156794 Z= 0.397 Angle : 0.604 39.138 235267 Z= 0.298 Chirality : 0.035 0.392 30124 Planarity : 0.022 0.596 12214 Dihedral : 23.092 179.693 90138 Min Nonbonded Distance : 1.429 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.97 % Favored : 95.88 % Rotamer: Outliers : 0.07 % Allowed : 0.37 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.11), residues: 5438 helix: 0.02 (0.12), residues: 1782 sheet: -0.52 (0.16), residues: 1065 loop : -0.44 (0.12), residues: 2591 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP b 23 HIS 0.011 0.001 HIS C 53 PHE 0.028 0.001 PHE d 107 TYR 0.019 0.002 TYR U 38 ARG 0.010 0.000 ARG d 184 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 1606 time to evaluate : 5.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 46 GLU cc_start: 0.8245 (pt0) cc_final: 0.7701 (pt0) REVERT: c 105 GLU cc_start: 0.7650 (tp30) cc_final: 0.7247 (tp30) REVERT: d 73 ARG cc_start: 0.8316 (tpt170) cc_final: 0.8059 (mmt-90) REVERT: d 78 GLU cc_start: 0.7448 (tp30) cc_final: 0.7135 (OUTLIER) REVERT: d 126 ASN cc_start: 0.8746 (m-40) cc_final: 0.8525 (m-40) REVERT: d 202 GLU cc_start: 0.7991 (pm20) cc_final: 0.7496 (pm20) REVERT: g 67 GLU cc_start: 0.8711 (tp30) cc_final: 0.8150 (tp30) REVERT: h 111 MET cc_start: 0.8083 (ptp) cc_final: 0.7848 (ptp) REVERT: i 29 VAL cc_start: 0.8816 (t) cc_final: 0.8571 (p) REVERT: k 94 GLU cc_start: 0.7973 (pp20) cc_final: 0.7737 (pp20) REVERT: m 11 ASP cc_start: 0.8273 (p0) cc_final: 0.8036 (p0) REVERT: m 54 ASP cc_start: 0.8004 (t0) cc_final: 0.7583 (t0) REVERT: m 109 ARG cc_start: 0.9152 (mmm160) cc_final: 0.8909 (mmm160) REVERT: t 9 LYS cc_start: 0.8449 (mtpt) cc_final: 0.7979 (tptp) REVERT: t 10 ARG cc_start: 0.8955 (mmm-85) cc_final: 0.8619 (mmm160) REVERT: t 24 ARG cc_start: 0.8606 (mmp80) cc_final: 0.8232 (mmp80) REVERT: t 26 SER cc_start: 0.9186 (m) cc_final: 0.8852 (p) REVERT: t 27 MET cc_start: 0.8182 (tmm) cc_final: 0.7723 (tmm) REVERT: t 60 ARG cc_start: 0.8663 (ttm170) cc_final: 0.8431 (ttp-110) REVERT: C 111 LYS cc_start: 0.8557 (ptpp) cc_final: 0.8234 (pttp) REVERT: E 136 GLN cc_start: 0.8912 (tp40) cc_final: 0.8485 (tp40) REVERT: G 88 GLN cc_start: 0.8236 (mm110) cc_final: 0.7910 (mt0) REVERT: N 94 THR cc_start: 0.9236 (p) cc_final: 0.8489 (p) REVERT: R 85 SER cc_start: 0.8447 (p) cc_final: 0.8047 (p) REVERT: 1 2 LYS cc_start: 0.8341 (pttm) cc_final: 0.7776 (pttp) REVERT: 3 20 ASN cc_start: 0.8649 (t0) cc_final: 0.8380 (t0) REVERT: 3 25 ARG cc_start: 0.8548 (mtm110) cc_final: 0.8046 (ptm-80) outliers start: 3 outliers final: 7 residues processed: 1607 average time/residue: 2.1771 time to fit residues: 5001.9981 Evaluate side-chains 1390 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 1384 time to evaluate : 5.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain k residue 57 LYS Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain U residue 67 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 847 optimal weight: 0.6980 chunk 760 optimal weight: 8.9990 chunk 422 optimal weight: 7.9990 chunk 259 optimal weight: 1.9990 chunk 513 optimal weight: 10.0000 chunk 406 optimal weight: 10.0000 chunk 786 optimal weight: 20.0000 chunk 304 optimal weight: 10.0000 chunk 478 optimal weight: 7.9990 chunk 585 optimal weight: 10.0000 chunk 911 optimal weight: 1.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 51 ASN b 94 HIS b 168 HIS c 69 HIS c 140 ASN d 59 GLN d 74 ASN d 85 ASN d 131 ASN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 198 HIS e 19 ASN ** e 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 78 ASN ** e 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 97 GLN e 135 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN i 31 ASN i 50 GLN i 75 GLN i 126 GLN j 56 HIS k 28 ASN l 5 ASN l 96 HIS m 105 ASN o 51 HIS p 79 ASN q 47 HIS q 51 ASN r 31 ASN r 52 GLN s 83 HIS t 68 HIS C 46 ASN C 90 ASN C 115 GLN C 153 GLN C 239 ASN D 42 ASN D 58 ASN D 67 HIS D 130 GLN D 164 GLN D 185 ASN E 29 HIS E 97 ASN E 156 ASN E 163 ASN G 20 ASN G 22 GLN G 143 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 HIS L 86 GLN L 138 GLN M 89 ASN N 104 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 23 ASN Q 38 GLN R 41 GLN R 77 HIS S 52 GLN S 72 ASN S 81 ASN T 89 HIS U 9 HIS V 28 ASN ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 GLN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 12 ASN Y 76 ASN Z 23 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 6 ASN 6 6 GLN 7 28 ASN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8816 moved from start: 0.0813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 156794 Z= 0.322 Angle : 0.654 18.177 235267 Z= 0.353 Chirality : 0.037 0.411 30124 Planarity : 0.007 0.135 12214 Dihedral : 23.456 179.850 79991 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.88 % Favored : 96.01 % Rotamer: Outliers : 3.75 % Allowed : 17.04 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.11), residues: 5438 helix: 0.53 (0.12), residues: 1824 sheet: -0.64 (0.16), residues: 1054 loop : -0.46 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP b 23 HIS 0.008 0.001 HIS C 53 PHE 0.022 0.002 PHE t 51 TYR 0.019 0.002 TYR S 25 ARG 0.009 0.001 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1560 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1400 time to evaluate : 6.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 LYS cc_start: 0.8569 (ptmt) cc_final: 0.8273 (ptpp) REVERT: b 108 ARG cc_start: 0.8387 (OUTLIER) cc_final: 0.8167 (ptp-110) REVERT: c 42 TYR cc_start: 0.8566 (t80) cc_final: 0.7820 (t80) REVERT: c 46 GLU cc_start: 0.8140 (pt0) cc_final: 0.7865 (pt0) REVERT: c 165 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8905 (p) REVERT: d 78 GLU cc_start: 0.7451 (tp30) cc_final: 0.7240 (tp30) REVERT: d 202 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: f 5 GLU cc_start: 0.7944 (tt0) cc_final: 0.7743 (tt0) REVERT: g 67 GLU cc_start: 0.8710 (tp30) cc_final: 0.8486 (tp30) REVERT: g 123 GLU cc_start: 0.9031 (tp30) cc_final: 0.8741 (tp30) REVERT: g 137 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8891 (ttmt) REVERT: h 3 MET cc_start: 0.8292 (tpp) cc_final: 0.8029 (tpp) REVERT: h 9 ASP cc_start: 0.8457 (t70) cc_final: 0.8175 (t0) REVERT: h 76 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.8229 (pt0) REVERT: h 111 MET cc_start: 0.8082 (ptp) cc_final: 0.7803 (ptp) REVERT: h 113 ASP cc_start: 0.8078 (t0) cc_final: 0.7826 (t0) REVERT: h 117 ARG cc_start: 0.8685 (ttp-170) cc_final: 0.8370 (ttp-170) REVERT: j 7 ARG cc_start: 0.8474 (mmt90) cc_final: 0.8206 (mtt180) REVERT: l 111 LYS cc_start: 0.9225 (mptp) cc_final: 0.8976 (mmtm) REVERT: l 112 GLN cc_start: 0.8767 (mt0) cc_final: 0.8309 (mt0) REVERT: l 121 ARG cc_start: 0.8332 (OUTLIER) cc_final: 0.8049 (ttm170) REVERT: m 7 ILE cc_start: 0.9457 (tt) cc_final: 0.9107 (pt) REVERT: m 11 ASP cc_start: 0.8233 (p0) cc_final: 0.7871 (p0) REVERT: m 54 ASP cc_start: 0.8111 (t0) cc_final: 0.7724 (t0) REVERT: n 23 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8278 (tppp) REVERT: n 43 ASN cc_start: 0.8398 (m-40) cc_final: 0.8192 (m-40) REVERT: o 10 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8367 (ttpp) REVERT: o 45 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8082 (pt0) REVERT: o 58 ARG cc_start: 0.8763 (tmt-80) cc_final: 0.8514 (ttt90) REVERT: o 65 LYS cc_start: 0.8904 (mmtp) cc_final: 0.8676 (mttp) REVERT: s 73 GLU cc_start: 0.8313 (tt0) cc_final: 0.8111 (tt0) REVERT: t 10 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8584 (mmm160) REVERT: t 14 SER cc_start: 0.8830 (t) cc_final: 0.8359 (p) REVERT: t 26 SER cc_start: 0.9302 (m) cc_final: 0.8934 (p) REVERT: t 43 ASP cc_start: 0.8169 (t0) cc_final: 0.7723 (p0) REVERT: t 60 ARG cc_start: 0.8649 (ttm170) cc_final: 0.8381 (ttp-110) REVERT: D 181 ASP cc_start: 0.7848 (t0) cc_final: 0.7167 (t0) REVERT: E 136 GLN cc_start: 0.8604 (tp40) cc_final: 0.8342 (tp40) REVERT: F 52 ASN cc_start: 0.8694 (m-40) cc_final: 0.8256 (m-40) REVERT: F 96 MET cc_start: 0.8759 (tmm) cc_final: 0.8441 (ttp) REVERT: F 101 GLU cc_start: 0.8072 (tm-30) cc_final: 0.7825 (tm-30) REVERT: F 137 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8973 (mp) REVERT: G 88 GLN cc_start: 0.8314 (mm110) cc_final: 0.8008 (mt0) REVERT: G 95 ARG cc_start: 0.7704 (ptm-80) cc_final: 0.7357 (ptm-80) REVERT: G 101 ASN cc_start: 0.8806 (p0) cc_final: 0.8554 (p0) REVERT: G 131 ILE cc_start: 0.9452 (mt) cc_final: 0.9190 (mt) REVERT: P 8 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8720 (mtt180) REVERT: R 93 ARG cc_start: 0.8344 (OUTLIER) cc_final: 0.7796 (ttt90) REVERT: S 16 LYS cc_start: 0.8938 (OUTLIER) cc_final: 0.8695 (ttpp) REVERT: S 51 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.7454 (mtt90) REVERT: W 79 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8815 (mtmm) REVERT: X 12 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7958 (pt0) REVERT: 1 43 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8168 (pp) outliers start: 160 outliers final: 64 residues processed: 1444 average time/residue: 2.0966 time to fit residues: 4375.5195 Evaluate side-chains 1447 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1366 time to evaluate : 5.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 108 ARG Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 51 SER Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 23 LYS Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain o residue 45 GLU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 8 ARG Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain W residue 72 ILE Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 18 ARG Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 5 residue 23 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 506 optimal weight: 20.0000 chunk 282 optimal weight: 6.9990 chunk 758 optimal weight: 2.9990 chunk 620 optimal weight: 6.9990 chunk 251 optimal weight: 8.9990 chunk 913 optimal weight: 0.7980 chunk 986 optimal weight: 3.9990 chunk 813 optimal weight: 2.9990 chunk 905 optimal weight: 2.9990 chunk 311 optimal weight: 10.0000 chunk 732 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 24 ASN ** b 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 74 ASN d 116 GLN d 131 ASN e 19 ASN e 77 ASN e 78 ASN e 82 GLN e 97 GLN e 132 ASN g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN p 59 HIS q 51 ASN r 31 ASN t 13 GLN C 115 GLN D 42 ASN D 58 ASN D 173 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN L 128 ASN L 138 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN V 28 ASN ** V 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 ASN ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 29 GLN 7 28 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 156794 Z= 0.195 Angle : 0.603 13.519 235267 Z= 0.331 Chirality : 0.033 0.399 30124 Planarity : 0.006 0.128 12214 Dihedral : 23.424 179.639 79980 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.40 % Favored : 96.47 % Rotamer: Outliers : 4.12 % Allowed : 20.65 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5438 helix: 0.84 (0.12), residues: 1834 sheet: -0.64 (0.16), residues: 1065 loop : -0.39 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 248 HIS 0.005 0.001 HIS g 142 PHE 0.022 0.001 PHE t 51 TYR 0.018 0.001 TYR i 7 ARG 0.008 0.000 ARG b 222 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1606 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1430 time to evaluate : 5.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 21 ARG cc_start: 0.8003 (ptp-110) cc_final: 0.7215 (ttp-170) REVERT: b 28 LYS cc_start: 0.8007 (tttm) cc_final: 0.7807 (tttt) REVERT: c 42 TYR cc_start: 0.8511 (t80) cc_final: 0.8225 (t80) REVERT: c 105 GLU cc_start: 0.7585 (tp30) cc_final: 0.7219 (tp30) REVERT: d 78 GLU cc_start: 0.7430 (tp30) cc_final: 0.7227 (tp30) REVERT: d 124 MET cc_start: 0.8043 (OUTLIER) cc_final: 0.7809 (mpt) REVERT: d 171 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.6017 (pp) REVERT: d 202 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7548 (pm20) REVERT: f 102 MET cc_start: 0.7957 (OUTLIER) cc_final: 0.7679 (mmm) REVERT: g 67 GLU cc_start: 0.8700 (tp30) cc_final: 0.8482 (tp30) REVERT: g 137 LYS cc_start: 0.9073 (OUTLIER) cc_final: 0.8828 (ttmt) REVERT: g 144 MET cc_start: 0.8759 (tmm) cc_final: 0.8397 (tmm) REVERT: h 3 MET cc_start: 0.8239 (tpp) cc_final: 0.7983 (tpp) REVERT: h 9 ASP cc_start: 0.8407 (t70) cc_final: 0.8134 (t0) REVERT: h 38 ASN cc_start: 0.8718 (t0) cc_final: 0.8359 (t0) REVERT: h 76 GLN cc_start: 0.8585 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: h 111 MET cc_start: 0.8070 (ptp) cc_final: 0.7844 (ptp) REVERT: i 29 VAL cc_start: 0.8861 (t) cc_final: 0.8653 (p) REVERT: j 7 ARG cc_start: 0.8331 (mmt90) cc_final: 0.8098 (mtt180) REVERT: k 26 SER cc_start: 0.9430 (OUTLIER) cc_final: 0.9227 (p) REVERT: l 111 LYS cc_start: 0.9175 (mptp) cc_final: 0.8942 (mmtm) REVERT: l 112 GLN cc_start: 0.8718 (mt0) cc_final: 0.8454 (mt0) REVERT: m 11 ASP cc_start: 0.8362 (p0) cc_final: 0.8136 (p0) REVERT: n 43 ASN cc_start: 0.8386 (m-40) cc_final: 0.8184 (m-40) REVERT: o 10 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8378 (ttpp) REVERT: p 60 TRP cc_start: 0.8196 (OUTLIER) cc_final: 0.7607 (m-90) REVERT: q 61 ILE cc_start: 0.8905 (pt) cc_final: 0.8662 (pt) REVERT: s 20 GLU cc_start: 0.8086 (pp20) cc_final: 0.7450 (pp20) REVERT: s 73 GLU cc_start: 0.8295 (tt0) cc_final: 0.8039 (tt0) REVERT: t 10 ARG cc_start: 0.8915 (mmm-85) cc_final: 0.8501 (mmm160) REVERT: t 14 SER cc_start: 0.8734 (t) cc_final: 0.8332 (p) REVERT: t 26 SER cc_start: 0.9302 (m) cc_final: 0.9086 (p) REVERT: t 59 ASP cc_start: 0.7842 (m-30) cc_final: 0.7618 (m-30) REVERT: t 60 ARG cc_start: 0.8616 (ttm170) cc_final: 0.8382 (ttp-110) REVERT: E 88 ARG cc_start: 0.7930 (OUTLIER) cc_final: 0.7559 (mmp80) REVERT: E 136 GLN cc_start: 0.8618 (tp40) cc_final: 0.8246 (tp40) REVERT: F 96 MET cc_start: 0.8783 (tmm) cc_final: 0.8385 (ttp) REVERT: F 101 GLU cc_start: 0.8028 (tm-30) cc_final: 0.7757 (tm-30) REVERT: G 88 GLN cc_start: 0.8252 (mm110) cc_final: 0.8036 (mt0) REVERT: G 114 ASP cc_start: 0.8687 (t70) cc_final: 0.8314 (t0) REVERT: G 131 ILE cc_start: 0.9381 (mt) cc_final: 0.9151 (mt) REVERT: O 127 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8462 (ttpt) REVERT: R 93 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7687 (ttt90) REVERT: S 16 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8648 (ttpp) REVERT: S 51 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7389 (mtt90) REVERT: W 79 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8785 (mtmm) REVERT: X 12 GLN cc_start: 0.8189 (OUTLIER) cc_final: 0.7974 (pt0) REVERT: 1 43 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8150 (pp) REVERT: 1 44 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8673 (tptm) REVERT: 2 9 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.8014 (tt0) REVERT: 8 36 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.8031 (ttt-90) outliers start: 176 outliers final: 62 residues processed: 1489 average time/residue: 2.1051 time to fit residues: 4520.8656 Evaluate side-chains 1441 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1359 time to evaluate : 5.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 51 SER Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 31 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 60 TRP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 64 LYS Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 2 residue 9 GLN Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 902 optimal weight: 8.9990 chunk 686 optimal weight: 10.0000 chunk 474 optimal weight: 10.0000 chunk 101 optimal weight: 20.0000 chunk 435 optimal weight: 10.0000 chunk 613 optimal weight: 50.0000 chunk 916 optimal weight: 8.9990 chunk 970 optimal weight: 0.9990 chunk 478 optimal weight: 7.9990 chunk 868 optimal weight: 3.9990 chunk 261 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 39 HIS d 59 GLN d 74 ASN d 116 GLN d 152 GLN e 19 ASN e 78 ASN e 89 HIS e 97 GLN e 132 ASN f 63 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN k 118 HIS o 80 GLN q 51 ASN r 31 ASN t 52 ASN D 58 ASN D 173 GLN F 21 ASN F 63 GLN G 104 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN L 138 GLN M 5 GLN N 54 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 86 GLN V 92 ASN 1 41 HIS ** 2 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8859 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 156794 Z= 0.466 Angle : 0.692 14.266 235267 Z= 0.373 Chirality : 0.041 0.412 30124 Planarity : 0.007 0.141 12214 Dihedral : 23.340 179.445 79978 Min Nonbonded Distance : 1.716 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.06 % Favored : 95.83 % Rotamer: Outliers : 5.55 % Allowed : 22.07 % Favored : 72.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.11), residues: 5438 helix: 0.83 (0.12), residues: 1814 sheet: -0.69 (0.16), residues: 1082 loop : -0.49 (0.12), residues: 2542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP q 73 HIS 0.007 0.001 HIS g 142 PHE 0.023 0.002 PHE t 51 TYR 0.021 0.002 TYR d 76 ARG 0.012 0.001 ARG e 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1617 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 1380 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 42 TYR cc_start: 0.8366 (t80) cc_final: 0.7800 (t80) REVERT: c 46 GLU cc_start: 0.8089 (pt0) cc_final: 0.7457 (pt0) REVERT: d 124 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7602 (mpt) REVERT: d 171 LEU cc_start: 0.6412 (OUTLIER) cc_final: 0.6039 (pp) REVERT: d 202 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: e 68 ARG cc_start: 0.8829 (ttm110) cc_final: 0.8619 (mtm-85) REVERT: g 137 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8890 (ttmt) REVERT: h 3 MET cc_start: 0.8259 (tpp) cc_final: 0.7970 (tpp) REVERT: h 9 ASP cc_start: 0.8481 (t70) cc_final: 0.8182 (t0) REVERT: h 38 ASN cc_start: 0.8679 (t0) cc_final: 0.8462 (t0) REVERT: h 76 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.8249 (pt0) REVERT: h 111 MET cc_start: 0.8144 (ptp) cc_final: 0.7862 (ptp) REVERT: k 98 ARG cc_start: 0.8311 (tpp80) cc_final: 0.8050 (tpp80) REVERT: l 62 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7221 (tm-30) REVERT: m 7 ILE cc_start: 0.9461 (OUTLIER) cc_final: 0.9078 (pt) REVERT: m 11 ASP cc_start: 0.8367 (p0) cc_final: 0.8045 (p0) REVERT: o 10 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8455 (ttpp) REVERT: s 21 LYS cc_start: 0.8871 (mptt) cc_final: 0.8436 (mptt) REVERT: s 73 GLU cc_start: 0.8355 (tt0) cc_final: 0.8127 (tt0) REVERT: t 10 ARG cc_start: 0.8965 (mmm-85) cc_final: 0.8527 (mmm160) REVERT: t 14 SER cc_start: 0.8856 (t) cc_final: 0.8420 (p) REVERT: t 26 SER cc_start: 0.9324 (m) cc_final: 0.9113 (p) REVERT: t 55 GLN cc_start: 0.8230 (tt0) cc_final: 0.8014 (tt0) REVERT: t 59 ASP cc_start: 0.8125 (m-30) cc_final: 0.7816 (m-30) REVERT: E 88 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7633 (mmp80) REVERT: E 136 GLN cc_start: 0.8747 (tp40) cc_final: 0.8404 (tp40) REVERT: F 96 MET cc_start: 0.8829 (tmm) cc_final: 0.8503 (ttp) REVERT: F 101 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7854 (tm-30) REVERT: G 88 GLN cc_start: 0.8344 (mm110) cc_final: 0.8043 (mt0) REVERT: G 102 VAL cc_start: 0.8985 (OUTLIER) cc_final: 0.8658 (t) REVERT: G 131 ILE cc_start: 0.9375 (mt) cc_final: 0.9131 (mt) REVERT: N 118 THR cc_start: 0.8864 (OUTLIER) cc_final: 0.8644 (p) REVERT: N 129 LYS cc_start: 0.8375 (OUTLIER) cc_final: 0.8128 (mttp) REVERT: O 127 LYS cc_start: 0.8793 (OUTLIER) cc_final: 0.8473 (ttpt) REVERT: P 2 ARG cc_start: 0.9016 (OUTLIER) cc_final: 0.8410 (ttp-110) REVERT: Q 60 GLU cc_start: 0.8620 (pm20) cc_final: 0.8387 (pm20) REVERT: R 89 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7624 (mtm-85) REVERT: R 93 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7777 (ttt90) REVERT: S 16 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8706 (ttpp) REVERT: S 51 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7318 (mtp85) REVERT: U 62 ASP cc_start: 0.8149 (m-30) cc_final: 0.7758 (m-30) REVERT: W 79 LYS cc_start: 0.9209 (OUTLIER) cc_final: 0.8813 (mtmm) REVERT: W 88 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7646 (mp0) REVERT: X 85 LYS cc_start: 0.9250 (OUTLIER) cc_final: 0.8911 (mtmm) REVERT: 1 43 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8392 (pp) REVERT: 2 37 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: 2 39 GLU cc_start: 0.8116 (OUTLIER) cc_final: 0.7891 (pm20) REVERT: 8 36 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8053 (ttt-90) outliers start: 237 outliers final: 125 residues processed: 1469 average time/residue: 2.1211 time to fit residues: 4485.0101 Evaluate side-chains 1495 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1345 time to evaluate : 5.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 108 ARG Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 33 LEU Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 78 GLU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 65 ILE Chi-restraints excluded: chain i residue 87 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain o residue 22 THR Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain q residue 79 VAL Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 102 VAL Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 137 ASP Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 89 ARG Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 37 GLU Chi-restraints excluded: chain 2 residue 39 GLU Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 5 residue 14 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 808 optimal weight: 2.9990 chunk 550 optimal weight: 10.0000 chunk 14 optimal weight: 20.0000 chunk 722 optimal weight: 2.9990 chunk 400 optimal weight: 30.0000 chunk 828 optimal weight: 2.9990 chunk 670 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 495 optimal weight: 7.9990 chunk 871 optimal weight: 6.9990 chunk 244 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 140 ASN d 59 GLN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 ASN e 78 ASN e 97 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 122 ASN ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 ASN r 31 ASN t 52 ASN D 58 ASN E 46 GLN E 115 GLN F 21 ASN G 104 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 128 ASN L 138 GLN ** N 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8840 moved from start: 0.1199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 156794 Z= 0.367 Angle : 0.660 13.864 235267 Z= 0.358 Chirality : 0.038 0.429 30124 Planarity : 0.007 0.136 12214 Dihedral : 23.370 179.398 79978 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.95 % Favored : 95.94 % Rotamer: Outliers : 5.27 % Allowed : 23.85 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 5438 helix: 0.87 (0.12), residues: 1823 sheet: -0.69 (0.16), residues: 1082 loop : -0.47 (0.12), residues: 2533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.008 0.001 HIS g 142 PHE 0.022 0.002 PHE t 51 TYR 0.024 0.002 TYR d 76 ARG 0.010 0.000 ARG b 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1370 time to evaluate : 5.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.7946 (ttp) cc_final: 0.7322 (tmm) REVERT: b 137 ARG cc_start: 0.8441 (ttm170) cc_final: 0.8241 (ttm110) REVERT: d 78 GLU cc_start: 0.7667 (tp30) cc_final: 0.7461 (tp30) REVERT: d 124 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7610 (mpt) REVERT: d 171 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.6060 (pp) REVERT: g 137 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8856 (ttmt) REVERT: h 3 MET cc_start: 0.8273 (tpp) cc_final: 0.7975 (tpp) REVERT: h 9 ASP cc_start: 0.8465 (t70) cc_final: 0.8169 (t0) REVERT: h 76 GLN cc_start: 0.8587 (OUTLIER) cc_final: 0.8227 (pt0) REVERT: h 111 MET cc_start: 0.8170 (ptp) cc_final: 0.7884 (ptp) REVERT: j 7 ARG cc_start: 0.8408 (mtt90) cc_final: 0.8069 (mtt180) REVERT: k 69 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8004 (ptm-80) REVERT: k 98 ARG cc_start: 0.8271 (tpp80) cc_final: 0.8067 (tpp80) REVERT: l 62 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7228 (tm-30) REVERT: l 111 LYS cc_start: 0.9213 (mptp) cc_final: 0.8982 (mmtm) REVERT: l 112 GLN cc_start: 0.8796 (mt0) cc_final: 0.8354 (mt0) REVERT: m 11 ASP cc_start: 0.8420 (p0) cc_final: 0.8160 (p0) REVERT: n 30 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.7922 (tt) REVERT: o 10 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8453 (ttpp) REVERT: p 60 TRP cc_start: 0.8321 (OUTLIER) cc_final: 0.7886 (m-90) REVERT: s 20 GLU cc_start: 0.8103 (pp20) cc_final: 0.7606 (pp20) REVERT: s 21 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8634 (mptt) REVERT: s 73 GLU cc_start: 0.8342 (tt0) cc_final: 0.8127 (tt0) REVERT: t 10 ARG cc_start: 0.8961 (mmm-85) cc_final: 0.8535 (mmm160) REVERT: t 14 SER cc_start: 0.8842 (t) cc_final: 0.8412 (p) REVERT: t 55 GLN cc_start: 0.8246 (tt0) cc_final: 0.8022 (tt0) REVERT: t 59 ASP cc_start: 0.8133 (m-30) cc_final: 0.7836 (m-30) REVERT: E 88 ARG cc_start: 0.8002 (OUTLIER) cc_final: 0.7629 (mmp80) REVERT: E 136 GLN cc_start: 0.8706 (tp40) cc_final: 0.8353 (tp40) REVERT: F 96 MET cc_start: 0.8805 (tmm) cc_final: 0.8438 (ttp) REVERT: F 101 GLU cc_start: 0.8131 (tm-30) cc_final: 0.7829 (tm-30) REVERT: G 88 GLN cc_start: 0.8329 (mm110) cc_final: 0.8065 (mt0) REVERT: G 131 ILE cc_start: 0.9356 (mt) cc_final: 0.9114 (mt) REVERT: N 118 THR cc_start: 0.8858 (OUTLIER) cc_final: 0.8637 (p) REVERT: N 129 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.8111 (mttp) REVERT: O 127 LYS cc_start: 0.8797 (OUTLIER) cc_final: 0.8476 (ttpt) REVERT: P 2 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8315 (ttp-110) REVERT: R 93 ARG cc_start: 0.8376 (OUTLIER) cc_final: 0.7736 (ttt90) REVERT: S 16 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8686 (ttpp) REVERT: S 51 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7186 (mtp85) REVERT: W 79 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8823 (mtmm) REVERT: W 88 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.7679 (mp0) REVERT: X 85 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8897 (mtmm) REVERT: 1 43 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8332 (pp) REVERT: 2 37 GLU cc_start: 0.7827 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: 2 39 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7762 (pm20) REVERT: 3 25 ARG cc_start: 0.8452 (mtp85) cc_final: 0.7997 (mtm180) REVERT: 8 36 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8035 (ttt-90) outliers start: 225 outliers final: 122 residues processed: 1458 average time/residue: 2.0652 time to fit residues: 4356.4310 Evaluate side-chains 1495 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1348 time to evaluate : 5.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 69 ARG Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 14 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 3 LEU Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain o residue 10 LYS Chi-restraints excluded: chain p residue 60 TRP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 28 MET Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain u residue 16 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain W residue 88 GLU Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 72 LYS Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 37 GLU Chi-restraints excluded: chain 2 residue 39 GLU Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 5 residue 14 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 326 optimal weight: 2.9990 chunk 873 optimal weight: 4.9990 chunk 191 optimal weight: 8.9990 chunk 569 optimal weight: 10.0000 chunk 239 optimal weight: 20.0000 chunk 971 optimal weight: 0.6980 chunk 806 optimal weight: 0.9980 chunk 449 optimal weight: 7.9990 chunk 80 optimal weight: 7.9990 chunk 321 optimal weight: 5.9990 chunk 509 optimal weight: 7.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 140 ASN d 59 GLN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 ASN e 43 ASN e 78 ASN e 97 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN q 51 ASN r 31 ASN t 52 ASN C 153 GLN D 58 ASN E 115 GLN F 21 ASN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN ** L 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN N 54 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8807 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 156794 Z= 0.257 Angle : 0.626 13.515 235267 Z= 0.342 Chirality : 0.035 0.523 30124 Planarity : 0.006 0.130 12214 Dihedral : 23.387 179.912 79978 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.66 % Favored : 96.23 % Rotamer: Outliers : 5.27 % Allowed : 24.88 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5438 helix: 0.97 (0.12), residues: 1829 sheet: -0.66 (0.16), residues: 1087 loop : -0.40 (0.12), residues: 2522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 248 HIS 0.008 0.001 HIS g 142 PHE 0.024 0.001 PHE 3 43 TYR 0.022 0.002 TYR d 76 ARG 0.012 0.000 ARG b 222 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1384 time to evaluate : 5.993 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 42 TYR cc_start: 0.8274 (t80) cc_final: 0.7810 (t80) REVERT: c 46 GLU cc_start: 0.7990 (pt0) cc_final: 0.7318 (pt0) REVERT: d 78 GLU cc_start: 0.7543 (tp30) cc_final: 0.7234 (tp30) REVERT: d 124 MET cc_start: 0.8067 (OUTLIER) cc_final: 0.7860 (mpt) REVERT: d 171 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5954 (pp) REVERT: d 202 GLU cc_start: 0.7890 (OUTLIER) cc_final: 0.7630 (pm20) REVERT: e 68 ARG cc_start: 0.8617 (mtm-85) cc_final: 0.8372 (mtt90) REVERT: e 122 ASN cc_start: 0.8699 (m-40) cc_final: 0.8490 (m-40) REVERT: f 102 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7729 (mmm) REVERT: g 67 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8337 (tm-30) REVERT: g 137 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.8825 (ttmt) REVERT: g 144 MET cc_start: 0.8983 (OUTLIER) cc_final: 0.8427 (tmm) REVERT: h 3 MET cc_start: 0.8279 (tpp) cc_final: 0.7982 (tpp) REVERT: h 76 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8240 (pt0) REVERT: h 111 MET cc_start: 0.8190 (ptp) cc_final: 0.7917 (ptp) REVERT: j 7 ARG cc_start: 0.8318 (mtt90) cc_final: 0.7968 (mtt180) REVERT: j 9 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8432 (mtp180) REVERT: l 62 GLU cc_start: 0.8106 (OUTLIER) cc_final: 0.7303 (tm-30) REVERT: l 111 LYS cc_start: 0.9204 (mptp) cc_final: 0.8927 (mmtm) REVERT: l 112 GLN cc_start: 0.8763 (mt0) cc_final: 0.8305 (mt0) REVERT: m 11 ASP cc_start: 0.8422 (p0) cc_final: 0.8167 (p0) REVERT: n 30 ILE cc_start: 0.8260 (OUTLIER) cc_final: 0.7806 (tt) REVERT: s 20 GLU cc_start: 0.8143 (pp20) cc_final: 0.7678 (pp20) REVERT: s 21 LYS cc_start: 0.8875 (OUTLIER) cc_final: 0.8602 (mptt) REVERT: s 73 GLU cc_start: 0.8301 (tt0) cc_final: 0.8017 (tt0) REVERT: t 10 ARG cc_start: 0.8953 (mmm-85) cc_final: 0.8538 (mmm160) REVERT: t 14 SER cc_start: 0.8806 (t) cc_final: 0.8390 (p) REVERT: t 55 GLN cc_start: 0.8249 (OUTLIER) cc_final: 0.8022 (tt0) REVERT: t 59 ASP cc_start: 0.8127 (m-30) cc_final: 0.7845 (m-30) REVERT: t 64 LYS cc_start: 0.8789 (tppt) cc_final: 0.8384 (tttt) REVERT: E 79 ARG cc_start: 0.9351 (OUTLIER) cc_final: 0.9114 (ttt-90) REVERT: E 88 ARG cc_start: 0.7980 (OUTLIER) cc_final: 0.7590 (mmp80) REVERT: E 136 GLN cc_start: 0.8667 (tp40) cc_final: 0.8283 (tp40) REVERT: F 96 MET cc_start: 0.8787 (tmm) cc_final: 0.8427 (ttp) REVERT: F 98 GLU cc_start: 0.8294 (mt-10) cc_final: 0.7998 (mt-10) REVERT: F 101 GLU cc_start: 0.8107 (tm-30) cc_final: 0.7786 (tm-30) REVERT: G 88 GLN cc_start: 0.8294 (mm110) cc_final: 0.8058 (mt0) REVERT: N 118 THR cc_start: 0.8871 (OUTLIER) cc_final: 0.8634 (p) REVERT: N 129 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.8108 (mttp) REVERT: O 127 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8477 (ttpt) REVERT: P 2 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8355 (ttp-110) REVERT: R 93 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7693 (ttt90) REVERT: S 16 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8647 (ttpp) REVERT: S 51 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.7181 (mtp85) REVERT: V 4 GLU cc_start: 0.8074 (pm20) cc_final: 0.7592 (pm20) REVERT: W 79 LYS cc_start: 0.9185 (OUTLIER) cc_final: 0.8785 (mtmm) REVERT: X 85 LYS cc_start: 0.9224 (OUTLIER) cc_final: 0.8895 (mtmm) REVERT: 1 43 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8217 (pp) REVERT: 1 44 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8677 (tptm) REVERT: 3 25 ARG cc_start: 0.8472 (mtp85) cc_final: 0.7926 (mtm110) REVERT: 8 36 ARG cc_start: 0.8437 (OUTLIER) cc_final: 0.8020 (ttt-90) outliers start: 225 outliers final: 127 residues processed: 1472 average time/residue: 2.0846 time to fit residues: 4459.4143 Evaluate side-chains 1500 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1346 time to evaluate : 5.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain f residue 102 MET Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 42 GLU Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 23 VAL Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 28 MET Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 55 GLN Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain O residue 127 LYS Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 4 residue 32 LYS Chi-restraints excluded: chain 5 residue 14 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 936 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 553 optimal weight: 10.0000 chunk 709 optimal weight: 0.9980 chunk 549 optimal weight: 20.0000 chunk 817 optimal weight: 5.9990 chunk 542 optimal weight: 10.0000 chunk 967 optimal weight: 8.9990 chunk 605 optimal weight: 10.0000 chunk 589 optimal weight: 7.9990 chunk 446 optimal weight: 7.9990 overall best weight: 5.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 19 ASN e 43 ASN e 78 ASN e 97 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** h 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 ASN r 31 ASN t 52 ASN t 61 GLN C 115 GLN D 58 ASN E 115 GLN ** G 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN L 128 ASN L 138 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN ** Z 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8858 moved from start: 0.1338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 156794 Z= 0.447 Angle : 0.691 14.194 235267 Z= 0.372 Chirality : 0.040 0.492 30124 Planarity : 0.007 0.139 12214 Dihedral : 23.326 179.373 79978 Min Nonbonded Distance : 1.718 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.32 % Favored : 95.57 % Rotamer: Outliers : 5.50 % Allowed : 25.66 % Favored : 68.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.11), residues: 5438 helix: 0.89 (0.12), residues: 1828 sheet: -0.74 (0.16), residues: 1081 loop : -0.46 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 62 HIS 0.010 0.001 HIS g 142 PHE 0.019 0.002 PHE Q 92 TYR 0.025 0.002 TYR d 76 ARG 0.014 0.001 ARG b 222 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 1360 time to evaluate : 6.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 42 TYR cc_start: 0.8310 (t80) cc_final: 0.7767 (t80) REVERT: c 46 GLU cc_start: 0.7967 (pt0) cc_final: 0.7252 (pt0) REVERT: d 78 GLU cc_start: 0.7572 (tp30) cc_final: 0.7306 (OUTLIER) REVERT: d 124 MET cc_start: 0.8113 (OUTLIER) cc_final: 0.7710 (mpt) REVERT: d 171 LEU cc_start: 0.6263 (OUTLIER) cc_final: 0.6032 (pp) REVERT: d 202 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7590 (pm20) REVERT: e 65 GLU cc_start: 0.7858 (tp30) cc_final: 0.7645 (tm-30) REVERT: g 67 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8331 (tm-30) REVERT: g 144 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8426 (tmm) REVERT: h 3 MET cc_start: 0.8296 (tpp) cc_final: 0.7997 (tpp) REVERT: h 9 ASP cc_start: 0.8486 (t70) cc_final: 0.8166 (t0) REVERT: h 76 GLN cc_start: 0.8615 (OUTLIER) cc_final: 0.8273 (pt0) REVERT: h 111 MET cc_start: 0.8185 (ptp) cc_final: 0.7946 (ptp) REVERT: j 9 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8402 (mtp180) REVERT: l 62 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: l 111 LYS cc_start: 0.9208 (mptp) cc_final: 0.8970 (mmtm) REVERT: l 121 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.7647 (ttm-80) REVERT: n 30 ILE cc_start: 0.8313 (OUTLIER) cc_final: 0.7850 (tt) REVERT: p 60 TRP cc_start: 0.8327 (OUTLIER) cc_final: 0.7944 (m-90) REVERT: q 42 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8904 (t) REVERT: s 20 GLU cc_start: 0.8218 (pp20) cc_final: 0.7764 (pp20) REVERT: s 21 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8576 (mptt) REVERT: s 37 ARG cc_start: 0.8946 (ptm160) cc_final: 0.8214 (ptm160) REVERT: t 10 ARG cc_start: 0.8972 (mmm-85) cc_final: 0.8609 (mmm-85) REVERT: t 14 SER cc_start: 0.8867 (t) cc_final: 0.8433 (p) REVERT: t 55 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.8068 (tt0) REVERT: t 59 ASP cc_start: 0.8275 (m-30) cc_final: 0.7992 (m-30) REVERT: t 64 LYS cc_start: 0.8801 (tppt) cc_final: 0.8469 (tttt) REVERT: E 88 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7601 (mmp80) REVERT: E 136 GLN cc_start: 0.8716 (tp40) cc_final: 0.8383 (tp40) REVERT: F 96 MET cc_start: 0.8811 (tmm) cc_final: 0.8488 (ttp) REVERT: F 98 GLU cc_start: 0.8301 (mt-10) cc_final: 0.8088 (mt-10) REVERT: F 101 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7887 (tm-30) REVERT: G 88 GLN cc_start: 0.8324 (mm110) cc_final: 0.8078 (mt0) REVERT: N 118 THR cc_start: 0.8882 (OUTLIER) cc_final: 0.8657 (p) REVERT: N 129 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.8149 (mttp) REVERT: P 2 ARG cc_start: 0.8999 (OUTLIER) cc_final: 0.8495 (ttp-110) REVERT: R 93 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7756 (ttt90) REVERT: S 11 ARG cc_start: 0.8052 (OUTLIER) cc_final: 0.7760 (tpm170) REVERT: S 15 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8369 (mtmm) REVERT: S 16 LYS cc_start: 0.8935 (OUTLIER) cc_final: 0.8695 (ttpp) REVERT: S 51 ARG cc_start: 0.8582 (OUTLIER) cc_final: 0.7253 (mtp85) REVERT: W 79 LYS cc_start: 0.9216 (OUTLIER) cc_final: 0.8815 (mtmm) REVERT: X 85 LYS cc_start: 0.9254 (OUTLIER) cc_final: 0.8918 (mtmm) REVERT: 1 43 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8414 (pp) REVERT: 1 44 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8765 (tptm) REVERT: 3 25 ARG cc_start: 0.8436 (mtp85) cc_final: 0.7961 (mtm180) REVERT: 7 44 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8945 (mt) REVERT: 8 36 ARG cc_start: 0.8457 (OUTLIER) cc_final: 0.8045 (ttt-90) outliers start: 235 outliers final: 153 residues processed: 1452 average time/residue: 2.0725 time to fit residues: 4347.2536 Evaluate side-chains 1523 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 181 poor density : 1342 time to evaluate : 5.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 108 LYS Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 71 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain j residue 9 ARG Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 25 VAL Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 60 TRP Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 67 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 28 MET Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 55 GLN Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 26 LEU Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 2 residue 5 ILE Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 5 residue 14 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 598 optimal weight: 3.9990 chunk 386 optimal weight: 20.0000 chunk 577 optimal weight: 5.9990 chunk 291 optimal weight: 9.9990 chunk 190 optimal weight: 8.9990 chunk 187 optimal weight: 6.9990 chunk 615 optimal weight: 10.0000 chunk 659 optimal weight: 6.9990 chunk 478 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 760 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 140 ASN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN e 19 ASN e 43 ASN e 78 ASN e 97 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN i 126 GLN l 5 ASN m 8 ASN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 40 GLN o 80 GLN q 51 ASN t 52 ASN D 58 ASN E 115 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN L 138 GLN N 54 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8854 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 156794 Z= 0.420 Angle : 0.684 14.027 235267 Z= 0.369 Chirality : 0.039 0.395 30124 Planarity : 0.007 0.137 12214 Dihedral : 23.356 179.417 79978 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.19 % Favored : 95.70 % Rotamer: Outliers : 5.41 % Allowed : 26.76 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.11), residues: 5438 helix: 0.87 (0.12), residues: 1826 sheet: -0.73 (0.16), residues: 1083 loop : -0.48 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G 62 HIS 0.010 0.001 HIS g 142 PHE 0.018 0.002 PHE Q 92 TYR 0.025 0.002 TYR d 76 ARG 0.014 0.001 ARG b 222 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1579 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 1348 time to evaluate : 6.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 6 MET cc_start: 0.7974 (ttp) cc_final: 0.7606 (tmm) REVERT: b 59 LYS cc_start: 0.8154 (ptpp) cc_final: 0.7919 (pttt) REVERT: b 154 MET cc_start: 0.8433 (ttt) cc_final: 0.7567 (tmt) REVERT: c 42 TYR cc_start: 0.8310 (t80) cc_final: 0.7762 (t80) REVERT: c 46 GLU cc_start: 0.7962 (pt0) cc_final: 0.7245 (pt0) REVERT: c 100 GLN cc_start: 0.9101 (pp30) cc_final: 0.8868 (pm20) REVERT: d 68 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8282 (mp) REVERT: d 78 GLU cc_start: 0.7600 (tp30) cc_final: 0.7339 (OUTLIER) REVERT: d 171 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6046 (pp) REVERT: d 202 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: e 61 GLN cc_start: 0.8461 (tp40) cc_final: 0.8208 (tp40) REVERT: e 68 ARG cc_start: 0.8687 (mtm-85) cc_final: 0.8429 (mtt90) REVERT: f 35 LYS cc_start: 0.8529 (mppt) cc_final: 0.8293 (mppt) REVERT: g 67 GLU cc_start: 0.8769 (OUTLIER) cc_final: 0.8344 (tm-30) REVERT: g 144 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8419 (tmm) REVERT: h 3 MET cc_start: 0.8325 (tpp) cc_final: 0.7996 (tpp) REVERT: h 9 ASP cc_start: 0.8488 (t70) cc_final: 0.8167 (t0) REVERT: h 76 GLN cc_start: 0.8606 (OUTLIER) cc_final: 0.8259 (pt0) REVERT: h 111 MET cc_start: 0.8210 (ptp) cc_final: 0.7980 (ptp) REVERT: h 117 ARG cc_start: 0.8683 (ttp-170) cc_final: 0.8342 (ttp-170) REVERT: l 62 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: l 121 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.7630 (ttm-80) REVERT: m 7 ILE cc_start: 0.9523 (OUTLIER) cc_final: 0.9174 (pt) REVERT: m 66 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8507 (mm-30) REVERT: n 30 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7798 (tt) REVERT: o 10 LYS cc_start: 0.9120 (ttpp) cc_final: 0.8711 (tptp) REVERT: q 42 THR cc_start: 0.9181 (OUTLIER) cc_final: 0.8897 (t) REVERT: s 20 GLU cc_start: 0.8221 (pp20) cc_final: 0.7825 (pp20) REVERT: s 21 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8600 (mptt) REVERT: t 10 ARG cc_start: 0.8967 (mmm-85) cc_final: 0.8615 (mmm-85) REVERT: t 14 SER cc_start: 0.8853 (t) cc_final: 0.8425 (p) REVERT: t 55 GLN cc_start: 0.8282 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: t 59 ASP cc_start: 0.8340 (m-30) cc_final: 0.8069 (m-30) REVERT: E 88 ARG cc_start: 0.8009 (OUTLIER) cc_final: 0.7600 (mmp80) REVERT: E 136 GLN cc_start: 0.8691 (tp40) cc_final: 0.8365 (tp40) REVERT: F 96 MET cc_start: 0.8798 (tmm) cc_final: 0.8497 (ttp) REVERT: F 98 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8066 (mt-10) REVERT: F 101 GLU cc_start: 0.8198 (tm-30) cc_final: 0.7887 (tm-30) REVERT: G 22 GLN cc_start: 0.8749 (tp-100) cc_final: 0.8458 (mm110) REVERT: G 88 GLN cc_start: 0.8333 (mm110) cc_final: 0.8095 (mt0) REVERT: G 116 GLN cc_start: 0.8629 (tp40) cc_final: 0.8417 (mm-40) REVERT: N 118 THR cc_start: 0.8892 (OUTLIER) cc_final: 0.8668 (p) REVERT: N 129 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8189 (mttp) REVERT: P 2 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8497 (ttp-110) REVERT: R 93 ARG cc_start: 0.8408 (OUTLIER) cc_final: 0.7756 (ttt90) REVERT: S 11 ARG cc_start: 0.8064 (OUTLIER) cc_final: 0.7765 (tpm170) REVERT: S 15 LYS cc_start: 0.8669 (OUTLIER) cc_final: 0.8364 (mtmm) REVERT: S 16 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8688 (ttpp) REVERT: S 51 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.7248 (mtp85) REVERT: W 79 LYS cc_start: 0.9221 (OUTLIER) cc_final: 0.8819 (mtmm) REVERT: X 85 LYS cc_start: 0.9251 (OUTLIER) cc_final: 0.8917 (mtmm) REVERT: 1 43 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8380 (pp) REVERT: 1 44 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8766 (tptm) REVERT: 2 37 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7338 (tm-30) REVERT: 3 25 ARG cc_start: 0.8420 (mtp85) cc_final: 0.8005 (mtm110) REVERT: 7 44 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8944 (mt) REVERT: 8 36 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.8030 (ttt-90) outliers start: 231 outliers final: 157 residues processed: 1433 average time/residue: 2.0991 time to fit residues: 4360.7588 Evaluate side-chains 1522 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1337 time to evaluate : 5.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 31 ILE Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 138 THR Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 210 VAL Chi-restraints excluded: chain c residue 85 GLU Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 68 LEU Chi-restraints excluded: chain d residue 85 ASN Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 169 THR Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 30 THR Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 32 VAL Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 76 GLN Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 113 ASP Chi-restraints excluded: chain h residue 125 ILE Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 26 SER Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 111 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 40 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain l residue 121 ARG Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 53 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 5 SER Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain p residue 68 SER Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 22 VAL Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 67 LEU Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 28 MET Chi-restraints excluded: chain t residue 54 MET Chi-restraints excluded: chain t residue 55 GLN Chi-restraints excluded: chain t residue 79 LEU Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 120 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 43 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain D residue 199 SER Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 175 ILE Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 23 ASN Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 164 GLU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 67 THR Chi-restraints excluded: chain G residue 110 SER Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain L residue 18 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain N residue 129 LYS Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 4 LYS Chi-restraints excluded: chain Q residue 5 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 28 VAL Chi-restraints excluded: chain Q residue 49 VAL Chi-restraints excluded: chain Q residue 61 GLN Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 19 SER Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 15 LYS Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain S residue 104 VAL Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 69 LEU Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 58 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 12 GLN Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Y residue 81 SER Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 43 GLU Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 34 SER Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 37 GLU Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 5 residue 14 SER Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 7 residue 44 LEU Chi-restraints excluded: chain 7 residue 54 ASP Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 880 optimal weight: 0.9990 chunk 927 optimal weight: 6.9990 chunk 845 optimal weight: 3.9990 chunk 901 optimal weight: 1.9990 chunk 926 optimal weight: 10.0000 chunk 542 optimal weight: 10.0000 chunk 392 optimal weight: 10.0000 chunk 708 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 814 optimal weight: 0.9990 chunk 852 optimal weight: 3.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 43 ASN e 78 ASN e 97 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN ** m 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 51 ASN C 153 GLN D 58 ASN E 115 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN L 138 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN ** Z 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 156794 Z= 0.186 Angle : 0.633 15.138 235267 Z= 0.345 Chirality : 0.034 0.407 30124 Planarity : 0.006 0.126 12214 Dihedral : 23.447 179.928 79978 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Rotamer: Outliers : 3.51 % Allowed : 28.98 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5438 helix: 0.93 (0.12), residues: 1839 sheet: -0.61 (0.16), residues: 1069 loop : -0.42 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP G 62 HIS 0.010 0.001 HIS g 142 PHE 0.018 0.001 PHE t 51 TYR 0.024 0.002 TYR d 76 ARG 0.014 0.001 ARG b 222 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 1382 time to evaluate : 5.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: c 42 TYR cc_start: 0.8249 (t80) cc_final: 0.7757 (t80) REVERT: c 46 GLU cc_start: 0.7927 (pt0) cc_final: 0.7238 (pt0) REVERT: c 100 GLN cc_start: 0.9129 (pp30) cc_final: 0.8912 (pm20) REVERT: d 78 GLU cc_start: 0.7529 (tp30) cc_final: 0.7285 (tp30) REVERT: d 124 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7607 (mpt) REVERT: d 171 LEU cc_start: 0.6191 (OUTLIER) cc_final: 0.5953 (pp) REVERT: d 202 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7538 (pm20) REVERT: e 61 GLN cc_start: 0.8369 (tp40) cc_final: 0.8155 (tp40) REVERT: e 70 ASN cc_start: 0.8391 (m-40) cc_final: 0.8093 (p0) REVERT: e 138 ARG cc_start: 0.9162 (mtp85) cc_final: 0.8961 (mtp85) REVERT: f 35 LYS cc_start: 0.8463 (mppt) cc_final: 0.8244 (mppt) REVERT: g 67 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: g 144 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8500 (tmm) REVERT: h 3 MET cc_start: 0.8289 (tpp) cc_final: 0.7975 (tpp) REVERT: h 9 ASP cc_start: 0.8446 (t70) cc_final: 0.8142 (t0) REVERT: h 111 MET cc_start: 0.8179 (ptp) cc_final: 0.7913 (ptp) REVERT: j 9 ARG cc_start: 0.9035 (mtt-85) cc_final: 0.8537 (ttt-90) REVERT: k 26 SER cc_start: 0.9433 (p) cc_final: 0.9221 (p) REVERT: l 62 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7370 (tm-30) REVERT: l 111 LYS cc_start: 0.9216 (mptp) cc_final: 0.8989 (mmtm) REVERT: n 30 ILE cc_start: 0.8127 (OUTLIER) cc_final: 0.7669 (tt) REVERT: o 10 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8710 (tptp) REVERT: q 42 THR cc_start: 0.9173 (OUTLIER) cc_final: 0.8869 (t) REVERT: s 6 LYS cc_start: 0.8939 (pttt) cc_final: 0.8738 (pttt) REVERT: s 20 GLU cc_start: 0.8171 (pp20) cc_final: 0.7842 (pp20) REVERT: s 21 LYS cc_start: 0.8881 (OUTLIER) cc_final: 0.8473 (mptt) REVERT: s 37 ARG cc_start: 0.8851 (ptm160) cc_final: 0.8583 (ptm160) REVERT: t 10 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8570 (mmm-85) REVERT: t 14 SER cc_start: 0.8813 (t) cc_final: 0.8388 (p) REVERT: E 88 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7557 (mmp80) REVERT: E 136 GLN cc_start: 0.8629 (tp40) cc_final: 0.8281 (tp40) REVERT: F 96 MET cc_start: 0.8767 (tmm) cc_final: 0.8450 (ttp) REVERT: F 101 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7787 (tm-30) REVERT: G 22 GLN cc_start: 0.8708 (tp-100) cc_final: 0.8433 (mm110) REVERT: G 88 GLN cc_start: 0.8269 (mm110) cc_final: 0.8066 (mt0) REVERT: G 95 ARG cc_start: 0.7678 (ptm-80) cc_final: 0.7443 (ptm160) REVERT: N 118 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8643 (p) REVERT: P 2 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.8381 (ttp-110) REVERT: R 93 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7675 (ttt90) REVERT: S 11 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7696 (tpm170) REVERT: S 16 LYS cc_start: 0.8854 (OUTLIER) cc_final: 0.8632 (ttpp) REVERT: S 51 ARG cc_start: 0.8438 (OUTLIER) cc_final: 0.7445 (mtt90) REVERT: W 79 LYS cc_start: 0.9189 (OUTLIER) cc_final: 0.8791 (mtmm) REVERT: X 85 LYS cc_start: 0.9225 (OUTLIER) cc_final: 0.8890 (mtmm) REVERT: 1 43 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8251 (pp) REVERT: 3 25 ARG cc_start: 0.8396 (mtp85) cc_final: 0.8011 (mtm110) REVERT: 8 36 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7980 (ttt-90) outliers start: 150 outliers final: 89 residues processed: 1435 average time/residue: 2.0748 time to fit residues: 4303.3635 Evaluate side-chains 1453 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1344 time to evaluate : 5.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 124 MET Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 113 ASP Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 165 GLU Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 7 GLN Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 73 LYS Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 898 optimal weight: 2.9990 chunk 592 optimal weight: 7.9990 chunk 953 optimal weight: 5.9990 chunk 582 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 662 optimal weight: 10.0000 chunk 1000 optimal weight: 6.9990 chunk 920 optimal weight: 10.0000 chunk 796 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 615 optimal weight: 10.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN e 43 ASN e 78 ASN e 97 GLN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN m 8 ASN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 80 GLN t 20 HIS D 58 ASN E 115 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8844 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.131 156794 Z= 0.398 Angle : 0.677 13.929 235267 Z= 0.366 Chirality : 0.039 0.402 30124 Planarity : 0.007 0.137 12214 Dihedral : 23.331 179.411 79978 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.10 % Favored : 95.79 % Rotamer: Outliers : 3.02 % Allowed : 30.03 % Favored : 66.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 5438 helix: 0.94 (0.12), residues: 1824 sheet: -0.68 (0.16), residues: 1079 loop : -0.44 (0.12), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 62 HIS 0.012 0.001 HIS g 142 PHE 0.017 0.002 PHE Q 92 TYR 0.027 0.002 TYR d 76 ARG 0.016 0.001 ARG q 27 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10876 Ramachandran restraints generated. 5438 Oldfield, 0 Emsley, 5438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1344 time to evaluate : 5.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 177 ASN cc_start: 0.8622 (m110) cc_final: 0.8221 (m110) REVERT: c 42 TYR cc_start: 0.8301 (t80) cc_final: 0.7742 (t80) REVERT: c 46 GLU cc_start: 0.7938 (pt0) cc_final: 0.7198 (pt0) REVERT: c 100 GLN cc_start: 0.9130 (pp30) cc_final: 0.8866 (pm20) REVERT: d 44 ARG cc_start: 0.7070 (ptp-170) cc_final: 0.6852 (ptp-170) REVERT: d 78 GLU cc_start: 0.7567 (tp30) cc_final: 0.7276 (OUTLIER) REVERT: d 124 MET cc_start: 0.8124 (mpt) cc_final: 0.7659 (mmm) REVERT: d 171 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5969 (pp) REVERT: d 202 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7616 (pm20) REVERT: e 61 GLN cc_start: 0.8418 (tp40) cc_final: 0.8178 (tp40) REVERT: e 122 ASN cc_start: 0.8706 (m-40) cc_final: 0.8400 (m110) REVERT: f 35 LYS cc_start: 0.8517 (mppt) cc_final: 0.8293 (mppt) REVERT: g 67 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8348 (tm-30) REVERT: g 144 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8438 (tmm) REVERT: h 3 MET cc_start: 0.8318 (tpp) cc_final: 0.7999 (tpp) REVERT: h 9 ASP cc_start: 0.8520 (t70) cc_final: 0.8219 (t0) REVERT: h 111 MET cc_start: 0.8212 (ptp) cc_final: 0.7983 (ptp) REVERT: h 117 ARG cc_start: 0.8625 (ttp-170) cc_final: 0.8258 (ttp-170) REVERT: i 18 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7283 (ptm160) REVERT: l 62 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7323 (tm-30) REVERT: l 111 LYS cc_start: 0.9215 (mptp) cc_final: 0.8956 (mmtm) REVERT: n 30 ILE cc_start: 0.8223 (OUTLIER) cc_final: 0.7779 (tt) REVERT: s 6 LYS cc_start: 0.8924 (pttt) cc_final: 0.8719 (pttt) REVERT: s 20 GLU cc_start: 0.8180 (pp20) cc_final: 0.7876 (pp20) REVERT: s 21 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8530 (mppt) REVERT: t 10 ARG cc_start: 0.8954 (mmm-85) cc_final: 0.8600 (mmm-85) REVERT: t 14 SER cc_start: 0.8856 (t) cc_final: 0.8429 (p) REVERT: E 79 ARG cc_start: 0.9369 (OUTLIER) cc_final: 0.9122 (ttt-90) REVERT: E 88 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7604 (mmp80) REVERT: E 136 GLN cc_start: 0.8659 (tp40) cc_final: 0.8357 (tp40) REVERT: F 96 MET cc_start: 0.8807 (tmm) cc_final: 0.8469 (ttp) REVERT: F 98 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7989 (mt-10) REVERT: F 101 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7915 (tm-30) REVERT: G 22 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8444 (mm110) REVERT: G 88 GLN cc_start: 0.8328 (mm110) cc_final: 0.8094 (mt0) REVERT: N 118 THR cc_start: 0.8897 (OUTLIER) cc_final: 0.8668 (p) REVERT: P 2 ARG cc_start: 0.8970 (OUTLIER) cc_final: 0.8293 (ttp-110) REVERT: R 93 ARG cc_start: 0.8389 (OUTLIER) cc_final: 0.7738 (ttt90) REVERT: S 11 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7757 (tpm170) REVERT: S 16 LYS cc_start: 0.8921 (OUTLIER) cc_final: 0.8675 (ttpp) REVERT: S 51 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7261 (mtp85) REVERT: W 79 LYS cc_start: 0.9205 (OUTLIER) cc_final: 0.8806 (mtmm) REVERT: X 85 LYS cc_start: 0.9260 (OUTLIER) cc_final: 0.8917 (mtmm) REVERT: 1 43 LEU cc_start: 0.8639 (OUTLIER) cc_final: 0.8354 (pp) REVERT: 1 44 LYS cc_start: 0.9180 (OUTLIER) cc_final: 0.8768 (tptm) REVERT: 3 25 ARG cc_start: 0.8483 (mtp85) cc_final: 0.7946 (mtm110) REVERT: 8 36 ARG cc_start: 0.8456 (OUTLIER) cc_final: 0.8031 (ttt-90) outliers start: 129 outliers final: 97 residues processed: 1394 average time/residue: 2.1079 time to fit residues: 4245.6062 Evaluate side-chains 1449 residues out of total 4546 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1332 time to evaluate : 5.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 163 VAL Chi-restraints excluded: chain c residue 165 THR Chi-restraints excluded: chain c residue 185 ASN Chi-restraints excluded: chain d residue 48 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 171 LEU Chi-restraints excluded: chain d residue 202 GLU Chi-restraints excluded: chain e residue 120 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 18 VAL Chi-restraints excluded: chain f residue 36 ILE Chi-restraints excluded: chain f residue 90 MET Chi-restraints excluded: chain g residue 67 GLU Chi-restraints excluded: chain g residue 104 ILE Chi-restraints excluded: chain g residue 144 MET Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 67 GLN Chi-restraints excluded: chain h residue 95 VAL Chi-restraints excluded: chain h residue 105 SER Chi-restraints excluded: chain h residue 113 ASP Chi-restraints excluded: chain i residue 18 ARG Chi-restraints excluded: chain i residue 19 VAL Chi-restraints excluded: chain i residue 29 VAL Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain i residue 111 VAL Chi-restraints excluded: chain k residue 20 VAL Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 46 THR Chi-restraints excluded: chain k residue 59 THR Chi-restraints excluded: chain l residue 21 VAL Chi-restraints excluded: chain l residue 62 GLU Chi-restraints excluded: chain l residue 108 LYS Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain m residue 64 VAL Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ARG Chi-restraints excluded: chain n residue 67 THR Chi-restraints excluded: chain o residue 5 THR Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 56 ARG Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 17 MET Chi-restraints excluded: chain q residue 23 VAL Chi-restraints excluded: chain r residue 71 THR Chi-restraints excluded: chain s residue 5 LEU Chi-restraints excluded: chain s residue 21 LYS Chi-restraints excluded: chain s residue 48 THR Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 23 SER Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 110 THR Chi-restraints excluded: chain E residue 79 ARG Chi-restraints excluded: chain E residue 88 ARG Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 191 ASP Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 36 THR Chi-restraints excluded: chain G residue 39 ASP Chi-restraints excluded: chain G residue 49 THR Chi-restraints excluded: chain G residue 169 VAL Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain M residue 66 LYS Chi-restraints excluded: chain M residue 67 LYS Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 143 GLU Chi-restraints excluded: chain O residue 134 THR Chi-restraints excluded: chain P residue 2 ARG Chi-restraints excluded: chain P residue 15 SER Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 62 LEU Chi-restraints excluded: chain Q residue 65 THR Chi-restraints excluded: chain Q residue 78 VAL Chi-restraints excluded: chain R residue 7 GLN Chi-restraints excluded: chain R residue 93 ARG Chi-restraints excluded: chain R residue 110 ILE Chi-restraints excluded: chain S residue 11 ARG Chi-restraints excluded: chain S residue 16 LYS Chi-restraints excluded: chain S residue 51 ARG Chi-restraints excluded: chain T residue 15 SER Chi-restraints excluded: chain T residue 46 GLU Chi-restraints excluded: chain T residue 66 HIS Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 67 ASP Chi-restraints excluded: chain U residue 72 THR Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain V residue 29 THR Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 78 SER Chi-restraints excluded: chain W residue 42 VAL Chi-restraints excluded: chain W residue 79 LYS Chi-restraints excluded: chain X residue 70 ILE Chi-restraints excluded: chain X residue 85 LYS Chi-restraints excluded: chain X residue 90 ASP Chi-restraints excluded: chain Z residue 2 SER Chi-restraints excluded: chain Z residue 65 ASP Chi-restraints excluded: chain 1 residue 9 LYS Chi-restraints excluded: chain 1 residue 43 LEU Chi-restraints excluded: chain 1 residue 44 LYS Chi-restraints excluded: chain 3 residue 57 VAL Chi-restraints excluded: chain 4 residue 9 THR Chi-restraints excluded: chain 4 residue 11 SER Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 4 residue 25 VAL Chi-restraints excluded: chain 5 residue 22 THR Chi-restraints excluded: chain 5 residue 23 THR Chi-restraints excluded: chain 8 residue 36 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1004 random chunks: chunk 488 optimal weight: 7.9990 chunk 632 optimal weight: 6.9990 chunk 848 optimal weight: 1.9990 chunk 244 optimal weight: 0.0270 chunk 734 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 221 optimal weight: 7.9990 chunk 797 optimal weight: 1.9990 chunk 333 optimal weight: 3.9990 chunk 819 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.7844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 93 ASN ** d 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 78 ASN e 97 GLN ** e 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 31 ASN i 50 GLN l 5 ASN ** n 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 62 GLN q 51 ASN C 115 GLN C 153 GLN D 58 ASN E 115 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 28 ASN L 86 GLN L 138 GLN N 54 GLN ** O 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 28 ASN ** X 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 28 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.100822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.067488 restraints weight = 274656.531| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 1.03 r_work: 0.2631 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2542 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8924 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 156794 Z= 0.188 Angle : 0.639 15.086 235267 Z= 0.348 Chirality : 0.034 0.409 30124 Planarity : 0.006 0.127 12214 Dihedral : 23.421 179.766 79978 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.77 % Favored : 96.12 % Rotamer: Outliers : 3.07 % Allowed : 30.41 % Favored : 66.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.64 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5438 helix: 0.94 (0.12), residues: 1835 sheet: -0.57 (0.16), residues: 1074 loop : -0.44 (0.12), residues: 2529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP G 62 HIS 0.011 0.001 HIS g 142 PHE 0.016 0.001 PHE t 51 TYR 0.023 0.002 TYR d 76 ARG 0.018 0.001 ARG q 27 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 58249.57 seconds wall clock time: 1006 minutes 31.94 seconds (60391.94 seconds total)