Starting phenix.real_space_refine on Tue Mar 26 07:15:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agu_15424/03_2024/8agu_15424_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agu_15424/03_2024/8agu_15424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agu_15424/03_2024/8agu_15424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agu_15424/03_2024/8agu_15424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agu_15424/03_2024/8agu_15424_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8agu_15424/03_2024/8agu_15424_updated.pdb" } resolution = 2.7 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= 0.020 sd= 0.128 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 7 6.06 5 P 3568 5.49 5 Mg 13 5.21 5 S 177 5.16 5 C 80608 2.51 5 N 27324 2.21 5 O 38051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 29": "OE1" <-> "OE2" Residue "A GLU 91": "OE1" <-> "OE2" Residue "B GLU 106": "OE1" <-> "OE2" Residue "B GLU 157": "OE1" <-> "OE2" Residue "B GLU 166": "OE1" <-> "OE2" Residue "C GLU 140": "OE1" <-> "OE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D GLU 173": "OE1" <-> "OE2" Residue "E GLU 72": "OE1" <-> "OE2" Residue "F GLU 34": "OE1" <-> "OE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F GLU 104": "OE1" <-> "OE2" Residue "G GLU 86": "OE1" <-> "OE2" Residue "G GLU 144": "OE1" <-> "OE2" Residue "H PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 121": "OE1" <-> "OE2" Residue "J GLU 4": "OE1" <-> "OE2" Residue "K GLU 70": "OE1" <-> "OE2" Residue "L GLU 67": "OE1" <-> "OE2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M GLU 108": "OE1" <-> "OE2" Residue "M GLU 109": "OE1" <-> "OE2" Residue "M GLU 119": "OE1" <-> "OE2" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 76": "OE1" <-> "OE2" Residue "Q GLU 35": "OE1" <-> "OE2" Residue "Q GLU 68": "OE1" <-> "OE2" Residue "Q GLU 81": "OE1" <-> "OE2" Residue "R GLU 83": "OE1" <-> "OE2" Residue "S GLU 58": "OE1" <-> "OE2" Residue "T GLU 87": "OE1" <-> "OE2" Residue "U GLU 8": "OE1" <-> "OE2" Residue "U GLU 15": "OE1" <-> "OE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 64": "OE1" <-> "OE2" Residue "V GLU 88": "OE1" <-> "OE2" Residue "b GLU 96": "OE1" <-> "OE2" Residue "c GLU 88": "OE1" <-> "OE2" Residue "j GLU 74": "OE1" <-> "OE2" Residue "j GLU 118": "OE1" <-> "OE2" Residue "k GLU 71": "OE1" <-> "OE2" Residue "k GLU 190": "OE1" <-> "OE2" Residue "k GLU 291": "OE1" <-> "OE2" Residue "k GLU 353": "OE1" <-> "OE2" Residue "l TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 117": "OE1" <-> "OE2" Residue "l TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 337": "OE1" <-> "OE2" Residue "m TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 148": "OE1" <-> "OE2" Residue "q GLU 143": "OE1" <-> "OE2" Residue "r GLU 45": "OE1" <-> "OE2" Residue "r GLU 58": "OE1" <-> "OE2" Residue "s GLU 15": "OE1" <-> "OE2" Residue "s GLU 38": "OE1" <-> "OE2" Residue "u GLU 37": "OE1" <-> "OE2" Residue "a ARG 99": "NH1" <-> "NH2" Residue "a GLU 162": "OE1" <-> "OE2" Residue "a PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 864": "OE1" <-> "OE2" Residue "a GLU 881": "OE1" <-> "OE2" Residue "e GLU 203": "OE1" <-> "OE2" Residue "e GLU 324": "OE1" <-> "OE2" Residue "e GLU 900": "OE1" <-> "OE2" Residue "e GLU 937": "OE1" <-> "OE2" Residue "e GLU 972": "OE1" <-> "OE2" Residue "e GLU 991": "OE1" <-> "OE2" Residue "e GLU 996": "OE1" <-> "OE2" Residue "v GLU 71": "OE1" <-> "OE2" Residue "0 ARG 61": "NH1" <-> "NH2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 149748 Number of models: 1 Model: "" Number of chains: 68 Chain: "A" Number of atoms: 1720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1720 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 7, 'TRANS': 195} Chain: "B" Number of atoms: 1555 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 197, 1555 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 8, 'TRANS': 188} Chain: "C" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1416 Classifications: {'peptide': 183} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 177} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3} Unresolved non-hydrogen planarities: 12 Chain: "D" Number of atoms: 1441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1441 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 9, 'TRANS': 175} Chain: "E" Number of atoms: 1258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1258 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 2, 'TRANS': 153} Chain: "F" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1437 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "G" Number of atoms: 1272 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1272 Classifications: {'peptide': 159} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "H" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 796 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "I" Number of atoms: 1003 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1003 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "J" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 518 Classifications: {'peptide': 63} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 60} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 964 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 115} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 984 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "M" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1080 Classifications: {'peptide': 135} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 128} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "N" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1169 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 140} 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: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 462 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 3, 'TRANS': 54} Chain: "P" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 737 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "Q" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 104} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1013 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 121} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 850 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Chain: "T" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 880 Classifications: {'peptide': 112} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 4, 'TRANS': 107} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "U" Number of atoms: 969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 969 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "V" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 95} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "W" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 645 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 1, 'TRANS': 78} Chain: "X" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 612 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "Y" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 436 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "Z" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 410 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "b" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 824 Classifications: {'peptide': 103} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 100} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "c" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 694 Classifications: {'peptide': 91} Link IDs: {'TRANS': 90} Chain: "d" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 207 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "f" Number of atoms: 68782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3216, 68782 Classifications: {'RNA': 3216} Modifications used: {'rna2p_pur': 330, 'rna2p_pyr': 219, 'rna3p_pur': 1449, 'rna3p_pyr': 1218} Link IDs: {'rna2p': 549, 'rna3p': 2666} Chain breaks: 3 Chain: "h" Number of atoms: 2579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 2579 Classifications: {'RNA': 121} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 7, 'rna3p_pur': 57, 'rna3p_pyr': 51} Link IDs: {'rna2p': 12, 'rna3p': 108} Chain: "i" Number of atoms: 3353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 3353 Classifications: {'RNA': 158} Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 14, 'rna3p_pur': 63, 'rna3p_pyr': 66} Link IDs: {'rna2p': 28, 'rna3p': 129} Chain: "j" Number of atoms: 1874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1874 Classifications: {'peptide': 246} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 234} Chain: "k" Number of atoms: 3075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3075 Classifications: {'peptide': 386} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 371} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 5 Chain: "l" Number of atoms: 2748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2748 Classifications: {'peptide': 361} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 343} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "m" Number of atoms: 2351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2351 Classifications: {'peptide': 294} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 283} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "n" Number of atoms: 1307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1307 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 157} Chain breaks: 1 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 11 Chain: "o" Number of atoms: 1784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1784 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 10, 'TRANS': 211} Chain: "p" Number of atoms: 1804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1804 Classifications: {'peptide': 233} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 12, 'TRANS': 220} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "q" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1508 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 186} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "r" Number of atoms: 1764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1764 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 10, 'TRANS': 207} Chain: "s" Number of atoms: 1346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1346 Classifications: {'peptide': 169} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 163} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "t" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1543 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 9, 'TRANS': 183} Chain: "u" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1053 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain: "a" Number of atoms: 6569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 848, 6569 Classifications: {'peptide': 848} Incomplete info: {'truncation_to_alanine': 98} Link IDs: {'PTRANS': 29, 'TRANS': 818} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 324 Unresolved non-hydrogen angles: 397 Unresolved non-hydrogen dihedrals: 261 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 6, 'ASP:plan': 12, 'TYR:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 166 Chain: "e" Number of atoms: 11509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1527, 11509 Classifications: {'peptide': 1527} Incomplete info: {'truncation_to_alanine': 271} Link IDs: {'PTRANS': 38, 'TRANS': 1488} Chain breaks: 3 Unresolved chain link angles: 7 Unresolved non-hydrogen bonds: 981 Unresolved non-hydrogen angles: 1251 Unresolved non-hydrogen dihedrals: 815 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 11, 'TYR:plan': 12, 'ASN:plan1': 23, 'TRP:plan': 1, 'ASP:plan': 21, 'PHE:plan': 27, 'GLU:plan': 25, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 566 Chain: "g" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1651 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "v" Number of atoms: 1085 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1085 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 136} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'5CT:plan-1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "w" Number of atoms: 1709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1709 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Chain: "y" Number of atoms: 1556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1556 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 62} Chain breaks: 1 Chain: "z" Number of atoms: 728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 728 Classifications: {'peptide': 148} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'PTRANS': 8, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 416 Unresolved non-hydrogen angles: 520 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 44 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 7, 'PHE:plan': 3, 'GLU:plan': 10, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 182 Chain: "0" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 961 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "1" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 85 Classifications: {'peptide': 17} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'TRANS': 16} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'UNK:plan-1': 17} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 13 Unusual residues: {' MG': 3, 'SPD': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 20901 SG CYS T 44 120.133 170.613 212.561 1.00 54.16 S ATOM 20919 SG CYS T 47 122.230 167.963 211.472 1.00 59.61 S ATOM 21191 SG CYS T 84 123.418 170.446 214.294 1.00 57.91 S ATOM 23302 SG CYS W 19 84.769 188.181 170.236 1.00 40.18 S ATOM 23327 SG CYS W 22 83.021 188.257 166.954 1.00 41.00 S ATOM 23427 SG CYS W 34 86.752 188.265 167.000 1.00 38.42 S ATOM 23445 SG CYS W 37 84.783 191.352 168.157 1.00 40.17 S ATOM 25002 SG CYS Z 96 133.207 139.531 76.595 1.00 54.37 S ATOM 25028 SG CYS Z 99 130.585 137.844 78.604 1.00 53.18 S ATOM 25115 SG CYS Z 110 130.460 137.313 74.924 1.00 52.08 S ATOM 25161 SG CYS Z 115 129.397 140.536 76.168 1.00 52.77 S ATOM 25359 SG CYS b 12 132.024 247.017 110.258 1.00 63.95 S ATOM 25394 SG CYS b 17 133.300 250.556 109.360 1.00 72.10 S ATOM 25858 SG CYS b 74 135.515 248.041 111.490 1.00 60.93 S ATOM 25880 SG CYS b 77 132.414 249.877 112.667 1.00 66.15 S ATOM 26403 SG CYS c 39 138.785 168.144 205.732 1.00 58.71 S ATOM 26426 SG CYS c 42 138.172 165.162 207.824 1.00 62.48 S ATOM 26535 SG CYS c 57 135.954 165.676 204.832 1.00 55.64 S ATOM 26553 SG CYS c 60 135.530 168.141 207.587 1.00 57.82 S ATOM A0W67 SG CYS e1527 39.261 124.463 188.831 1.00285.10 S ATOM A0W6R SG CYS e1530 37.002 122.403 186.968 1.00279.23 S ATOM A0WBJ SG CYS e1551 38.390 125.443 185.586 1.00286.27 S ATOM A0WC4 SG CYS e1554 36.160 126.612 188.096 1.00284.05 S ATOM A0W25 SG CYS e1508 41.101 118.913 177.749 1.00285.58 S ATOM A0W8H SG CYS e1538 42.836 121.636 175.171 1.00281.30 S Residues with excluded nonbonded symmetry interactions: 197 residue: pdb=" N AVAL B 3 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 3 " occ=0.50 residue: pdb=" N AGLU B 4 " occ=0.50 ... (7 atoms not shown) pdb=" OE2AGLU B 4 " occ=0.50 residue: pdb=" N APRO B 5 " occ=0.50 ... (5 atoms not shown) pdb=" CD APRO B 5 " occ=0.50 residue: pdb=" N AVAL B 6 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 6 " occ=0.50 residue: pdb=" N AVAL B 7 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 7 " occ=0.50 residue: pdb=" N AVAL B 8 " occ=0.50 ... (5 atoms not shown) pdb=" CG2AVAL B 8 " occ=0.50 residue: pdb=" N AILE B 9 " occ=0.50 ... (6 atoms not shown) pdb=" CD1AILE B 9 " occ=0.50 residue: pdb=" N AASP B 10 " occ=0.50 ... (6 atoms not shown) pdb=" OD2AASP B 10 " occ=0.50 residue: pdb=" N AGLY B 11 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 11 " occ=0.50 residue: pdb=" N ALYS B 12 " occ=0.50 ... (7 atoms not shown) pdb=" NZ ALYS B 12 " occ=0.50 residue: pdb=" N AGLY B 13 " occ=0.50 ... (2 atoms not shown) pdb=" O AGLY B 13 " occ=0.50 residue: pdb=" N AHIS B 14 " occ=0.50 ... (8 atoms not shown) pdb=" NE2AHIS B 14 " occ=0.50 ... (remaining 185 not shown) Time building chain proxies: 58.49, per 1000 atoms: 0.39 Number of scatterers: 149748 At special positions: 0 Unit cell: (239.334, 282.753, 262.632, 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 7 29.99 S 177 16.00 P 3568 15.00 Mg 13 11.99 O 38051 8.00 N 27324 7.00 C 80608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 57.21 Conformation dependent library (CDL) restraints added in 9.5 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN T 201 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 47 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 44 " pdb="ZN ZN T 201 " - pdb=" SG CYS T 84 " pdb=" ZN W 101 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 22 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 19 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 37 " pdb="ZN ZN W 101 " - pdb=" SG CYS W 34 " pdb=" ZN Z 201 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 99 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 110 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 115 " pdb="ZN ZN Z 201 " - pdb=" SG CYS Z 96 " pdb=" ZN b 201 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 77 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 12 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 17 " pdb="ZN ZN b 201 " - pdb=" SG CYS b 74 " pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 39 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 57 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 42 " pdb="ZN ZN c 501 " - pdb=" SG CYS c 60 " pdb=" ZN e2001 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1530 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1527 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1554 " pdb="ZN ZN e2001 " - pdb=" SG CYS e1551 " pdb=" ZN e2002 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1508 " pdb="ZN ZN e2002 " - pdb=" SG CYS e1538 " pdb="ZN ZN e2002 " - pdb=" ND1 HIS e1535 " Number of angles added : 30 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17762 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: 367 helices and 87 sheets defined 48.9% alpha, 12.8% beta 1159 base pairs and 1966 stacking pairs defined. Time for finding SS restraints: 92.41 Creating SS restraints... Processing helix chain 'A' and resid 2 through 14 removed outlier: 4.806A pdb=" N TYR A 6 " --> pdb=" O GLY A 2 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LYS A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 34 removed outlier: 3.753A pdb=" N TRP A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LYS A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N ASN A 34 " --> pdb=" O TYR A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 52 Processing helix chain 'A' and resid 83 through 88 removed outlier: 3.843A pdb=" N GLN A 87 " --> pdb=" O LYS A 83 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLY A 88 " --> pdb=" O PRO A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 83 through 88' Processing helix chain 'A' and resid 97 through 111 Processing helix chain 'A' and resid 139 through 145 removed outlier: 4.410A pdb=" N ASP A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 153 removed outlier: 5.054A pdb=" N TRP A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N CYS A 152 " --> pdb=" O TYR A 148 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ASP A 153 " --> pdb=" O ASN A 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 146 through 153' Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 165 through 173 Processing helix chain 'A' and resid 186 through 196 Processing helix chain 'B' and resid 15 through 30 removed outlier: 3.689A pdb=" N ALYS B 25 " --> pdb=" O ASER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 60 removed outlier: 4.078A pdb=" N ALYS B 60 " --> pdb=" O AASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 70 removed outlier: 4.023A pdb=" N AGLY B 69 " --> pdb=" O AASN B 65 " (cutoff:3.500A) Proline residue: B 70 - end of helix No H-bonds generated for 'chain 'B' and resid 65 through 70' Processing helix chain 'B' and resid 75 through 89 removed outlier: 3.834A pdb=" N AMET B 87 " --> pdb=" O AALA B 83 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N ASER B 89 " --> pdb=" O AARG B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 103 removed outlier: 3.928A pdb=" N AARG B 101 " --> pdb=" O AALA B 97 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N ALEU B 102 " --> pdb=" O AALA B 98 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N ALYS B 103 " --> pdb=" O ALEU B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 114 removed outlier: 4.915A pdb=" N ALYS B 114 " --> pdb=" O APRO B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 129 Processing helix chain 'B' and resid 137 through 146 Processing helix chain 'B' and resid 151 through 186 removed outlier: 3.814A pdb=" N ALYS B 170 " --> pdb=" O AGLU B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'C' and resid 10 through 15 removed outlier: 3.730A pdb=" N SER C 14 " --> pdb=" O ASN C 10 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ALA C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 10 through 15' Processing helix chain 'C' and resid 25 through 37 removed outlier: 3.640A pdb=" N GLU C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE C 36 " --> pdb=" O THR C 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 54 Processing helix chain 'C' and resid 84 through 106 Processing helix chain 'C' and resid 169 through 183 Processing helix chain 'C' and resid 70 through 76 removed outlier: 3.765A pdb=" N GLY C 73 " --> pdb=" O THR C 70 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU C 75 " --> pdb=" O GLN C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 23 through 40 Processing helix chain 'D' and resid 42 through 54 removed outlier: 3.961A pdb=" N LYS D 46 " --> pdb=" O ALA D 42 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N PHE D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LEU D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 60 Proline residue: D 60 - end of helix Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.813A pdb=" N GLN D 73 " --> pdb=" O ARG D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 118 Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 147 through 154 removed outlier: 4.144A pdb=" N ARG D 151 " --> pdb=" O ARG D 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N HIS D 152 " --> pdb=" O GLU D 148 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE D 153 " --> pdb=" O ALA D 149 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLY D 154 " --> pdb=" O VAL D 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 147 through 154' Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 18 through 23 removed outlier: 3.908A pdb=" N VAL E 22 " --> pdb=" O GLY E 18 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TRP E 23 " --> pdb=" O LYS E 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 18 through 23' Processing helix chain 'E' and resid 28 through 36 removed outlier: 5.179A pdb=" N ASN E 36 " --> pdb=" O ILE E 32 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 48 Processing helix chain 'E' and resid 60 through 73 Processing helix chain 'E' and resid 77 through 82 removed outlier: 3.710A pdb=" N ARG E 81 " --> pdb=" O GLY E 77 " (cutoff:3.500A) removed outlier: 5.973A pdb=" N LYS E 82 " --> pdb=" O TYR E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 77 through 82' Processing helix chain 'E' and resid 84 through 113 Proline residue: E 90 - end of helix removed outlier: 6.826A pdb=" N VAL E 93 " --> pdb=" O LEU E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 130 removed outlier: 3.685A pdb=" N VAL E 122 " --> pdb=" O HIS E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 157 Processing helix chain 'F' and resid 33 through 49 Processing helix chain 'F' and resid 98 through 114 Processing helix chain 'F' and resid 117 through 122 removed outlier: 5.661A pdb=" N HIS F 122 " --> pdb=" O PHE F 118 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 4.880A pdb=" N PHE F 143 " --> pdb=" O TYR F 139 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU F 144 " --> pdb=" O VAL F 140 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N THR F 145 " --> pdb=" O LYS F 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 32 removed outlier: 4.512A pdb=" N TYR G 30 " --> pdb=" O HIS G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 4.286A pdb=" N ILE G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N LYS G 97 " --> pdb=" O VAL G 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 92 through 97' Processing helix chain 'G' and resid 99 through 121 removed outlier: 3.890A pdb=" N GLN G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ALA G 121 " --> pdb=" O ALA G 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 26 removed outlier: 4.167A pdb=" N ASN H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY H 26 " --> pdb=" O PRO H 22 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 41 Processing helix chain 'H' and resid 72 through 88 Processing helix chain 'I' and resid 66 through 71 removed outlier: 5.400A pdb=" N LYS I 71 " --> pdb=" O PRO I 67 " (cutoff:3.500A) Processing helix chain 'I' and resid 119 through 127 removed outlier: 3.884A pdb=" N LEU I 125 " --> pdb=" O GLU I 121 " (cutoff:3.500A) Proline residue: I 127 - end of helix Processing helix chain 'I' and resid 128 through 133 Processing helix chain 'J' and resid 33 through 43 Processing helix chain 'J' and resid 45 through 50 removed outlier: 3.562A pdb=" N ILE J 49 " --> pdb=" O ASN J 45 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ALA J 50 " --> pdb=" O PRO J 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 45 through 50' Processing helix chain 'J' and resid 52 through 60 Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.644A pdb=" N ILE K 63 " --> pdb=" O SER K 59 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLU K 64 " --> pdb=" O TYR K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 78 removed outlier: 3.733A pdb=" N LYS K 75 " --> pdb=" O THR K 71 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N VAL K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU K 77 " --> pdb=" O MET K 73 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ASP K 78 " --> pdb=" O LYS K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 103 Processing helix chain 'K' and resid 131 through 140 removed outlier: 3.836A pdb=" N ASN K 137 " --> pdb=" O LEU K 133 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ARG K 138 " --> pdb=" O ASP K 134 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 Processing helix chain 'L' and resid 23 through 32 removed outlier: 4.027A pdb=" N VAL L 29 " --> pdb=" O SER L 25 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N SER L 32 " --> pdb=" O ARG L 28 " (cutoff:3.500A) Processing helix chain 'L' and resid 36 through 44 Processing helix chain 'L' and resid 100 through 105 removed outlier: 3.568A pdb=" N LEU L 104 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N VAL L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 100 through 105' Processing helix chain 'L' and resid 112 through 123 Processing helix chain 'M' and resid 58 through 67 removed outlier: 5.381A pdb=" N VAL M 62 " --> pdb=" O GLY M 58 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N LYS M 67 " --> pdb=" O ALA M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 76 through 81 removed outlier: 3.567A pdb=" N LEU M 80 " --> pdb=" O ASN M 76 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU M 81 " --> pdb=" O TYR M 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 76 through 81' Processing helix chain 'M' and resid 92 through 97 removed outlier: 5.472A pdb=" N SER M 97 " --> pdb=" O LYS M 93 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 125 removed outlier: 3.596A pdb=" N VAL M 113 " --> pdb=" O GLU M 109 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N GLY M 125 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'N' and resid 2 through 7 removed outlier: 4.161A pdb=" N THR N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS N 7 " --> pdb=" O SER N 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 2 through 7' Processing helix chain 'N' and resid 41 through 49 Processing helix chain 'N' and resid 64 through 69 removed outlier: 4.420A pdb=" N PHE N 68 " --> pdb=" O GLN N 64 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N TRP N 69 " --> pdb=" O GLN N 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 64 through 69' Processing helix chain 'N' and resid 74 through 83 removed outlier: 4.578A pdb=" N TRP N 79 " --> pdb=" O LEU N 75 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N LEU N 81 " --> pdb=" O LYS N 77 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ILE N 82 " --> pdb=" O LEU N 78 " (cutoff:3.500A) Proline residue: N 83 - end of helix Processing helix chain 'N' and resid 86 through 94 removed outlier: 4.083A pdb=" N ALA N 94 " --> pdb=" O TYR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 Processing helix chain 'N' and resid 131 through 142 Processing helix chain 'O' and resid 11 through 20 removed outlier: 4.643A pdb=" N ASN O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 36 through 59 removed outlier: 3.531A pdb=" N ASN O 42 " --> pdb=" O LYS O 38 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N HIS O 45 " --> pdb=" O ARG O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 9 through 20 Processing helix chain 'P' and resid 26 through 37 Processing helix chain 'P' and resid 49 through 64 Processing helix chain 'P' and resid 73 through 82 removed outlier: 3.830A pdb=" N THR P 79 " --> pdb=" O ASN P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.972A pdb=" N LEU P 104 " --> pdb=" O ILE P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 15 through 21 removed outlier: 3.857A pdb=" N ARG Q 19 " --> pdb=" O ASN Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 27 through 45 Processing helix chain 'Q' and resid 52 through 61 Processing helix chain 'R' and resid 21 through 26 removed outlier: 5.153A pdb=" N HIS R 26 " --> pdb=" O SER R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 40 through 45 Processing helix chain 'R' and resid 78 through 87 removed outlier: 3.853A pdb=" N THR R 84 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) removed outlier: 4.546A pdb=" N THR R 86 " --> pdb=" O LEU R 82 " (cutoff:3.500A) removed outlier: 5.517A pdb=" N MET R 87 " --> pdb=" O GLU R 83 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 116 removed outlier: 4.185A pdb=" N VAL R 107 " --> pdb=" O LYS R 103 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 45 removed outlier: 4.452A pdb=" N PHE S 43 " --> pdb=" O GLN S 39 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR S 44 " --> pdb=" O ASP S 40 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEU S 45 " --> pdb=" O ALA S 41 " (cutoff:3.500A) Processing helix chain 'T' and resid 58 through 66 removed outlier: 3.621A pdb=" N TYR T 62 " --> pdb=" O ARG T 58 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA T 63 " --> pdb=" O PRO T 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N THR T 64 " --> pdb=" O ARG T 60 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N VAL T 65 " --> pdb=" O GLN T 61 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N SER T 66 " --> pdb=" O TYR T 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 58 through 66' Processing helix chain 'T' and resid 81 through 113 removed outlier: 3.753A pdb=" N GLU T 110 " --> pdb=" O LYS T 106 " (cutoff:3.500A) Processing helix chain 'U' and resid 5 through 12 removed outlier: 4.178A pdb=" N THR U 11 " --> pdb=" O TYR U 7 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N LYS U 12 " --> pdb=" O GLU U 8 " (cutoff:3.500A) Processing helix chain 'U' and resid 13 through 38 removed outlier: 3.564A pdb=" N GLN U 34 " --> pdb=" O GLU U 30 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N LEU U 36 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N SER U 37 " --> pdb=" O VAL U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 71 removed outlier: 4.591A pdb=" N THR U 46 " --> pdb=" O PRO U 42 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL U 47 " --> pdb=" O LYS U 43 " (cutoff:3.500A) Processing helix chain 'U' and resid 77 through 82 removed outlier: 5.175A pdb=" N ALA U 82 " --> pdb=" O LYS U 78 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 91 Processing helix chain 'U' and resid 93 through 99 Processing helix chain 'U' and resid 101 through 111 Processing helix chain 'V' and resid 25 through 30 removed outlier: 4.460A pdb=" N LYS V 29 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LYS V 30 " --> pdb=" O ILE V 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 25 through 30' Processing helix chain 'V' and resid 34 through 49 Processing helix chain 'V' and resid 51 through 64 Processing helix chain 'V' and resid 65 through 77 Processing helix chain 'V' and resid 79 through 100 Processing helix chain 'W' and resid 4 through 11 removed outlier: 3.650A pdb=" N GLY W 9 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS W 10 " --> pdb=" O PRO W 6 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG W 11 " --> pdb=" O SER W 7 " (cutoff:3.500A) Processing helix chain 'W' and resid 50 through 58 Processing helix chain 'W' and resid 65 through 77 removed outlier: 5.840A pdb=" N HIS W 69 " --> pdb=" O ARG W 65 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL W 70 " --> pdb=" O TYR W 66 " (cutoff:3.500A) removed outlier: 4.852A pdb=" N SER W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 17 removed outlier: 3.795A pdb=" N ARG X 16 " --> pdb=" O LEU X 12 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ARG X 17 " --> pdb=" O GLU X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 69 Processing helix chain 'Y' and resid 6 through 21 removed outlier: 5.318A pdb=" N ARG Y 21 " --> pdb=" O LYS Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 30 removed outlier: 4.498A pdb=" N ARG Y 28 " --> pdb=" O PRO Y 24 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N LEU Y 29 " --> pdb=" O GLN Y 25 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG Y 30 " --> pdb=" O TRP Y 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 24 through 30' Processing helix chain 'Z' and resid 79 through 91 removed outlier: 3.873A pdb=" N TYR Z 89 " --> pdb=" O LEU Z 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 48 Processing helix chain 'c' and resid 19 through 35 removed outlier: 3.578A pdb=" N GLN c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN c 32 " --> pdb=" O LYS c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 73 through 92 removed outlier: 4.149A pdb=" N GLU c 91 " --> pdb=" O ARG c 87 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ALA c 92 " --> pdb=" O GLU c 88 " (cutoff:3.500A) Processing helix chain 'd' and resid 4 through 25 removed outlier: 5.694A pdb=" N TRP d 8 " --> pdb=" O MET d 4 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 5 through 11 removed outlier: 4.394A pdb=" N GLY j 11 " --> pdb=" O ASN j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 33 through 39 removed outlier: 5.744A pdb=" N ARG j 37 " --> pdb=" O ASP j 33 " (cutoff:3.500A) Processing helix chain 'j' and resid 103 through 108 removed outlier: 4.097A pdb=" N VAL j 107 " --> pdb=" O PRO j 103 " (cutoff:3.500A) Proline residue: j 108 - end of helix No H-bonds generated for 'chain 'j' and resid 103 through 108' Processing helix chain 'j' and resid 181 through 193 removed outlier: 4.173A pdb=" N LEU j 191 " --> pdb=" O HIS j 187 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N LYS j 192 " --> pdb=" O LYS j 188 " (cutoff:3.500A) Processing helix chain 'j' and resid 200 through 205 removed outlier: 3.826A pdb=" N MET j 204 " --> pdb=" O ARG j 200 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N ASN j 205 " --> pdb=" O GLY j 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 200 through 205' Processing helix chain 'j' and resid 173 through 178 removed outlier: 3.642A pdb=" N ASP j 176 " --> pdb=" O GLY j 173 " (cutoff:3.500A) Proline residue: j 178 - end of helix Processing helix chain 'k' and resid 111 through 120 removed outlier: 4.415A pdb=" N ARG k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N PHE k 118 " --> pdb=" O VAL k 114 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N TYR k 119 " --> pdb=" O LYS k 115 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N LYS k 120 " --> pdb=" O ARG k 116 " (cutoff:3.500A) Processing helix chain 'k' and resid 130 through 139 removed outlier: 3.973A pdb=" N ALA k 138 " --> pdb=" O SER k 134 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N GLN k 139 " --> pdb=" O ALA k 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 142 through 154 removed outlier: 4.413A pdb=" N ARG k 146 " --> pdb=" O ALA k 142 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N GLU k 147 " --> pdb=" O GLY k 143 " (cutoff:3.500A) Processing helix chain 'k' and resid 165 through 170 removed outlier: 4.238A pdb=" N THR k 169 " --> pdb=" O GLN k 165 " (cutoff:3.500A) Proline residue: k 170 - end of helix No H-bonds generated for 'chain 'k' and resid 165 through 170' Processing helix chain 'k' and resid 187 through 199 Processing helix chain 'k' and resid 204 through 209 removed outlier: 4.182A pdb=" N VAL k 208 " --> pdb=" O ALA k 204 " (cutoff:3.500A) Processing helix chain 'k' and resid 228 through 233 Processing helix chain 'k' and resid 347 through 352 removed outlier: 6.411A pdb=" N LEU k 351 " --> pdb=" O SER k 347 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU k 352 " --> pdb=" O ARG k 348 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 347 through 352' Processing helix chain 'k' and resid 372 through 381 Processing helix chain 'l' and resid 31 through 46 removed outlier: 3.787A pdb=" N SER l 41 " --> pdb=" O THR l 37 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS l 44 " --> pdb=" O THR l 40 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ASN l 45 " --> pdb=" O SER l 41 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LYS l 46 " --> pdb=" O VAL l 42 " (cutoff:3.500A) Processing helix chain 'l' and resid 114 through 131 removed outlier: 3.922A pdb=" N ALA l 130 " --> pdb=" O ILE l 126 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N VAL l 131 " --> pdb=" O ALA l 127 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 139 Processing helix chain 'l' and resid 154 through 159 removed outlier: 4.895A pdb=" N SER l 158 " --> pdb=" O THR l 154 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE l 159 " --> pdb=" O ASP l 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 154 through 159' Processing helix chain 'l' and resid 161 through 173 Processing helix chain 'l' and resid 174 through 185 removed outlier: 4.235A pdb=" N LYS l 185 " --> pdb=" O VAL l 181 " (cutoff:3.500A) Processing helix chain 'l' and resid 191 through 196 removed outlier: 3.778A pdb=" N ARG l 195 " --> pdb=" O LYS l 191 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASN l 196 " --> pdb=" O GLY l 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 191 through 196' Processing helix chain 'l' and resid 214 through 221 removed outlier: 4.755A pdb=" N ASN l 221 " --> pdb=" O LYS l 217 " (cutoff:3.500A) Processing helix chain 'l' and resid 234 through 240 Proline residue: l 240 - end of helix Processing helix chain 'l' and resid 251 through 262 removed outlier: 4.668A pdb=" N ASP l 259 " --> pdb=" O PHE l 255 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N GLN l 260 " --> pdb=" O THR l 256 " (cutoff:3.500A) Processing helix chain 'l' and resid 285 through 292 Processing helix chain 'l' and resid 293 through 299 removed outlier: 3.686A pdb=" N ALA l 298 " --> pdb=" O GLU l 294 " (cutoff:3.500A) Processing helix chain 'l' and resid 320 through 328 Processing helix chain 'l' and resid 329 through 338 removed outlier: 4.448A pdb=" N VAL l 333 " --> pdb=" O PRO l 329 " (cutoff:3.500A) Processing helix chain 'l' and resid 352 through 361 Processing helix chain 'm' and resid 9 through 16 Processing helix chain 'm' and resid 20 through 26 Processing helix chain 'm' and resid 29 through 37 removed outlier: 3.681A pdb=" N ARG m 35 " --> pdb=" O TYR m 31 " (cutoff:3.500A) Processing helix chain 'm' and resid 79 through 87 removed outlier: 4.613A pdb=" N LEU m 83 " --> pdb=" O TYR m 79 " (cutoff:3.500A) Proline residue: m 84 - end of helix Processing helix chain 'm' and resid 94 through 114 Processing helix chain 'm' and resid 115 through 120 removed outlier: 4.700A pdb=" N TYR m 119 " --> pdb=" O LEU m 115 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LYS m 120 " --> pdb=" O ASP m 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 115 through 120' Processing helix chain 'm' and resid 157 through 170 removed outlier: 3.763A pdb=" N GLY m 161 " --> pdb=" O ALA m 157 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY m 170 " --> pdb=" O ALA m 166 " (cutoff:3.500A) Processing helix chain 'm' and resid 191 through 201 removed outlier: 3.619A pdb=" N LEU m 195 " --> pdb=" O ASP m 191 " (cutoff:3.500A) Processing helix chain 'm' and resid 202 through 215 removed outlier: 3.708A pdb=" N TYR m 207 " --> pdb=" O HIS m 203 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ASP m 214 " --> pdb=" O GLU m 210 " (cutoff:3.500A) Processing helix chain 'm' and resid 216 through 223 removed outlier: 4.783A pdb=" N PHE m 223 " --> pdb=" O PHE m 219 " (cutoff:3.500A) Processing helix chain 'm' and resid 224 through 230 Processing helix chain 'm' and resid 234 through 250 removed outlier: 4.367A pdb=" N ASP m 238 " --> pdb=" O ASP m 234 " (cutoff:3.500A) Processing helix chain 'm' and resid 261 through 273 removed outlier: 3.767A pdb=" N GLU m 268 " --> pdb=" O GLN m 264 " (cutoff:3.500A) Processing helix chain 'm' and resid 278 through 294 Processing helix chain 'n' and resid 80 through 85 removed outlier: 3.994A pdb=" N VAL n 84 " --> pdb=" O ASN n 80 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N ILE n 85 " --> pdb=" O ALA n 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 80 through 85' Processing helix chain 'n' and resid 102 through 107 removed outlier: 3.963A pdb=" N PHE n 106 " --> pdb=" O ASN n 102 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N ALA n 107 " --> pdb=" O VAL n 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 102 through 107' Processing helix chain 'n' and resid 131 through 150 removed outlier: 3.875A pdb=" N LYS n 143 " --> pdb=" O LYS n 139 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA n 144 " --> pdb=" O VAL n 140 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA n 147 " --> pdb=" O LYS n 143 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU n 148 " --> pdb=" O ALA n 144 " (cutoff:3.500A) Processing helix chain 'n' and resid 154 through 162 removed outlier: 5.285A pdb=" N SER n 162 " --> pdb=" O TYR n 158 " (cutoff:3.500A) Processing helix chain 'o' and resid 27 through 73 Processing helix chain 'o' and resid 96 through 107 Processing helix chain 'o' and resid 120 through 131 removed outlier: 4.041A pdb=" N LEU o 126 " --> pdb=" O ALA o 122 " (cutoff:3.500A) Processing helix chain 'o' and resid 140 through 151 Processing helix chain 'o' and resid 165 through 173 removed outlier: 4.156A pdb=" N ILE o 169 " --> pdb=" O ASP o 165 " (cutoff:3.500A) Processing helix chain 'o' and resid 180 through 191 removed outlier: 4.171A pdb=" N VAL o 191 " --> pdb=" O GLU o 187 " (cutoff:3.500A) Processing helix chain 'o' and resid 194 through 203 removed outlier: 5.109A pdb=" N TRP o 203 " --> pdb=" O ASN o 199 " (cutoff:3.500A) Processing helix chain 'o' and resid 235 through 244 removed outlier: 3.631A pdb=" N LEU o 239 " --> pdb=" O PHE o 235 " (cutoff:3.500A) Processing helix chain 'p' and resid 53 through 69 removed outlier: 4.222A pdb=" N LYS p 63 " --> pdb=" O GLN p 59 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N ILE p 67 " --> pdb=" O LYS p 63 " (cutoff:3.500A) Processing helix chain 'p' and resid 72 through 80 removed outlier: 4.847A pdb=" N ALA p 76 " --> pdb=" O PRO p 72 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N PHE p 78 " --> pdb=" O THR p 74 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N GLN p 79 " --> pdb=" O ILE p 75 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N TYR p 80 " --> pdb=" O ALA p 76 " (cutoff:3.500A) Processing helix chain 'p' and resid 83 through 98 removed outlier: 4.002A pdb=" N LYS p 96 " --> pdb=" O LYS p 92 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N TYR p 97 " --> pdb=" O LEU p 93 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ARG p 98 " --> pdb=" O PHE p 94 " (cutoff:3.500A) Processing helix chain 'p' and resid 101 through 119 Processing helix chain 'p' and resid 135 through 146 Processing helix chain 'p' and resid 159 through 174 removed outlier: 4.604A pdb=" N VAL p 163 " --> pdb=" O PRO p 159 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N PHE p 165 " --> pdb=" O GLU p 161 " (cutoff:3.500A) removed outlier: 5.759A pdb=" N LEU p 166 " --> pdb=" O LEU p 162 " (cutoff:3.500A) Proline residue: p 167 - end of helix Processing helix chain 'p' and resid 182 through 191 Processing helix chain 'p' and resid 204 through 222 removed outlier: 3.674A pdb=" N GLU p 208 " --> pdb=" O ARG p 204 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N ALA p 209 " --> pdb=" O ALA p 205 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA p 210 " --> pdb=" O GLU p 206 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N THR p 217 " --> pdb=" O LYS p 213 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ALA p 220 " --> pdb=" O SER p 216 " (cutoff:3.500A) Processing helix chain 'p' and resid 225 through 233 removed outlier: 4.682A pdb=" N LYS p 231 " --> pdb=" O ASP p 227 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS p 232 " --> pdb=" O GLU p 228 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N TRP p 233 " --> pdb=" O VAL p 229 " (cutoff:3.500A) Processing helix chain 'p' and resid 239 through 255 removed outlier: 4.215A pdb=" N SER p 255 " --> pdb=" O LYS p 251 " (cutoff:3.500A) Processing helix chain 'q' and resid 61 through 84 removed outlier: 3.641A pdb=" N ARG q 69 " --> pdb=" O VAL q 65 " (cutoff:3.500A) Processing helix chain 'q' and resid 150 through 166 removed outlier: 4.142A pdb=" N CYS q 165 " --> pdb=" O LEU q 161 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG q 166 " --> pdb=" O GLN q 162 " (cutoff:3.500A) Processing helix chain 'q' and resid 171 through 176 removed outlier: 4.108A pdb=" N LEU q 176 " --> pdb=" O ILE q 172 " (cutoff:3.500A) Processing helix chain 'r' and resid 5 through 10 removed outlier: 4.429A pdb=" N TYR r 9 " --> pdb=" O PRO r 5 " (cutoff:3.500A) Processing helix chain 'r' and resid 42 through 47 removed outlier: 4.412A pdb=" N PHE r 46 " --> pdb=" O THR r 42 " (cutoff:3.500A) Proline residue: r 47 - end of helix No H-bonds generated for 'chain 'r' and resid 42 through 47' Processing helix chain 'r' and resid 61 through 80 Processing helix chain 'r' and resid 107 through 112 removed outlier: 4.663A pdb=" N LEU r 111 " --> pdb=" O GLY r 107 " (cutoff:3.500A) Processing helix chain 'r' and resid 144 through 160 removed outlier: 3.558A pdb=" N GLU r 150 " --> pdb=" O ASP r 146 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N TYR r 157 " --> pdb=" O ARG r 153 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N LYS r 158 " --> pdb=" O ARG r 154 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE r 159 " --> pdb=" O ALA r 155 " (cutoff:3.500A) Proline residue: r 160 - end of helix Processing helix chain 'r' and resid 177 through 188 removed outlier: 4.306A pdb=" N ALA r 187 " --> pdb=" O LYS r 183 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY r 188 " --> pdb=" O LYS r 184 " (cutoff:3.500A) Processing helix chain 'r' and resid 205 through 213 removed outlier: 4.577A pdb=" N PHE r 213 " --> pdb=" O ASN r 209 " (cutoff:3.500A) Processing helix chain 'r' and resid 214 through 219 removed outlier: 4.578A pdb=" N ALA r 219 " --> pdb=" O GLU r 215 " (cutoff:3.500A) Processing helix chain 's' and resid 27 through 42 Processing helix chain 's' and resid 73 through 88 Processing helix chain 's' and resid 108 through 113 removed outlier: 4.451A pdb=" N LEU s 112 " --> pdb=" O GLU s 108 " (cutoff:3.500A) Processing helix chain 's' and resid 136 through 141 removed outlier: 3.837A pdb=" N ARG s 140 " --> pdb=" O ALA s 136 " (cutoff:3.500A) Processing helix chain 's' and resid 155 through 167 removed outlier: 4.922A pdb=" N TYR s 167 " --> pdb=" O PHE s 163 " (cutoff:3.500A) Processing helix chain 't' and resid 17 through 22 removed outlier: 4.154A pdb=" N ARG t 21 " --> pdb=" O HIS t 17 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL t 22 " --> pdb=" O TRP t 18 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 17 through 22' Processing helix chain 't' and resid 27 through 47 Processing helix chain 't' and resid 76 through 84 Processing helix chain 't' and resid 86 through 94 Processing helix chain 't' and resid 105 through 123 Processing helix chain 't' and resid 140 through 146 Proline residue: t 146 - end of helix Processing helix chain 't' and resid 165 through 180 removed outlier: 6.293A pdb=" N THR t 169 " --> pdb=" O SER t 165 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU t 170 " --> pdb=" O ALA t 166 " (cutoff:3.500A) Processing helix chain 't' and resid 181 through 193 Processing helix chain 'u' and resid 59 through 64 removed outlier: 4.074A pdb=" N VAL u 63 " --> pdb=" O ASN u 59 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N VAL u 64 " --> pdb=" O LEU u 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 59 through 64' Processing helix chain 'u' and resid 77 through 89 Processing helix chain 'u' and resid 90 through 98 removed outlier: 3.837A pdb=" N SER u 97 " --> pdb=" O LYS u 93 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N SER u 98 " --> pdb=" O TRP u 94 " (cutoff:3.500A) Processing helix chain 'u' and resid 99 through 112 Processing helix chain 'u' and resid 113 through 138 removed outlier: 4.239A pdb=" N ALA u 136 " --> pdb=" O LYS u 132 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LYS u 137 " --> pdb=" O LYS u 133 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N ALA u 138 " --> pdb=" O ALA u 134 " (cutoff:3.500A) Processing helix chain 'a' and resid 6 through 21 removed outlier: 3.741A pdb=" N GLU a 16 " --> pdb=" O LEU a 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 84 Processing helix chain 'a' and resid 153 through 160 removed outlier: 5.501A pdb=" N ASN a 160 " --> pdb=" O LEU a 156 " (cutoff:3.500A) Processing helix chain 'a' and resid 161 through 175 removed outlier: 5.509A pdb=" N GLU a 175 " --> pdb=" O ASN a 171 " (cutoff:3.500A) Processing helix chain 'a' and resid 177 through 206 removed outlier: 4.065A pdb=" N GLY a 206 " --> pdb=" O LEU a 202 " (cutoff:3.500A) Processing helix chain 'a' and resid 219 through 229 Proline residue: a 229 - end of helix Processing helix chain 'a' and resid 232 through 244 Processing helix chain 'a' and resid 250 through 258 Processing helix chain 'a' and resid 259 through 278 Processing helix chain 'a' and resid 299 through 305 removed outlier: 4.707A pdb=" N ILE a 305 " --> pdb=" O ASP a 301 " (cutoff:3.500A) Processing helix chain 'a' and resid 317 through 324 removed outlier: 3.811A pdb=" N ASP a 322 " --> pdb=" O GLY a 318 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER a 323 " --> pdb=" O GLY a 319 " (cutoff:3.500A) Processing helix chain 'a' and resid 332 through 395 removed outlier: 6.669A pdb=" N THR a 336 " --> pdb=" O PRO a 332 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLU a 357 " --> pdb=" O ILE a 353 " (cutoff:3.500A) Processing helix chain 'a' and resid 396 through 413 Processing helix chain 'a' and resid 415 through 430 Processing helix chain 'a' and resid 431 through 438 removed outlier: 5.633A pdb=" N ASN a 438 " --> pdb=" O ALA a 434 " (cutoff:3.500A) Processing helix chain 'a' and resid 513 through 527 Processing helix chain 'a' and resid 529 through 554 removed outlier: 3.780A pdb=" N GLY a 540 " --> pdb=" O GLU a 536 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS a 541 " --> pdb=" O LYS a 537 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 578 removed outlier: 4.079A pdb=" N LYS a 576 " --> pdb=" O TYR a 572 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TYR a 577 " --> pdb=" O PHE a 573 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N SER a 578 " --> pdb=" O PHE a 574 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 572 through 578' Processing helix chain 'a' and resid 593 through 604 Processing helix chain 'a' and resid 631 through 647 Processing helix chain 'a' and resid 661 through 666 removed outlier: 3.819A pdb=" N VAL a 665 " --> pdb=" O PHE a 661 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N SER a 666 " --> pdb=" O ALA a 662 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 661 through 666' Processing helix chain 'a' and resid 839 through 851 removed outlier: 3.661A pdb=" N LYS a 843 " --> pdb=" O GLY a 839 " (cutoff:3.500A) Processing helix chain 'a' and resid 855 through 867 Processing helix chain 'a' and resid 868 through 910 removed outlier: 3.656A pdb=" N LYS a 909 " --> pdb=" O LEU a 905 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LYS a 910 " --> pdb=" O LYS a 906 " (cutoff:3.500A) Processing helix chain 'a' and resid 916 through 925 removed outlier: 3.697A pdb=" N HIS a 920 " --> pdb=" O ASN a 916 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N LYS a 925 " --> pdb=" O LYS a 921 " (cutoff:3.500A) Processing helix chain 'a' and resid 943 through 951 removed outlier: 4.625A pdb=" N LYS a 949 " --> pdb=" O PRO a 945 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N TYR a 950 " --> pdb=" O ALA a 946 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LYS a 951 " --> pdb=" O LEU a 947 " (cutoff:3.500A) Processing helix chain 'a' and resid 962 through 977 removed outlier: 3.917A pdb=" N ARG a 977 " --> pdb=" O TYR a 973 " (cutoff:3.500A) Processing helix chain 'a' and resid 990 through 1001 removed outlier: 5.579A pdb=" N LYS a1001 " --> pdb=" O ILE a 997 " (cutoff:3.500A) Processing helix chain 'a' and resid 1002 through 1010 removed outlier: 3.503A pdb=" N LEU a1007 " --> pdb=" O GLN a1003 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N CYS a1010 " --> pdb=" O VAL a1006 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 35 through 42 Processing helix chain 'e' and resid 44 through 57 removed outlier: 5.429A pdb=" N ARG e 57 " --> pdb=" O SER e 53 " (cutoff:3.500A) Processing helix chain 'e' and resid 58 through 76 removed outlier: 3.902A pdb=" N PHE e 76 " --> pdb=" O LEU e 72 " (cutoff:3.500A) Processing helix chain 'e' and resid 79 through 84 removed outlier: 5.031A pdb=" N ASN e 84 " --> pdb=" O GLU e 80 " (cutoff:3.500A) Processing helix chain 'e' and resid 85 through 99 removed outlier: 3.970A pdb=" N LYS e 97 " --> pdb=" O GLN e 93 " (cutoff:3.500A) Processing helix chain 'e' and resid 103 through 122 Processing helix chain 'e' and resid 127 through 141 removed outlier: 4.201A pdb=" N ASP e 131 " --> pdb=" O LYS e 127 " (cutoff:3.500A) Proline residue: e 134 - end of helix Processing helix chain 'e' and resid 144 through 160 Proline residue: e 150 - end of helix Processing helix chain 'e' and resid 162 through 174 removed outlier: 3.543A pdb=" N ILE e 166 " --> pdb=" O ASP e 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 186 Processing helix chain 'e' and resid 189 through 195 removed outlier: 4.287A pdb=" N ASP e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 200 through 226 removed outlier: 3.956A pdb=" N SER e 204 " --> pdb=" O SER e 200 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU e 205 " --> pdb=" O LYS e 201 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE e 206 " --> pdb=" O GLU e 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 227 through 234 removed outlier: 4.296A pdb=" N GLU e 231 " --> pdb=" O LYS e 227 " (cutoff:3.500A) Processing helix chain 'e' and resid 235 through 244 removed outlier: 5.618A pdb=" N GLU e 244 " --> pdb=" O ILE e 240 " (cutoff:3.500A) Processing helix chain 'e' and resid 245 through 251 removed outlier: 3.549A pdb=" N LEU e 250 " --> pdb=" O ILE e 246 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N ASN e 251 " --> pdb=" O TRP e 247 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 275 removed outlier: 4.475A pdb=" N TYR e 261 " --> pdb=" O ASN e 257 " (cutoff:3.500A) Processing helix chain 'e' and resid 276 through 281 removed outlier: 4.114A pdb=" N LYS e 281 " --> pdb=" O MET e 277 " (cutoff:3.500A) Processing helix chain 'e' and resid 282 through 299 removed outlier: 5.505A pdb=" N THR e 299 " --> pdb=" O LEU e 295 " (cutoff:3.500A) Processing helix chain 'e' and resid 302 through 310 Proline residue: e 308 - end of helix Processing helix chain 'e' and resid 311 through 325 removed outlier: 5.233A pdb=" N GLU e 324 " --> pdb=" O LEU e 320 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ASP e 325 " --> pdb=" O ASP e 321 " (cutoff:3.500A) Processing helix chain 'e' and resid 326 through 333 removed outlier: 4.065A pdb=" N ASP e 332 " --> pdb=" O ILE e 328 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS e 333 " --> pdb=" O TRP e 329 " (cutoff:3.500A) Processing helix chain 'e' and resid 334 through 350 removed outlier: 3.756A pdb=" N SER e 349 " --> pdb=" O VAL e 345 " (cutoff:3.500A) Proline residue: e 350 - end of helix Processing helix chain 'e' and resid 353 through 369 removed outlier: 4.012A pdb=" N ARG e 367 " --> pdb=" O SER e 363 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N HIS e 368 " --> pdb=" O SER e 364 " (cutoff:3.500A) Processing helix chain 'e' and resid 375 through 392 Proline residue: e 379 - end of helix removed outlier: 3.834A pdb=" N GLY e 392 " --> pdb=" O LEU e 388 " (cutoff:3.500A) Processing helix chain 'e' and resid 398 through 417 Processing helix chain 'e' and resid 418 through 436 Processing helix chain 'e' and resid 437 through 443 removed outlier: 4.978A pdb=" N THR e 443 " --> pdb=" O LEU e 439 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 450 removed outlier: 4.989A pdb=" N SER e 450 " --> pdb=" O ASN e 446 " (cutoff:3.500A) Processing helix chain 'e' and resid 454 through 468 Processing helix chain 'e' and resid 469 through 477 removed outlier: 5.035A pdb=" N VAL e 477 " --> pdb=" O ARG e 473 " (cutoff:3.500A) Processing helix chain 'e' and resid 478 through 491 Proline residue: e 491 - end of helix Processing helix chain 'e' and resid 492 through 512 removed outlier: 4.875A pdb=" N ALA e 496 " --> pdb=" O ASN e 492 " (cutoff:3.500A) Proline residue: e 512 - end of helix Processing helix chain 'e' and resid 513 through 519 Processing helix chain 'e' and resid 520 through 533 removed outlier: 4.880A pdb=" N ASP e 533 " --> pdb=" O PHE e 529 " (cutoff:3.500A) Processing helix chain 'e' and resid 534 through 552 Proline residue: e 549 - end of helix Processing helix chain 'e' and resid 556 through 571 removed outlier: 4.938A pdb=" N LYS e 571 " --> pdb=" O TYR e 567 " (cutoff:3.500A) Processing helix chain 'e' and resid 572 through 577 removed outlier: 5.094A pdb=" N THR e 577 " --> pdb=" O PHE e 573 " (cutoff:3.500A) Processing helix chain 'e' and resid 578 through 594 removed outlier: 4.847A pdb=" N ASN e 594 " --> pdb=" O ALA e 590 " (cutoff:3.500A) Processing helix chain 'e' and resid 596 through 608 removed outlier: 4.950A pdb=" N ASP e 608 " --> pdb=" O MET e 604 " (cutoff:3.500A) Processing helix chain 'e' and resid 609 through 619 removed outlier: 4.990A pdb=" N ASP e 619 " --> pdb=" O LEU e 615 " (cutoff:3.500A) Processing helix chain 'e' and resid 622 through 635 removed outlier: 5.119A pdb=" N LYS e 635 " --> pdb=" O MET e 631 " (cutoff:3.500A) Processing helix chain 'e' and resid 640 through 647 removed outlier: 4.681A pdb=" N ASN e 646 " --> pdb=" O ILE e 642 " (cutoff:3.500A) Processing helix chain 'e' and resid 651 through 666 Processing helix chain 'e' and resid 667 through 679 removed outlier: 4.634A pdb=" N ASP e 679 " --> pdb=" O LEU e 675 " (cutoff:3.500A) Processing helix chain 'e' and resid 680 through 691 removed outlier: 4.546A pdb=" N ASP e 691 " --> pdb=" O LEU e 687 " (cutoff:3.500A) Processing helix chain 'e' and resid 692 through 700 removed outlier: 5.635A pdb=" N TYR e 698 " --> pdb=" O SER e 694 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N GLU e 699 " --> pdb=" O CYS e 695 " (cutoff:3.500A) Processing helix chain 'e' and resid 702 through 717 Processing helix chain 'e' and resid 719 through 737 Processing helix chain 'e' and resid 742 through 757 removed outlier: 3.700A pdb=" N TYR e 746 " --> pdb=" O ALA e 742 " (cutoff:3.500A) Processing helix chain 'e' and resid 758 through 766 Proline residue: e 766 - end of helix Processing helix chain 'e' and resid 768 through 777 removed outlier: 4.142A pdb=" N VAL e 772 " --> pdb=" O ASN e 768 " (cutoff:3.500A) Processing helix chain 'e' and resid 781 through 789 removed outlier: 3.629A pdb=" N VAL e 787 " --> pdb=" O ARG e 783 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N SER e 789 " --> pdb=" O SER e 785 " (cutoff:3.500A) Processing helix chain 'e' and resid 792 through 798 removed outlier: 4.913A pdb=" N LEU e 796 " --> pdb=" O THR e 792 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU e 797 " --> pdb=" O ASN e 793 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LEU e 798 " --> pdb=" O THR e 794 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 792 through 798' Processing helix chain 'e' and resid 805 through 827 Proline residue: e 827 - end of helix Processing helix chain 'e' and resid 831 through 852 Processing helix chain 'e' and resid 856 through 862 removed outlier: 5.264A pdb=" N PHE e 862 " --> pdb=" O LEU e 858 " (cutoff:3.500A) Processing helix chain 'e' and resid 875 through 886 Proline residue: e 886 - end of helix Processing helix chain 'e' and resid 895 through 903 removed outlier: 3.747A pdb=" N ASN e 902 " --> pdb=" O ILE e 898 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N SER e 903 " --> pdb=" O ALA e 899 " (cutoff:3.500A) Processing helix chain 'e' and resid 904 through 921 Processing helix chain 'e' and resid 927 through 944 removed outlier: 3.668A pdb=" N SER e 935 " --> pdb=" O GLY e 931 " (cutoff:3.500A) Processing helix chain 'e' and resid 950 through 965 Processing helix chain 'e' and resid 970 through 987 removed outlier: 5.338A pdb=" N GLY e 986 " --> pdb=" O SER e 982 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N ILE e 987 " --> pdb=" O GLN e 983 " (cutoff:3.500A) Processing helix chain 'e' and resid 988 through 995 Processing helix chain 'e' and resid 996 through 1008 Processing helix chain 'e' and resid 1020 through 1038 removed outlier: 4.497A pdb=" N ASP e1038 " --> pdb=" O TRP e1034 " (cutoff:3.500A) Processing helix chain 'e' and resid 1044 through 1063 removed outlier: 4.387A pdb=" N VAL e1048 " --> pdb=" O SER e1044 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU e1063 " --> pdb=" O LEU e1059 " (cutoff:3.500A) Processing helix chain 'e' and resid 1064 through 1070 removed outlier: 4.530A pdb=" N ILE e1070 " --> pdb=" O ARG e1066 " (cutoff:3.500A) Processing helix chain 'e' and resid 1071 through 1090 removed outlier: 4.759A pdb=" N ASP e1090 " --> pdb=" O MET e1086 " (cutoff:3.500A) Processing helix chain 'e' and resid 1094 through 1111 Processing helix chain 'e' and resid 1123 through 1137 Processing helix chain 'e' and resid 1145 through 1163 removed outlier: 4.975A pdb=" N GLU e1163 " --> pdb=" O ILE e1159 " (cutoff:3.500A) Processing helix chain 'e' and resid 1165 through 1179 removed outlier: 4.089A pdb=" N LYS e1172 " --> pdb=" O GLU e1168 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ARG e1173 " --> pdb=" O SER e1169 " (cutoff:3.500A) Processing helix chain 'e' and resid 1180 through 1188 removed outlier: 3.977A pdb=" N ILE e1184 " --> pdb=" O ASN e1180 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ASN e1187 " --> pdb=" O ASP e1183 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE e1188 " --> pdb=" O ILE e1184 " (cutoff:3.500A) Processing helix chain 'e' and resid 1189 through 1217 Processing helix chain 'e' and resid 1235 through 1240 removed outlier: 5.256A pdb=" N LEU e1240 " --> pdb=" O SER e1236 " (cutoff:3.500A) Processing helix chain 'e' and resid 1241 through 1252 removed outlier: 4.624A pdb=" N VAL e1252 " --> pdb=" O VAL e1248 " (cutoff:3.500A) Processing helix chain 'e' and resid 1261 through 1281 removed outlier: 3.683A pdb=" N ASP e1281 " --> pdb=" O MET e1277 " (cutoff:3.500A) Processing helix chain 'e' and resid 1283 through 1298 Processing helix chain 'e' and resid 1299 through 1312 removed outlier: 4.990A pdb=" N ASP e1312 " --> pdb=" O THR e1308 " (cutoff:3.500A) Processing helix chain 'e' and resid 1315 through 1323 removed outlier: 4.426A pdb=" N TRP e1319 " --> pdb=" O ASP e1315 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ASP e1323 " --> pdb=" O TRP e1319 " (cutoff:3.500A) Processing helix chain 'e' and resid 1324 through 1330 removed outlier: 4.428A pdb=" N TYR e1330 " --> pdb=" O GLU e1326 " (cutoff:3.500A) Processing helix chain 'e' and resid 1331 through 1336 removed outlier: 3.827A pdb=" N ASN e1335 " --> pdb=" O ASN e1331 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ASN e1336 " --> pdb=" O ILE e1332 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 1331 through 1336' Processing helix chain 'e' and resid 1340 through 1364 removed outlier: 4.322A pdb=" N GLY e1364 " --> pdb=" O PHE e1360 " (cutoff:3.500A) Processing helix chain 'e' and resid 1365 through 1375 removed outlier: 5.593A pdb=" N LYS e1375 " --> pdb=" O TRP e1371 " (cutoff:3.500A) Processing helix chain 'e' and resid 1376 through 1390 Processing helix chain 'e' and resid 1391 through 1411 removed outlier: 4.566A pdb=" N ASP e1408 " --> pdb=" O ASN e1404 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N ARG e1409 " --> pdb=" O SER e1405 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU e1410 " --> pdb=" O LYS e1406 " (cutoff:3.500A) Processing helix chain 'e' and resid 1448 through 1453 removed outlier: 4.407A pdb=" N ASN e1453 " --> pdb=" O TYR e1449 " (cutoff:3.500A) Processing helix chain 'e' and resid 1465 through 1482 removed outlier: 3.508A pdb=" N ILE e1480 " --> pdb=" O THR e1476 " (cutoff:3.500A) Processing helix chain 'e' and resid 1486 through 1503 removed outlier: 3.695A pdb=" N SER e1490 " --> pdb=" O SER e1486 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE e1502 " --> pdb=" O VAL e1498 " (cutoff:3.500A) Processing helix chain 'e' and resid 1535 through 1546 Processing helix chain 'g' and resid 12 through 17 removed outlier: 4.234A pdb=" N PHE g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 31 through 42 removed outlier: 3.829A pdb=" N PHE g 38 " --> pdb=" O PHE g 34 " (cutoff:3.500A) Processing helix chain 'g' and resid 58 through 63 removed outlier: 4.797A pdb=" N MET g 62 " --> pdb=" O ILE g 58 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 88 Processing helix chain 'g' and resid 103 through 108 Processing helix chain 'g' and resid 122 through 133 Processing helix chain 'g' and resid 147 through 152 Processing helix chain 'g' and resid 166 through 178 Processing helix chain 'g' and resid 192 through 197 Processing helix chain 'g' and resid 211 through 223 Processing helix chain 'v' and resid 22 through 27 removed outlier: 5.216A pdb=" N ARG v 27 " --> pdb=" O CYS v 23 " (cutoff:3.500A) Processing helix chain 'v' and resid 118 through 131 Processing helix chain 'w' and resid 5 through 21 Processing helix chain 'w' and resid 70 through 81 removed outlier: 3.728A pdb=" N SER w 79 " --> pdb=" O ASP w 75 " (cutoff:3.500A) Processing helix chain 'w' and resid 86 through 94 removed outlier: 3.660A pdb=" N ASN w 94 " --> pdb=" O LEU w 90 " (cutoff:3.500A) Processing helix chain 'w' and resid 96 through 108 removed outlier: 4.877A pdb=" N ASN w 108 " --> pdb=" O SER w 104 " (cutoff:3.500A) Processing helix chain 'w' and resid 113 through 124 removed outlier: 4.555A pdb=" N LYS w 118 " --> pdb=" O GLU w 114 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N GLN w 119 " --> pdb=" O VAL w 115 " (cutoff:3.500A) Proline residue: w 121 - end of helix Processing helix chain 'w' and resid 126 through 132 Processing helix chain 'w' and resid 143 through 154 Processing helix chain 'w' and resid 175 through 195 removed outlier: 5.072A pdb=" N LYS w 195 " --> pdb=" O VAL w 191 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 37 Proline residue: z 34 - end of helix Processing helix chain 'z' and resid 39 through 53 removed outlier: 4.149A pdb=" N PHE z 53 " --> pdb=" O ALA z 49 " (cutoff:3.500A) Processing helix chain 'z' and resid 77 through 87 removed outlier: 5.034A pdb=" N GLU z 87 " --> pdb=" O THR z 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 106 through 118 Processing helix chain 'z' and resid 125 through 138 removed outlier: 4.664A pdb=" N SER z 138 " --> pdb=" O GLY z 134 " (cutoff:3.500A) Processing helix chain 'z' and resid 151 through 156 removed outlier: 5.015A pdb=" N ASN z 156 " --> pdb=" O ILE z 152 " (cutoff:3.500A) Processing helix chain 'z' and resid 158 through 163 Proline residue: z 163 - end of helix Processing helix chain '0' and resid 3 through 23 removed outlier: 4.980A pdb=" N LYS 0 23 " --> pdb=" O LEU 0 19 " (cutoff:3.500A) Processing helix chain '0' and resid 34 through 46 Processing helix chain '0' and resid 55 through 71 removed outlier: 4.922A pdb=" N SER 0 68 " --> pdb=" O ARG 0 64 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ASP 0 69 " --> pdb=" O GLY 0 65 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N LEU 0 70 " --> pdb=" O PHE 0 66 " (cutoff:3.500A) Proline residue: 0 71 - end of helix Processing helix chain '0' and resid 72 through 81 removed outlier: 4.428A pdb=" N LEU 0 76 " --> pdb=" O ASP 0 72 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 0 77 " --> pdb=" O PHE 0 73 " (cutoff:3.500A) Proline residue: 0 78 - end of helix removed outlier: 4.205A pdb=" N LYS 0 81 " --> pdb=" O LEU 0 77 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 72 through 81' Processing helix chain '0' and resid 93 through 103 Processing sheet with id= 1, first strand: chain 'A' and resid 35 through 39 removed outlier: 6.465A pdb=" N VAL A 35 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 61 " --> pdb=" O ALA A 39 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLY A 58 " --> pdb=" O ASP A 136 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE A 133 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 117 through 121 removed outlier: 3.634A pdb=" N ASN A 117 " --> pdb=" O ILE A 133 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR A 129 " --> pdb=" O VAL A 121 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 6 through 10 Processing sheet with id= 4, first strand: chain 'C' and resid 16 through 20 Processing sheet with id= 5, first strand: chain 'C' and resid 57 through 60 removed outlier: 5.435A pdb=" N LYS C 80 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 124 through 131 No H-bonds generated for sheet with id= 6 Processing sheet with id= 7, first strand: chain 'D' and resid 119 through 122 removed outlier: 4.879A pdb=" N THR D 100 " --> pdb=" O LYS D 79 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'F' and resid 24 through 31 removed outlier: 6.706A pdb=" N ILE F 10 " --> pdb=" O VAL F 59 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'F' and resid 87 through 96 removed outlier: 5.101A pdb=" N ASN F 74 " --> pdb=" O ILE F 129 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'F' and resid 6 through 10 removed outlier: 4.567A pdb=" N GLU F 6 " --> pdb=" O ILE F 64 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'G' and resid 38 through 43 removed outlier: 4.577A pdb=" N ASP G 38 " --> pdb=" O VAL G 64 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS G 60 " --> pdb=" O ILE G 42 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.172A pdb=" N ASN H 101 " --> pdb=" O THR H 14 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'I' and resid 79 through 82 removed outlier: 3.921A pdb=" N ALA I 82 " --> pdb=" O ASP I 97 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N ASP I 97 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN I 98 " --> pdb=" O ILE I 22 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA I 21 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N MET I 59 " --> pdb=" O ILE I 37 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ASP I 56 " --> pdb=" O VAL I 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'I' and resid 84 through 87 removed outlier: 4.506A pdb=" N VAL I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'I' and resid 75 through 78 Processing sheet with id= 16, first strand: chain 'J' and resid 3 through 6 removed outlier: 6.441A pdb=" N GLU J 4 " --> pdb=" O LYS J 12 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS J 12 " --> pdb=" O GLU J 4 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASP J 6 " --> pdb=" O GLY J 10 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'J' and resid 18 through 22 Processing sheet with id= 18, first strand: chain 'K' and resid 81 through 86 removed outlier: 3.734A pdb=" N LYS K 120 " --> pdb=" O VAL K 86 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N THR K 119 " --> pdb=" O ARG K 115 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'L' and resid 56 through 59 removed outlier: 4.092A pdb=" N GLN L 66 " --> pdb=" O VAL L 58 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'L' and resid 72 through 75 Processing sheet with id= 21, first strand: chain 'L' and resid 86 through 89 removed outlier: 4.343A pdb=" N ALA L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'M' and resid 8 through 13 removed outlier: 4.145A pdb=" N LYS M 9 " --> pdb=" O ILE M 25 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LYS M 21 " --> pdb=" O VAL M 13 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'M' and resid 27 through 30 removed outlier: 4.643A pdb=" N LYS M 27 " --> pdb=" O LEU M 42 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'N' and resid 99 through 102 Processing sheet with id= 25, first strand: chain 'P' and resid 22 through 25 removed outlier: 6.372A pdb=" N LYS P 22 " --> pdb=" O LEU P 93 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU P 41 " --> pdb=" O ILE P 92 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS P 66 " --> pdb=" O LYS P 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 48 through 51 removed outlier: 4.934A pdb=" N ASP Q 48 " --> pdb=" O LEU Q 89 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL Q 8 " --> pdb=" O ARG Q 77 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR Q 9 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'R' and resid 71 through 77 Processing sheet with id= 28, first strand: chain 'S' and resid 11 through 15 removed outlier: 6.754A pdb=" N LEU S 29 " --> pdb=" O LEU S 14 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ARG S 82 " --> pdb=" O THR S 72 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS S 63 " --> pdb=" O ALA S 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS S 47 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG S 48 " --> pdb=" O PHE S 101 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'S' and resid 8 through 14 removed outlier: 4.046A pdb=" N ALA S 96 " --> pdb=" O HIS S 13 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'T' and resid 19 through 24 removed outlier: 4.587A pdb=" N LYS T 19 " --> pdb=" O VAL T 35 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'X' and resid 2 through 5 removed outlier: 4.535A pdb=" N VAL X 55 " --> pdb=" O ILE X 5 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N THR X 22 " --> pdb=" O ARG X 46 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Z' and resid 100 through 103 removed outlier: 4.137A pdb=" N ALA Z 101 " --> pdb=" O CYS Z 96 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LYS Z 93 " --> pdb=" O LYS Z 124 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N GLN Z 120 " --> pdb=" O ARG Z 97 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'b' and resid 7 through 10 removed outlier: 4.478A pdb=" N VAL b 68 " --> pdb=" O LEU b 85 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR b 79 " --> pdb=" O CYS b 74 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 47 through 50 removed outlier: 6.880A pdb=" N ILE c 54 " --> pdb=" O GLY c 50 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N GLY c 53 " --> pdb=" O GLY c 66 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N LYS c 62 " --> pdb=" O CYS c 57 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'j' and resid 47 through 50 removed outlier: 3.921A pdb=" N GLN j 47 " --> pdb=" O LYS j 60 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N LYS j 60 " --> pdb=" O LYS j 46 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLN j 86 " --> pdb=" O VAL j 45 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'j' and resid 111 through 114 removed outlier: 4.419A pdb=" N THR j 111 " --> pdb=" O ILE j 136 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG j 147 " --> pdb=" O ILE j 137 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'j' and resid 58 through 64 Processing sheet with id= 38, first strand: chain 'j' and resid 145 through 150 removed outlier: 4.406A pdb=" N ALA j 154 " --> pdb=" O LEU j 150 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'k' and resid 41 through 44 removed outlier: 4.889A pdb=" N ALA k 42 " --> pdb=" O ASN k 184 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N GLN k 182 " --> pdb=" O THR k 44 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N HIS k 177 " --> pdb=" O THR k 164 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LEU k 161 " --> pdb=" O VAL k 87 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LYS k 201 " --> pdb=" O VAL k 86 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'k' and resid 53 through 59 removed outlier: 6.661A pdb=" N VAL k 78 " --> pdb=" O ALA k 51 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG k 334 " --> pdb=" O LYS k 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N ILE k 335 " --> pdb=" O VAL k 220 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N VAL k 220 " --> pdb=" O ILE k 335 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N HIS k 273 " --> pdb=" O THR k 221 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'k' and resid 98 through 101 Processing sheet with id= 42, first strand: chain 'k' and resid 284 through 288 removed outlier: 3.740A pdb=" N GLY k 288 " --> pdb=" O ASN k 319 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N ASN k 319 " --> pdb=" O GLY k 288 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'k' and resid 76 through 80 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'k' and resid 88 through 93 removed outlier: 3.745A pdb=" N GLY k 88 " --> pdb=" O LEU k 161 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'k' and resid 213 through 216 removed outlier: 4.188A pdb=" N GLU k 213 " --> pdb=" O ILE k 282 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'l' and resid 75 through 78 removed outlier: 4.384A pdb=" N GLN l 87 " --> pdb=" O VAL l 77 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'l' and resid 205 through 208 Processing sheet with id= 48, first strand: chain 'm' and resid 72 through 75 removed outlier: 6.834A pdb=" N ILE m 64 " --> pdb=" O LEU m 75 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'n' and resid 37 through 42 removed outlier: 3.956A pdb=" N THR n 38 " --> pdb=" O TYR n 54 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS n 50 " --> pdb=" O LEU n 42 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'o' and resid 133 through 138 removed outlier: 7.864A pdb=" N TYR o 133 " --> pdb=" O ILE o 89 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS o 82 " --> pdb=" O VAL o 119 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER o 113 " --> pdb=" O ARG o 88 " (cutoff:3.500A) removed outlier: 5.441A pdb=" N ASN o 112 " --> pdb=" O LEU o 207 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'o' and resid 152 through 155 removed outlier: 8.624A pdb=" N GLY o 152 " --> pdb=" O LEU o 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'p' and resid 176 through 181 Processing sheet with id= 53, first strand: chain 'q' and resid 5 through 12 removed outlier: 4.945A pdb=" N GLN q 51 " --> pdb=" O VAL q 12 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N LEU q 52 " --> pdb=" O VAL q 48 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'q' and resid 17 through 20 removed outlier: 5.995A pdb=" N ARG q 23 " --> pdb=" O LEU q 38 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'q' and resid 132 through 137 removed outlier: 4.964A pdb=" N GLU q 143 " --> pdb=" O SER q 137 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ASP q 142 " --> pdb=" O TYR q 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 86 through 90 Processing sheet with id= 57, first strand: chain 'r' and resid 34 through 37 removed outlier: 6.338A pdb=" N TYR r 34 " --> pdb=" O VAL r 89 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU r 52 " --> pdb=" O ILE r 135 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N GLN r 133 " --> pdb=" O SER r 54 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'r' and resid 56 through 59 No H-bonds generated for sheet with id= 58 Processing sheet with id= 59, first strand: chain 'r' and resid 189 through 193 removed outlier: 7.658A pdb=" N GLU r 189 " --> pdb=" O LEU r 200 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N PHE r 196 " --> pdb=" O ASP r 193 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'r' and resid 49 through 55 removed outlier: 5.069A pdb=" N CYS r 49 " --> pdb=" O SER r 168 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLN r 162 " --> pdb=" O ASN r 55 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 's' and resid 45 through 49 removed outlier: 5.683A pdb=" N SER s 22 " --> pdb=" O GLY s 124 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N GLY s 124 " --> pdb=" O SER s 22 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 's' and resid 52 through 55 removed outlier: 7.192A pdb=" N TYR s 52 " --> pdb=" O ARG s 61 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N ARG s 61 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 's' and resid 89 through 92 removed outlier: 3.627A pdb=" N ASP s 170 " --> pdb=" O TYR s 89 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU s 91 " --> pdb=" O ASP s 170 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 56 through 59 Processing sheet with id= 65, first strand: chain 'u' and resid 19 through 24 removed outlier: 4.472A pdb=" N ARG u 19 " --> pdb=" O ILE u 35 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS u 31 " --> pdb=" O ILE u 23 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 36 through 39 removed outlier: 6.764A pdb=" N LYS u 43 " --> pdb=" O ILE u 39 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'a' and resid 27 through 32 removed outlier: 3.586A pdb=" N ASN a 28 " --> pdb=" O LYS a 42 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE a 32 " --> pdb=" O GLN a 38 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLN a 38 " --> pdb=" O ILE a 32 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'a' and resid 91 through 95 removed outlier: 3.850A pdb=" N ALA a 91 " --> pdb=" O GLN a 104 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ILE a 100 " --> pdb=" O VAL a 95 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ARG a 99 " --> pdb=" O PHE a 116 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU a 115 " --> pdb=" O ASN a 121 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASN a 121 " --> pdb=" O GLU a 115 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'a' and resid 308 through 311 removed outlier: 3.864A pdb=" N THR a 308 " --> pdb=" O LEU a 286 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'a' and resid 446 through 454 removed outlier: 9.175A pdb=" N ASN a 446 " --> pdb=" O LEU a 510 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N GLU a 502 " --> pdb=" O LEU a 454 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'a' and resid 609 through 613 Processing sheet with id= 72, first strand: chain 'a' and resid 657 through 660 Processing sheet with id= 73, first strand: chain 'a' and resid 939 through 942 removed outlier: 3.780A pdb=" N PHE a 703 " --> pdb=" O TYR a 952 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N TYR a 952 " --> pdb=" O PHE a 703 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'e' and resid 1417 through 1423 removed outlier: 6.101A pdb=" N ASN e1426 " --> pdb=" O LEU e1445 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA e1430 " --> pdb=" O ILE e1441 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ILE e1441 " --> pdb=" O ALA e1430 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N GLU e1440 " --> pdb=" O VAL e1459 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'g' and resid 23 through 27 Processing sheet with id= 76, first strand: chain 'g' and resid 69 through 73 Processing sheet with id= 77, first strand: chain 'g' and resid 114 through 117 Processing sheet with id= 78, first strand: chain 'g' and resid 158 through 161 Processing sheet with id= 79, first strand: chain 'v' and resid 18 through 21 removed outlier: 3.677A pdb=" N SER v 149 " --> pdb=" O THR v 137 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain 'v' and resid 30 through 33 removed outlier: 4.740A pdb=" N GLY v 30 " --> pdb=" O ILE v 41 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL v 60 " --> pdb=" O VAL v 42 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'v' and resid 101 through 104 removed outlier: 3.654A pdb=" N ASP v 108 " --> pdb=" O ASN v 104 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain 'v' and resid 57 through 63 removed outlier: 4.294A pdb=" N LYS v 68 " --> pdb=" O ASP v 63 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain 'w' and resid 49 through 53 removed outlier: 7.222A pdb=" N PHE w 49 " --> pdb=" O LEU w 159 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain 'w' and resid 65 through 68 Processing sheet with id= 85, first strand: chain 'w' and resid 163 through 169 removed outlier: 6.356A pdb=" N LEU w 163 " --> pdb=" O LEU w 38 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL w 32 " --> pdb=" O VAL w 169 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU w 204 " --> pdb=" O LEU w 216 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'z' and resid 11 through 17 removed outlier: 3.527A pdb=" N LYS z 11 " --> pdb=" O GLN z 65 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N VAL z 60 " --> pdb=" O PRO z 75 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain '0' and resid 49 through 53 removed outlier: 3.838A pdb=" N SER 0 24 " --> pdb=" O THR 0 89 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL 0 27 " --> pdb=" O VAL 0 188 " (cutoff:3.500A) 3386 hydrogen bonds defined for protein. 10065 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2848 hydrogen bonds 4538 hydrogen bond angles 0 basepair planarities 1159 basepair parallelities 1966 stacking parallelities Total time for adding SS restraints: 272.87 Time building geometry restraints manager: 62.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 17673 1.32 - 1.44: 63017 1.44 - 1.57: 71981 1.57 - 1.69: 7128 1.69 - 1.82: 279 Bond restraints: 160078 Sorted by residual: bond pdb=" C LYS j 221 " pdb=" O LYS j 221 " ideal model delta sigma weight residual 1.234 1.191 0.043 1.00e-02 1.00e+04 1.87e+01 bond pdb=" CA LYS j 221 " pdb=" C LYS j 221 " ideal model delta sigma weight residual 1.530 1.487 0.044 1.12e-02 7.97e+03 1.53e+01 bond pdb=" C LEU m 83 " pdb=" N PRO m 84 " ideal model delta sigma weight residual 1.335 1.377 -0.043 1.28e-02 6.10e+03 1.12e+01 bond pdb=" N LYS j 221 " pdb=" CA LYS j 221 " ideal model delta sigma weight residual 1.455 1.424 0.032 1.09e-02 8.42e+03 8.48e+00 bond pdb=" CG LEU o 126 " pdb=" CD1 LEU o 126 " ideal model delta sigma weight residual 1.521 1.426 0.095 3.30e-02 9.18e+02 8.35e+00 ... (remaining 160073 not shown) Histogram of bond angle deviations from ideal: 96.00 - 104.12: 13732 104.12 - 112.25: 89904 112.25 - 120.37: 72641 120.37 - 128.50: 52831 128.50 - 136.62: 4555 Bond angle restraints: 233663 Sorted by residual: angle pdb=" C GLY H 51 " pdb=" N ASN H 52 " pdb=" CA ASN H 52 " ideal model delta sigma weight residual 121.54 136.62 -15.08 1.91e+00 2.74e-01 6.24e+01 angle pdb=" N GLY v 53 " pdb=" CA GLY v 53 " pdb=" C GLY v 53 " ideal model delta sigma weight residual 112.51 124.23 -11.72 1.53e+00 4.27e-01 5.87e+01 angle pdb=" N ILE e 884 " pdb=" CA ILE e 884 " pdb=" C ILE e 884 " ideal model delta sigma weight residual 110.62 102.85 7.77 1.02e+00 9.61e-01 5.80e+01 angle pdb=" N GLY e1298 " pdb=" CA GLY e1298 " pdb=" C GLY e1298 " ideal model delta sigma weight residual 115.30 104.97 10.33 1.39e+00 5.18e-01 5.53e+01 angle pdb=" C GLU z 87 " pdb=" N PRO z 88 " pdb=" CA PRO z 88 " ideal model delta sigma weight residual 120.38 112.79 7.59 1.03e+00 9.43e-01 5.43e+01 ... (remaining 233658 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 91999 35.98 - 71.96: 8215 71.96 - 107.94: 841 107.94 - 143.91: 20 143.91 - 179.89: 56 Dihedral angle restraints: 101131 sinusoidal: 73679 harmonic: 27452 Sorted by residual: dihedral pdb=" CA GLY e 392 " pdb=" C GLY e 392 " pdb=" N PHE e 393 " pdb=" CA PHE e 393 " ideal model delta harmonic sigma weight residual -180.00 -87.59 -92.41 0 5.00e+00 4.00e-02 3.42e+02 dihedral pdb=" CA THR p 30 " pdb=" C THR p 30 " pdb=" N PRO p 31 " pdb=" CA PRO p 31 " ideal model delta harmonic sigma weight residual -180.00 -124.96 -55.04 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA GLY O 20 " pdb=" C GLY O 20 " pdb=" N ILE O 21 " pdb=" CA ILE O 21 " ideal model delta harmonic sigma weight residual -180.00 -132.45 -47.55 0 5.00e+00 4.00e-02 9.04e+01 ... (remaining 101128 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 28484 0.149 - 0.299: 631 0.299 - 0.448: 33 0.448 - 0.597: 3 0.597 - 0.747: 1 Chirality restraints: 29152 Sorted by residual: chirality pdb=" CB ILE U 118 " pdb=" CA ILE U 118 " pdb=" CG1 ILE U 118 " pdb=" CG2 ILE U 118 " both_signs ideal model delta sigma weight residual False 2.64 1.90 0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" CA ASP p 158 " pdb=" N ASP p 158 " pdb=" C ASP p 158 " pdb=" CB ASP p 158 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" C3' G f 282 " pdb=" C4' G f 282 " pdb=" O3' G f 282 " pdb=" C2' G f 282 " both_signs ideal model delta sigma weight residual False -2.48 -2.01 -0.46 2.00e-01 2.50e+01 5.40e+00 ... (remaining 29149 not shown) Planarity restraints: 16403 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP m 95 " -0.034 2.00e-02 2.50e+03 3.45e-02 2.97e+01 pdb=" CG TRP m 95 " 0.090 2.00e-02 2.50e+03 pdb=" CD1 TRP m 95 " -0.048 2.00e-02 2.50e+03 pdb=" CD2 TRP m 95 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP m 95 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP m 95 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP m 95 " 0.008 2.00e-02 2.50e+03 pdb=" CZ3 TRP m 95 " -0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP m 95 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG d 5 " -0.024 2.00e-02 2.50e+03 4.79e-02 2.29e+01 pdb=" C ARG d 5 " 0.083 2.00e-02 2.50e+03 pdb=" O ARG d 5 " -0.031 2.00e-02 2.50e+03 pdb=" N ALA d 6 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 60 " 0.014 2.00e-02 2.50e+03 3.11e-02 1.93e+01 pdb=" CG TYR N 60 " -0.067 2.00e-02 2.50e+03 pdb=" CD1 TYR N 60 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 TYR N 60 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR N 60 " -0.018 2.00e-02 2.50e+03 pdb=" CE2 TYR N 60 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR N 60 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 60 " -0.006 2.00e-02 2.50e+03 ... (remaining 16400 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 22 1.81 - 2.58: 1385 2.58 - 3.36: 173585 3.36 - 4.13: 474618 4.13 - 4.90: 703993 Nonbonded interactions: 1353603 Sorted by model distance: nonbonded pdb=" CB ALA e 399 " pdb=" CB SER e 438 " model vdw 1.041 3.860 nonbonded pdb=" CA ALA e 399 " pdb=" CB SER e 438 " model vdw 1.051 3.870 nonbonded pdb=" O2' A y 58 " pdb=" OP2 U y 60 " model vdw 1.155 2.440 nonbonded pdb=" CE1 PHE e 765 " pdb=" CB LEU e 822 " model vdw 1.396 3.740 nonbonded pdb=" C TRP e1319 " pdb=" CE1 PHE e1390 " model vdw 1.422 3.570 ... (remaining 1353598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.01 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.820 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: 0.150 Extract box with map and model: 22.910 Check model and map are aligned: 1.670 Set scattering table: 1.020 Process input model: 617.330 Find NCS groups from input model: 3.430 Set up NCS constraints: 0.420 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: 0.040 Load rotamer database and sin/cos tables:13.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 665.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 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 : 0.006 0.095 160078 Z= 0.365 Angle : 0.900 15.083 233663 Z= 0.506 Chirality : 0.055 0.747 29152 Planarity : 0.007 0.101 16403 Dihedral : 21.588 179.892 83369 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 1.81 % Allowed : 2.53 % Favored : 95.66 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.11 % 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: 0.14 (0.08), residues: 9312 helix: 1.35 (0.08), residues: 3925 sheet: 0.05 (0.15), residues: 1194 loop : -1.11 (0.09), residues: 4193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.002 TRP m 95 HIS 0.018 0.002 HIS r 123 PHE 0.045 0.002 PHE o 229 TYR 0.067 0.002 TYR N 60 ARG 0.026 0.001 ARG A 50 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1299 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 1162 time to evaluate : 8.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 155 MET cc_start: 0.8895 (tpt) cc_final: 0.8654 (tpt) REVERT: G 99 SER cc_start: 0.8770 (t) cc_final: 0.8484 (t) REVERT: M 106 GLN cc_start: 0.8751 (mt0) cc_final: 0.7964 (mt0) REVERT: P 98 SER cc_start: 0.8758 (t) cc_final: 0.8491 (t) REVERT: R 92 TYR cc_start: 0.8978 (m-80) cc_final: 0.8770 (m-80) REVERT: V 66 GLU cc_start: 0.7551 (mt-10) cc_final: 0.7343 (mt-10) REVERT: Z 87 SER cc_start: 0.8606 (p) cc_final: 0.8343 (m) REVERT: n 132 THR cc_start: 0.8481 (p) cc_final: 0.7889 (p) REVERT: n 137 ASP cc_start: 0.7800 (m-30) cc_final: 0.6719 (m-30) REVERT: q 150 SER cc_start: 0.8952 (t) cc_final: 0.8246 (t) REVERT: r 208 ASN cc_start: 0.8179 (m110) cc_final: 0.7786 (m-40) REVERT: s 101 ASN cc_start: 0.8734 (m-40) cc_final: 0.8514 (m110) REVERT: s 131 MET cc_start: 0.8480 (mmm) cc_final: 0.7837 (mmm) REVERT: s 173 ASP cc_start: 0.8098 (p0) cc_final: 0.7344 (p0) REVERT: a 9 ASP cc_start: 0.7501 (OUTLIER) cc_final: 0.6388 (m-30) REVERT: a 589 MET cc_start: 0.8947 (OUTLIER) cc_final: 0.8678 (mmm) REVERT: a 590 MET cc_start: 0.8740 (tmm) cc_final: 0.8243 (tmt) REVERT: a 605 ILE cc_start: 0.8027 (OUTLIER) cc_final: 0.7076 (mp) REVERT: e 67 MET cc_start: 0.8673 (tpp) cc_final: 0.8356 (mmm) REVERT: e 137 LEU cc_start: 0.9692 (mt) cc_final: 0.9365 (tp) REVERT: e 807 LYS cc_start: 0.8663 (OUTLIER) cc_final: 0.8229 (tppt) REVERT: e 820 ASP cc_start: 0.7452 (OUTLIER) cc_final: 0.7070 (t0) REVERT: e 963 MET cc_start: -0.1186 (mmt) cc_final: -0.1754 (mmt) REVERT: e 1432 TYR cc_start: 0.3143 (OUTLIER) cc_final: 0.1369 (p90) REVERT: e 1474 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8201 (mtp) REVERT: g 6 GLN cc_start: 0.6067 (mt0) cc_final: 0.5589 (pp30) REVERT: g 140 GLN cc_start: 0.8685 (tp40) cc_final: 0.8177 (mp10) REVERT: v 81 GLU cc_start: 0.8189 (tp30) cc_final: 0.7982 (tp30) REVERT: v 125 GLN cc_start: 0.8995 (tp40) cc_final: 0.8362 (tp-100) REVERT: v 136 VAL cc_start: 0.8385 (t) cc_final: 0.7840 (p) REVERT: w 68 PHE cc_start: 0.8592 (m-10) cc_final: 0.8167 (m-80) REVERT: 0 22 TYR cc_start: 0.8986 (m-80) cc_final: 0.8339 (m-80) REVERT: 0 38 MET cc_start: 0.9493 (mmm) cc_final: 0.8535 (tmm) REVERT: 0 58 MET cc_start: 0.8583 (tpt) cc_final: 0.8074 (tpp) REVERT: 0 191 TYR cc_start: 0.8552 (t80) cc_final: 0.7669 (t80) outliers start: 137 outliers final: 26 residues processed: 1287 average time/residue: 2.1097 time to fit residues: 3953.7557 Evaluate side-chains 841 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 808 time to evaluate : 8.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 GLU Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 89 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 605 ILE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 649 TRP Chi-restraints excluded: chain a residue 928 LEU Chi-restraints excluded: chain a residue 934 VAL Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 264 VAL Chi-restraints excluded: chain e residue 358 VAL Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 403 ASN Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 782 TYR Chi-restraints excluded: chain e residue 807 LYS Chi-restraints excluded: chain e residue 819 LEU Chi-restraints excluded: chain e residue 820 ASP Chi-restraints excluded: chain e residue 823 LEU Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 990 VAL Chi-restraints excluded: chain e residue 1084 LEU Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1474 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 1077 optimal weight: 9.9990 chunk 967 optimal weight: 20.0000 chunk 536 optimal weight: 10.0000 chunk 330 optimal weight: 7.9990 chunk 652 optimal weight: 10.0000 chunk 516 optimal weight: 10.0000 chunk 1000 optimal weight: 20.0000 chunk 387 optimal weight: 8.9990 chunk 608 optimal weight: 10.0000 chunk 744 optimal weight: 3.9990 chunk 1158 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN A B 50 ASN A B 122 GLN A ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 138 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN M 122 HIS N 65 GLN P 75 ASN W 76 ASN X 28 ASN j 83 HIS j 132 ASN l 116 ASN l 361 HIS m 39 GLN n 167 ASN ** o 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 59 GLN p 77 GLN ** r 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 208 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 114 GLN u 27 GLN ** a 412 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 413 GLN a 445 GLN a 517 ASN a 599 GLN a 687 ASN a 690 ASN a 957 GLN e 79 ASN e 160 ASN e 174 GLN e 805 ASN e 902 ASN e1138 ASN e1141 GLN e1206 GLN e1288 GLN e1293 GLN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1532 ASN ** g 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 56 ASN ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.099 160078 Z= 0.529 Angle : 0.722 17.978 233663 Z= 0.377 Chirality : 0.046 0.351 29152 Planarity : 0.006 0.111 16403 Dihedral : 22.558 179.765 65676 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.79 % Favored : 96.14 % Rotamer: Outliers : 2.92 % Allowed : 11.22 % Favored : 85.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.09 % 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 (0.08), residues: 9312 helix: 1.26 (0.08), residues: 3951 sheet: -0.00 (0.15), residues: 1142 loop : -0.95 (0.09), residues: 4219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.056 0.003 TRP e1319 HIS 0.012 0.002 HIS C 145 PHE 0.042 0.002 PHE 0 66 TYR 0.032 0.002 TYR l 194 ARG 0.013 0.001 ARG X 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1046 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 825 time to evaluate : 8.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 120 ASN cc_start: 0.8783 (OUTLIER) cc_final: 0.8440 (p0) REVERT: E 28 GLU cc_start: 0.7984 (mp0) cc_final: 0.7721 (mp0) REVERT: M 84 ARG cc_start: 0.9047 (OUTLIER) cc_final: 0.8092 (ptp90) REVERT: P 98 SER cc_start: 0.8808 (t) cc_final: 0.8605 (t) REVERT: S 31 LYS cc_start: 0.9129 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: X 10 GLN cc_start: 0.8601 (tt0) cc_final: 0.8354 (tt0) REVERT: X 76 ASN cc_start: 0.8201 (t0) cc_final: 0.7956 (t0) REVERT: Z 126 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.7768 (mttt) REVERT: b 18 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8036 (mtt90) REVERT: j 24 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8225 (mt0) REVERT: k 289 ASP cc_start: 0.7219 (p0) cc_final: 0.6668 (p0) REVERT: n 132 THR cc_start: 0.8517 (p) cc_final: 0.8178 (p) REVERT: n 133 GLU cc_start: 0.7360 (tp30) cc_final: 0.7020 (tp30) REVERT: n 137 ASP cc_start: 0.7747 (m-30) cc_final: 0.7120 (m-30) REVERT: q 150 SER cc_start: 0.9061 (t) cc_final: 0.8712 (p) REVERT: q 153 ASP cc_start: 0.7885 (m-30) cc_final: 0.7411 (m-30) REVERT: s 38 GLU cc_start: 0.8484 (pp20) cc_final: 0.8217 (pp20) REVERT: s 52 TYR cc_start: 0.8369 (m-80) cc_final: 0.7930 (m-80) REVERT: s 89 TYR cc_start: 0.8673 (m-10) cc_final: 0.8342 (m-10) REVERT: u 16 GLU cc_start: 0.8391 (pm20) cc_final: 0.8053 (pm20) REVERT: u 121 MET cc_start: 0.8452 (tmm) cc_final: 0.8167 (ttt) REVERT: a 543 MET cc_start: 0.9144 (ttm) cc_final: 0.8553 (tpp) REVERT: a 589 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8848 (mmm) REVERT: a 590 MET cc_start: 0.8824 (tmm) cc_final: 0.8247 (tmt) REVERT: a 605 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.8154 (mp) REVERT: a 884 MET cc_start: 0.9491 (ptp) cc_final: 0.9241 (ptp) REVERT: e 67 MET cc_start: 0.8415 (tpp) cc_final: 0.8057 (mmm) REVERT: e 116 MET cc_start: 0.9277 (mtp) cc_final: 0.8921 (mtt) REVERT: e 137 LEU cc_start: 0.9624 (mt) cc_final: 0.9290 (tp) REVERT: e 394 SER cc_start: 0.5077 (OUTLIER) cc_final: 0.4844 (p) REVERT: e 807 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8015 (tppt) REVERT: e 963 MET cc_start: -0.0702 (mmt) cc_final: -0.1065 (mmt) REVERT: e 1093 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7857 (tp) REVERT: e 1286 MET cc_start: 0.6511 (ptt) cc_final: 0.6038 (ptt) REVERT: e 1432 TYR cc_start: 0.2922 (OUTLIER) cc_final: 0.1679 (p90) REVERT: g 6 GLN cc_start: 0.5817 (mt0) cc_final: 0.5429 (pp30) REVERT: g 68 ARG cc_start: 0.8017 (mpp80) cc_final: 0.7691 (mpp80) REVERT: g 96 ARG cc_start: 0.8932 (ttm110) cc_final: 0.7725 (mtp-110) REVERT: g 140 GLN cc_start: 0.8797 (tp40) cc_final: 0.8119 (mp10) REVERT: v 88 ASN cc_start: 0.7827 (t0) cc_final: 0.6644 (t0) REVERT: v 125 GLN cc_start: 0.9032 (tp40) cc_final: 0.8464 (tp-100) REVERT: w 45 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8700 (tmm-80) REVERT: w 60 ARG cc_start: 0.8658 (mtm-85) cc_final: 0.8430 (ttm170) REVERT: w 72 PHE cc_start: 0.8280 (t80) cc_final: 0.6414 (OUTLIER) REVERT: w 76 ARG cc_start: 0.8545 (mtm180) cc_final: 0.7926 (mtm180) REVERT: w 174 MET cc_start: 0.6806 (mpt) cc_final: 0.6412 (mpt) REVERT: 0 10 GLU cc_start: 0.9431 (pp20) cc_final: 0.9171 (pp20) REVERT: 0 11 TYR cc_start: 0.8981 (t80) cc_final: 0.8705 (t80) REVERT: 0 22 TYR cc_start: 0.8763 (m-80) cc_final: 0.8412 (m-80) REVERT: 0 58 MET cc_start: 0.8738 (tpt) cc_final: 0.8527 (tpp) REVERT: 0 60 ARG cc_start: 0.9180 (mpt-90) cc_final: 0.8977 (mpt-90) REVERT: 0 191 TYR cc_start: 0.8035 (t80) cc_final: 0.7316 (t80) outliers start: 221 outliers final: 85 residues processed: 960 average time/residue: 2.1274 time to fit residues: 2984.5086 Evaluate side-chains 850 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 754 time to evaluate : 8.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 182 ASN Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 87 ASN Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 72 THR Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain Z residue 126 LYS Chi-restraints excluded: chain b residue 18 ARG Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 40 SER Chi-restraints excluded: chain d residue 4 MET Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 65 ILE Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 605 ILE Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 697 LEU Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 99 ILE Chi-restraints excluded: chain e residue 125 ILE Chi-restraints excluded: chain e residue 264 VAL Chi-restraints excluded: chain e residue 394 SER Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 733 HIS Chi-restraints excluded: chain e residue 807 LYS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 990 VAL Chi-restraints excluded: chain e residue 1093 LEU Chi-restraints excluded: chain e residue 1365 CYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain v residue 34 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 94 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 643 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 964 optimal weight: 50.0000 chunk 789 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 1160 optimal weight: 10.0000 chunk 1254 optimal weight: 0.5980 chunk 1033 optimal weight: 5.9990 chunk 1151 optimal weight: 8.9990 chunk 395 optimal weight: 10.0000 chunk 931 optimal weight: 9.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 123 GLN N 65 GLN V 92 ASN W 13 ASN j 97 ASN p 77 GLN ** p 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 90 GLN ** s 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 102 GLN t 114 GLN a 412 GLN e1138 ASN e1206 GLN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1457 ASN g 75 GLN ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 160078 Z= 0.405 Angle : 0.639 13.928 233663 Z= 0.336 Chirality : 0.042 0.320 29152 Planarity : 0.005 0.106 16403 Dihedral : 22.529 178.947 65651 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.93 % Favored : 96.02 % Rotamer: Outliers : 2.91 % Allowed : 13.49 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.09 % 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: 0.31 (0.08), residues: 9312 helix: 1.38 (0.08), residues: 3956 sheet: 0.05 (0.15), residues: 1148 loop : -0.87 (0.09), residues: 4208 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP n 9 HIS 0.008 0.001 HIS e1499 PHE 0.028 0.002 PHE o 229 TYR 0.025 0.002 TYR e 323 ARG 0.012 0.001 ARG I 88 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1016 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 796 time to evaluate : 8.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8805 (OUTLIER) cc_final: 0.8224 (ttt90) REVERT: C 182 ILE cc_start: 0.8895 (OUTLIER) cc_final: 0.8551 (tp) REVERT: G 104 GLU cc_start: 0.7823 (tm-30) cc_final: 0.6726 (tm-30) REVERT: H 49 ASN cc_start: 0.7646 (t0) cc_final: 0.7432 (t0) REVERT: M 84 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8086 (ptp90) REVERT: M 89 VAL cc_start: 0.9091 (OUTLIER) cc_final: 0.8852 (p) REVERT: P 57 GLU cc_start: 0.7890 (mt-10) cc_final: 0.7589 (mt-10) REVERT: P 98 SER cc_start: 0.8830 (t) cc_final: 0.8617 (t) REVERT: R 19 ARG cc_start: 0.9291 (OUTLIER) cc_final: 0.7377 (ttp-170) REVERT: S 31 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8408 (ttmm) REVERT: S 58 GLU cc_start: 0.7403 (tm-30) cc_final: 0.7195 (tm-30) REVERT: U 79 ASP cc_start: 0.8593 (OUTLIER) cc_final: 0.8365 (p0) REVERT: X 10 GLN cc_start: 0.8580 (tt0) cc_final: 0.8328 (tt0) REVERT: X 76 ASN cc_start: 0.8254 (t0) cc_final: 0.7974 (t0) REVERT: j 24 GLN cc_start: 0.8553 (OUTLIER) cc_final: 0.8296 (mt0) REVERT: j 142 ASP cc_start: 0.7672 (p0) cc_final: 0.7412 (p0) REVERT: k 289 ASP cc_start: 0.7293 (p0) cc_final: 0.6674 (p0) REVERT: m 95 TRP cc_start: 0.9423 (OUTLIER) cc_final: 0.7829 (t60) REVERT: n 13 GLU cc_start: 0.7858 (mt-10) cc_final: 0.7575 (mt-10) REVERT: n 133 GLU cc_start: 0.7258 (tp30) cc_final: 0.6995 (tp30) REVERT: n 137 ASP cc_start: 0.7741 (m-30) cc_final: 0.6641 (m-30) REVERT: s 52 TYR cc_start: 0.8368 (m-80) cc_final: 0.7890 (m-80) REVERT: u 12 TRP cc_start: 0.8326 (OUTLIER) cc_final: 0.7890 (p90) REVERT: u 16 GLU cc_start: 0.8355 (pm20) cc_final: 0.8067 (pm20) REVERT: a 543 MET cc_start: 0.9134 (ttm) cc_final: 0.8374 (tpp) REVERT: a 589 MET cc_start: 0.9074 (OUTLIER) cc_final: 0.8650 (mmm) REVERT: a 590 MET cc_start: 0.8870 (tmm) cc_final: 0.8422 (tmm) REVERT: a 649 TRP cc_start: 0.6700 (t-100) cc_final: 0.6126 (t-100) REVERT: a 682 ARG cc_start: 0.8493 (OUTLIER) cc_final: 0.7705 (ppt90) REVERT: a 884 MET cc_start: 0.9400 (ptp) cc_final: 0.9198 (ptt) REVERT: e 28 ASN cc_start: 0.8473 (OUTLIER) cc_final: 0.8070 (m-40) REVERT: e 67 MET cc_start: 0.8442 (tpp) cc_final: 0.8066 (mmm) REVERT: e 116 MET cc_start: 0.9342 (mtp) cc_final: 0.9015 (mtt) REVERT: e 137 LEU cc_start: 0.9614 (mt) cc_final: 0.9302 (tp) REVERT: e 807 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7802 (tppt) REVERT: e 963 MET cc_start: -0.0789 (mmt) cc_final: -0.1119 (mmt) REVERT: e 1135 MET cc_start: 0.2639 (mtp) cc_final: 0.2375 (mtp) REVERT: e 1277 MET cc_start: 0.7456 (mtt) cc_final: 0.7249 (mtp) REVERT: e 1286 MET cc_start: 0.6598 (ptt) cc_final: 0.6313 (ptt) REVERT: e 1432 TYR cc_start: 0.2587 (OUTLIER) cc_final: 0.1269 (p90) REVERT: g 6 GLN cc_start: 0.5672 (mt0) cc_final: 0.5172 (pp30) REVERT: g 67 ARG cc_start: 0.8145 (ttm110) cc_final: 0.7643 (mtp-110) REVERT: g 96 ARG cc_start: 0.8956 (ttm110) cc_final: 0.7725 (mtp-110) REVERT: g 140 GLN cc_start: 0.8825 (tp40) cc_final: 0.8140 (mp10) REVERT: g 197 MET cc_start: 0.8697 (ppp) cc_final: 0.8377 (ppp) REVERT: v 125 GLN cc_start: 0.9073 (tp40) cc_final: 0.8545 (tp-100) REVERT: v 136 VAL cc_start: 0.8748 (t) cc_final: 0.8338 (p) REVERT: w 60 ARG cc_start: 0.8696 (mtm-85) cc_final: 0.8177 (mtm-85) REVERT: w 72 PHE cc_start: 0.8363 (t80) cc_final: 0.6394 (OUTLIER) REVERT: w 76 ARG cc_start: 0.8617 (mtm180) cc_final: 0.7981 (mtm180) REVERT: w 157 PHE cc_start: 0.8928 (m-10) cc_final: 0.8342 (m-10) REVERT: w 174 MET cc_start: 0.7076 (mpt) cc_final: 0.6270 (mpt) REVERT: w 190 PHE cc_start: 0.9285 (t80) cc_final: 0.9007 (t80) REVERT: w 210 MET cc_start: 0.7344 (mmm) cc_final: 0.4664 (mmt) REVERT: w 214 PHE cc_start: 0.8498 (m-80) cc_final: 0.8178 (m-80) REVERT: 0 7 LYS cc_start: 0.9248 (tppp) cc_final: 0.8959 (tppp) REVERT: 0 10 GLU cc_start: 0.9557 (pp20) cc_final: 0.9277 (pp20) REVERT: 0 14 LYS cc_start: 0.8722 (ttpp) cc_final: 0.8386 (tptp) REVERT: 0 38 MET cc_start: 0.9243 (tpp) cc_final: 0.8333 (tmm) REVERT: 0 58 MET cc_start: 0.8724 (tpt) cc_final: 0.8463 (tpp) REVERT: 0 97 LYS cc_start: 0.9486 (ptmm) cc_final: 0.9075 (ptmm) REVERT: 0 191 TYR cc_start: 0.7971 (t80) cc_final: 0.7307 (t80) outliers start: 220 outliers final: 105 residues processed: 939 average time/residue: 2.1590 time to fit residues: 2993.2801 Evaluate side-chains 869 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 750 time to evaluate : 8.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 106 ASP Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 32 LYS Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 25 GLN Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 336 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain q residue 177 ASP Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 807 LYS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 1038 ASP Chi-restraints excluded: chain e residue 1206 GLN Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 139 ARG Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 49 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 145 TYR Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 1146 optimal weight: 50.0000 chunk 872 optimal weight: 9.9990 chunk 602 optimal weight: 7.9990 chunk 128 optimal weight: 2.9990 chunk 554 optimal weight: 40.0000 chunk 779 optimal weight: 5.9990 chunk 1165 optimal weight: 30.0000 chunk 1233 optimal weight: 6.9990 chunk 608 optimal weight: 10.0000 chunk 1104 optimal weight: 30.0000 chunk 332 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN F 138 GLN G 127 GLN I 98 ASN M 106 GLN V 92 ASN ** p 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 95 ASN a 690 ASN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN v 58 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 160078 Z= 0.424 Angle : 0.645 20.601 233663 Z= 0.338 Chirality : 0.042 0.324 29152 Planarity : 0.005 0.106 16403 Dihedral : 22.486 178.989 65644 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.15 % Favored : 95.82 % Rotamer: Outliers : 3.20 % Allowed : 15.29 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.60 % Twisted General : 0.09 % 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: 0.36 (0.09), residues: 9312 helix: 1.44 (0.08), residues: 3967 sheet: 0.02 (0.15), residues: 1184 loop : -0.85 (0.09), residues: 4161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP n 9 HIS 0.012 0.001 HIS e 733 PHE 0.028 0.002 PHE o 229 TYR 0.028 0.002 TYR F 172 ARG 0.009 0.001 ARG K 138 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1035 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 793 time to evaluate : 8.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8795 (OUTLIER) cc_final: 0.8187 (ttt90) REVERT: B 151 ASP cc_start: 0.8723 (OUTLIER) cc_final: 0.8519 (m-30) REVERT: C 120 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8350 (p0) REVERT: C 182 ILE cc_start: 0.8898 (OUTLIER) cc_final: 0.8559 (tp) REVERT: D 173 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8142 (mt-10) REVERT: G 104 GLU cc_start: 0.7698 (tm-30) cc_final: 0.7449 (tm-30) REVERT: H 49 ASN cc_start: 0.7963 (t0) cc_final: 0.7612 (t0) REVERT: M 84 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8095 (ptp90) REVERT: N 120 ASN cc_start: 0.8701 (t0) cc_final: 0.8378 (t0) REVERT: P 57 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7601 (mt-10) REVERT: R 19 ARG cc_start: 0.9303 (OUTLIER) cc_final: 0.7354 (ttp-170) REVERT: S 31 LYS cc_start: 0.9161 (OUTLIER) cc_final: 0.8431 (ttmm) REVERT: S 58 GLU cc_start: 0.7349 (tm-30) cc_final: 0.7136 (tm-30) REVERT: U 79 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8368 (p0) REVERT: V 92 ASN cc_start: 0.8949 (m-40) cc_final: 0.8658 (m110) REVERT: X 10 GLN cc_start: 0.8463 (tt0) cc_final: 0.8205 (tt0) REVERT: X 76 ASN cc_start: 0.8311 (t0) cc_final: 0.8008 (t0) REVERT: k 289 ASP cc_start: 0.7350 (p0) cc_final: 0.6809 (p0) REVERT: l 288 ARG cc_start: 0.7986 (mtm110) cc_final: 0.7715 (mtm110) REVERT: m 95 TRP cc_start: 0.9452 (OUTLIER) cc_final: 0.7821 (t60) REVERT: n 102 ASN cc_start: 0.9023 (OUTLIER) cc_final: 0.8820 (p0) REVERT: n 133 GLU cc_start: 0.7368 (tp30) cc_final: 0.7085 (tp30) REVERT: n 137 ASP cc_start: 0.7720 (m-30) cc_final: 0.6680 (m-30) REVERT: s 52 TYR cc_start: 0.8401 (m-80) cc_final: 0.7955 (m-80) REVERT: u 12 TRP cc_start: 0.8585 (OUTLIER) cc_final: 0.7646 (p90) REVERT: u 16 GLU cc_start: 0.8354 (pm20) cc_final: 0.8059 (pm20) REVERT: a 543 MET cc_start: 0.9113 (ttm) cc_final: 0.8387 (tpp) REVERT: a 589 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8663 (mmm) REVERT: a 590 MET cc_start: 0.8846 (tmm) cc_final: 0.8396 (tmm) REVERT: a 682 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7757 (ppt90) REVERT: a 884 MET cc_start: 0.9452 (ptp) cc_final: 0.9242 (ptt) REVERT: e 28 ASN cc_start: 0.8466 (OUTLIER) cc_final: 0.7999 (m-40) REVERT: e 67 MET cc_start: 0.8461 (tpp) cc_final: 0.8081 (mmm) REVERT: e 116 MET cc_start: 0.9291 (mtp) cc_final: 0.8965 (mtt) REVERT: e 137 LEU cc_start: 0.9605 (mt) cc_final: 0.9301 (tp) REVERT: e 807 LYS cc_start: 0.8578 (OUTLIER) cc_final: 0.7870 (tppt) REVERT: e 963 MET cc_start: -0.0652 (mmt) cc_final: -0.0940 (mmt) REVERT: e 1060 MET cc_start: 0.1374 (mmt) cc_final: 0.1116 (mpt) REVERT: e 1068 MET cc_start: 0.1060 (OUTLIER) cc_final: 0.0636 (pp-130) REVERT: e 1093 LEU cc_start: 0.8040 (mt) cc_final: 0.7689 (tp) REVERT: e 1135 MET cc_start: 0.2712 (mtp) cc_final: 0.2457 (mtp) REVERT: e 1277 MET cc_start: 0.7495 (mtt) cc_final: 0.7293 (mtp) REVERT: e 1286 MET cc_start: 0.6626 (ptt) cc_final: 0.6333 (ptt) REVERT: e 1432 TYR cc_start: 0.2536 (OUTLIER) cc_final: 0.1052 (p90) REVERT: g 1 MET cc_start: 0.4602 (ttt) cc_final: 0.3473 (ttt) REVERT: g 6 GLN cc_start: 0.5734 (mt0) cc_final: 0.4941 (pp30) REVERT: g 67 ARG cc_start: 0.8153 (ttm110) cc_final: 0.7610 (mtp-110) REVERT: g 68 ARG cc_start: 0.7794 (mpp80) cc_final: 0.7355 (mpp80) REVERT: g 95 GLN cc_start: 0.9017 (tp-100) cc_final: 0.8776 (tp-100) REVERT: g 123 ARG cc_start: 0.8257 (mmp80) cc_final: 0.8005 (mmp80) REVERT: g 140 GLN cc_start: 0.8826 (tp40) cc_final: 0.8153 (mp10) REVERT: g 197 MET cc_start: 0.8773 (ppp) cc_final: 0.8388 (ppp) REVERT: v 125 GLN cc_start: 0.9020 (tp40) cc_final: 0.8497 (tp-100) REVERT: w 72 PHE cc_start: 0.8388 (t80) cc_final: 0.6446 (OUTLIER) REVERT: w 76 ARG cc_start: 0.8693 (mtm180) cc_final: 0.8090 (mtm180) REVERT: w 157 PHE cc_start: 0.8943 (m-10) cc_final: 0.8208 (m-10) REVERT: w 190 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8892 (t80) REVERT: w 210 MET cc_start: 0.7263 (mmm) cc_final: 0.7014 (mmt) REVERT: 0 7 LYS cc_start: 0.9275 (tppp) cc_final: 0.8936 (tppp) REVERT: 0 10 GLU cc_start: 0.9581 (pp20) cc_final: 0.9328 (pp20) REVERT: 0 22 TYR cc_start: 0.8500 (m-80) cc_final: 0.7997 (m-80) REVERT: 0 38 MET cc_start: 0.9226 (tpp) cc_final: 0.8246 (tmm) REVERT: 0 58 MET cc_start: 0.8705 (tpt) cc_final: 0.8416 (tpp) REVERT: 0 60 ARG cc_start: 0.9324 (mpt-90) cc_final: 0.9082 (mpt-90) REVERT: 0 191 TYR cc_start: 0.8027 (t80) cc_final: 0.7373 (t80) outliers start: 242 outliers final: 129 residues processed: 961 average time/residue: 2.0817 time to fit residues: 2949.1537 Evaluate side-chains 894 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 747 time to evaluate : 8.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain H residue 20 SER Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 68 ILE Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain N residue 125 VAL Chi-restraints excluded: chain P residue 32 LYS Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 89 GLU Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain Z residue 98 LYS Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 59 ASP Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 336 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 102 ASN Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 177 ASP Chi-restraints excluded: chain r residue 26 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 658 TRP Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 807 LYS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 904 VAL Chi-restraints excluded: chain e residue 1038 ASP Chi-restraints excluded: chain e residue 1068 MET Chi-restraints excluded: chain e residue 1184 ILE Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 192 VAL Chi-restraints excluded: chain v residue 33 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 190 PHE Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 1027 optimal weight: 8.9990 chunk 700 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 918 optimal weight: 3.9990 chunk 508 optimal weight: 8.9990 chunk 1052 optimal weight: 10.0000 chunk 852 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 629 optimal weight: 10.0000 chunk 1107 optimal weight: 10.0000 chunk 311 optimal weight: 0.8980 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN Q 57 GLN m 81 HIS o 64 GLN q 9 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e1206 GLN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN ** w 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 160078 Z= 0.226 Angle : 0.571 18.590 233663 Z= 0.301 Chirality : 0.037 0.290 29152 Planarity : 0.004 0.101 16403 Dihedral : 22.482 178.228 65644 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.90 % Favored : 96.07 % Rotamer: Outliers : 2.47 % Allowed : 16.98 % Favored : 80.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % 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: 0.52 (0.09), residues: 9312 helix: 1.58 (0.08), residues: 3972 sheet: 0.16 (0.15), residues: 1143 loop : -0.79 (0.09), residues: 4197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP w 198 HIS 0.005 0.001 HIS r 123 PHE 0.027 0.001 PHE v 150 TYR 0.041 0.001 TYR v 90 ARG 0.011 0.000 ARG K 138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 811 time to evaluate : 8.351 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8748 (OUTLIER) cc_final: 0.8147 (ttt90) REVERT: B 151 ASP cc_start: 0.8718 (OUTLIER) cc_final: 0.8513 (m-30) REVERT: G 134 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8208 (mp-120) REVERT: H 49 ASN cc_start: 0.8125 (t0) cc_final: 0.7744 (t0) REVERT: K 138 ARG cc_start: 0.8442 (ttp80) cc_final: 0.8193 (ttp80) REVERT: N 120 ASN cc_start: 0.8615 (t0) cc_final: 0.8320 (t0) REVERT: R 19 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.7449 (ttp-170) REVERT: S 31 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8403 (ttmm) REVERT: j 24 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.8216 (mt0) REVERT: j 143 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7948 (pp20) REVERT: k 289 ASP cc_start: 0.7306 (p0) cc_final: 0.6769 (p0) REVERT: m 95 TRP cc_start: 0.9413 (OUTLIER) cc_final: 0.7767 (t60) REVERT: n 13 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7493 (mt-10) REVERT: n 137 ASP cc_start: 0.7735 (m-30) cc_final: 0.6547 (m-30) REVERT: o 182 ASP cc_start: 0.7710 (OUTLIER) cc_final: 0.7472 (m-30) REVERT: s 52 TYR cc_start: 0.8359 (m-80) cc_final: 0.7920 (m-80) REVERT: u 12 TRP cc_start: 0.8639 (OUTLIER) cc_final: 0.7937 (p90) REVERT: u 16 GLU cc_start: 0.8298 (pm20) cc_final: 0.8003 (pm20) REVERT: a 543 MET cc_start: 0.9069 (ttm) cc_final: 0.8405 (tpp) REVERT: a 589 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8696 (mmm) REVERT: a 590 MET cc_start: 0.8894 (tmm) cc_final: 0.8494 (tmm) REVERT: a 649 TRP cc_start: 0.6606 (OUTLIER) cc_final: 0.6333 (t60) REVERT: a 682 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7789 (ppt90) REVERT: a 884 MET cc_start: 0.9432 (ptp) cc_final: 0.9213 (ptt) REVERT: e 28 ASN cc_start: 0.8355 (OUTLIER) cc_final: 0.7880 (m-40) REVERT: e 67 MET cc_start: 0.8433 (tpp) cc_final: 0.8052 (mmm) REVERT: e 116 MET cc_start: 0.9285 (mtp) cc_final: 0.9019 (mtt) REVERT: e 137 LEU cc_start: 0.9596 (mt) cc_final: 0.9265 (tp) REVERT: e 963 MET cc_start: -0.0853 (mmt) cc_final: -0.1168 (mmt) REVERT: e 1060 MET cc_start: 0.1483 (mmt) cc_final: 0.1129 (mpt) REVERT: e 1068 MET cc_start: 0.0956 (ptt) cc_final: 0.0581 (pp-130) REVERT: e 1093 LEU cc_start: 0.7948 (mt) cc_final: 0.7646 (tp) REVERT: e 1135 MET cc_start: 0.2632 (mtp) cc_final: 0.2405 (mtp) REVERT: e 1277 MET cc_start: 0.7547 (mtt) cc_final: 0.7343 (mtp) REVERT: e 1286 MET cc_start: 0.6676 (ptt) cc_final: 0.6178 (ptt) REVERT: e 1432 TYR cc_start: 0.2361 (OUTLIER) cc_final: 0.1002 (p90) REVERT: g 4 ARG cc_start: 0.7957 (mmt90) cc_final: 0.7597 (mmt90) REVERT: g 6 GLN cc_start: 0.5684 (mt0) cc_final: 0.4899 (pp30) REVERT: g 67 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7687 (mtp-110) REVERT: g 68 ARG cc_start: 0.7774 (mpp80) cc_final: 0.7308 (mpp80) REVERT: g 96 ARG cc_start: 0.8871 (ttm110) cc_final: 0.7822 (mtp-110) REVERT: v 125 GLN cc_start: 0.9059 (tp40) cc_final: 0.8547 (tp-100) REVERT: w 72 PHE cc_start: 0.8421 (t80) cc_final: 0.6489 (OUTLIER) REVERT: w 76 ARG cc_start: 0.8651 (mtm180) cc_final: 0.8075 (mtm180) REVERT: w 157 PHE cc_start: 0.8868 (m-10) cc_final: 0.8350 (m-10) REVERT: 0 7 LYS cc_start: 0.9319 (tppp) cc_final: 0.9015 (tppp) REVERT: 0 10 GLU cc_start: 0.9595 (pp20) cc_final: 0.9351 (pp20) REVERT: 0 14 LYS cc_start: 0.8843 (ttpp) cc_final: 0.8470 (tptp) REVERT: 0 22 TYR cc_start: 0.8478 (m-80) cc_final: 0.7990 (m-80) REVERT: 0 38 MET cc_start: 0.9186 (tpp) cc_final: 0.8222 (tmm) REVERT: 0 60 ARG cc_start: 0.9311 (mpt-90) cc_final: 0.9068 (mpt-90) REVERT: 0 191 TYR cc_start: 0.7945 (t80) cc_final: 0.7316 (t80) outliers start: 187 outliers final: 107 residues processed: 939 average time/residue: 2.0803 time to fit residues: 2879.1097 Evaluate side-chains 890 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 769 time to evaluate : 8.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 61 MET Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 24 GLN Chi-restraints excluded: chain j residue 143 GLU Chi-restraints excluded: chain k residue 59 ASP Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain n residue 152 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 182 ASP Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain r residue 26 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 158 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 649 TRP Chi-restraints excluded: chain a residue 658 TRP Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 833 HIS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain g residue 171 GLU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 88 ASN Chi-restraints excluded: chain w residue 19 TYR Chi-restraints excluded: chain w residue 48 ARG Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 66 PHE Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 414 optimal weight: 8.9990 chunk 1110 optimal weight: 10.0000 chunk 243 optimal weight: 4.9990 chunk 724 optimal weight: 9.9990 chunk 304 optimal weight: 9.9990 chunk 1234 optimal weight: 20.0000 chunk 1024 optimal weight: 50.0000 chunk 571 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 408 optimal weight: 10.0000 chunk 648 optimal weight: 10.0000 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN V 92 ASN ** p 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 562 HIS ** e 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 75 GLN ** 0 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.092 160078 Z= 0.505 Angle : 0.671 19.137 233663 Z= 0.349 Chirality : 0.044 0.345 29152 Planarity : 0.005 0.106 16403 Dihedral : 22.423 179.383 65640 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.18 % Favored : 95.79 % Rotamer: Outliers : 3.15 % Allowed : 17.42 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % 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: 0.43 (0.09), residues: 9312 helix: 1.52 (0.08), residues: 3981 sheet: 0.02 (0.15), residues: 1176 loop : -0.84 (0.09), residues: 4155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP n 9 HIS 0.009 0.001 HIS l 311 PHE 0.034 0.002 PHE v 150 TYR 0.040 0.002 TYR v 90 ARG 0.012 0.001 ARG g 139 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 761 time to evaluate : 8.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8799 (OUTLIER) cc_final: 0.8094 (ttt90) REVERT: B 151 ASP cc_start: 0.8725 (OUTLIER) cc_final: 0.8521 (m-30) REVERT: C 120 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8384 (p0) REVERT: E 92 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.7792 (tt0) REVERT: H 44 GLU cc_start: 0.7600 (pm20) cc_final: 0.7393 (pm20) REVERT: H 49 ASN cc_start: 0.8297 (t0) cc_final: 0.7879 (t0) REVERT: I 88 ARG cc_start: 0.7710 (mpt180) cc_final: 0.7466 (mpt180) REVERT: J 12 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8164 (mtpp) REVERT: K 138 ARG cc_start: 0.8543 (ttp80) cc_final: 0.8293 (ttp80) REVERT: N 120 ASN cc_start: 0.8717 (t0) cc_final: 0.8415 (t0) REVERT: R 19 ARG cc_start: 0.9326 (OUTLIER) cc_final: 0.7394 (ttp-170) REVERT: S 31 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8441 (ttmm) REVERT: S 58 GLU cc_start: 0.7324 (tm-30) cc_final: 0.7095 (tm-30) REVERT: U 27 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7520 (tp30) REVERT: U 79 ASP cc_start: 0.8612 (OUTLIER) cc_final: 0.8381 (p0) REVERT: V 92 ASN cc_start: 0.8890 (m-40) cc_final: 0.8632 (m110) REVERT: b 72 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9104 (mt) REVERT: k 289 ASP cc_start: 0.7307 (p0) cc_final: 0.6762 (p0) REVERT: m 95 TRP cc_start: 0.9498 (OUTLIER) cc_final: 0.7775 (t60) REVERT: m 158 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7957 (ptt-90) REVERT: n 13 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7641 (mt-10) REVERT: n 133 GLU cc_start: 0.7325 (tp30) cc_final: 0.6892 (tp30) REVERT: n 137 ASP cc_start: 0.7329 (m-30) cc_final: 0.6737 (m-30) REVERT: o 68 ASP cc_start: 0.8220 (m-30) cc_final: 0.7929 (m-30) REVERT: q 76 ASP cc_start: 0.8137 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: q 153 ASP cc_start: 0.7745 (m-30) cc_final: 0.7399 (m-30) REVERT: s 47 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8905 (mt0) REVERT: s 52 TYR cc_start: 0.8437 (m-80) cc_final: 0.8024 (m-80) REVERT: s 78 GLU cc_start: 0.8355 (pp20) cc_final: 0.8088 (pp20) REVERT: u 12 TRP cc_start: 0.8895 (OUTLIER) cc_final: 0.8231 (p90) REVERT: u 16 GLU cc_start: 0.8380 (pm20) cc_final: 0.8076 (pm20) REVERT: a 543 MET cc_start: 0.9098 (ttm) cc_final: 0.8366 (tpp) REVERT: a 589 MET cc_start: 0.9098 (OUTLIER) cc_final: 0.8574 (mmm) REVERT: a 590 MET cc_start: 0.8902 (tmm) cc_final: 0.8492 (tmm) REVERT: a 682 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8001 (ppt90) REVERT: a 884 MET cc_start: 0.9414 (ptp) cc_final: 0.9160 (ptt) REVERT: e 28 ASN cc_start: 0.8436 (OUTLIER) cc_final: 0.7913 (m-40) REVERT: e 67 MET cc_start: 0.8495 (tpp) cc_final: 0.8113 (mmm) REVERT: e 116 MET cc_start: 0.9300 (mtp) cc_final: 0.8971 (mtt) REVERT: e 137 LEU cc_start: 0.9604 (mt) cc_final: 0.9290 (tp) REVERT: e 963 MET cc_start: -0.0754 (mmt) cc_final: -0.1042 (mmt) REVERT: e 1060 MET cc_start: 0.1602 (mmt) cc_final: 0.1304 (mpt) REVERT: e 1068 MET cc_start: 0.1166 (ptt) cc_final: 0.0715 (pp-130) REVERT: e 1286 MET cc_start: 0.6573 (ptt) cc_final: 0.6249 (ptt) REVERT: e 1432 TYR cc_start: 0.2430 (OUTLIER) cc_final: 0.1196 (p90) REVERT: e 1483 MET cc_start: 0.8028 (tpt) cc_final: 0.7570 (pmt) REVERT: g 1 MET cc_start: 0.4293 (ttt) cc_final: 0.4020 (ttt) REVERT: g 4 ARG cc_start: 0.7997 (mmt90) cc_final: 0.7613 (mmt90) REVERT: g 6 GLN cc_start: 0.5602 (mt0) cc_final: 0.4753 (pp30) REVERT: g 67 ARG cc_start: 0.8245 (ttm110) cc_final: 0.7683 (mtp-110) REVERT: g 68 ARG cc_start: 0.7798 (mpp80) cc_final: 0.7331 (mpp80) REVERT: g 96 ARG cc_start: 0.8901 (ttm110) cc_final: 0.7770 (mtp-110) REVERT: g 123 ARG cc_start: 0.8397 (mmp80) cc_final: 0.7886 (mmp80) REVERT: g 139 ARG cc_start: 0.8746 (ttm110) cc_final: 0.7816 (mtt-85) REVERT: g 140 GLN cc_start: 0.8741 (tp-100) cc_final: 0.8530 (tp40) REVERT: g 197 MET cc_start: 0.8727 (ppp) cc_final: 0.8266 (ppp) REVERT: v 125 GLN cc_start: 0.9051 (tp40) cc_final: 0.8550 (tp-100) REVERT: v 136 VAL cc_start: 0.8910 (t) cc_final: 0.8662 (p) REVERT: w 72 PHE cc_start: 0.8483 (t80) cc_final: 0.6403 (OUTLIER) REVERT: w 76 ARG cc_start: 0.8696 (mtm180) cc_final: 0.8140 (mtm180) REVERT: w 157 PHE cc_start: 0.8922 (m-10) cc_final: 0.8350 (m-10) REVERT: w 210 MET cc_start: 0.7607 (mmp) cc_final: 0.6491 (mmt) REVERT: 0 7 LYS cc_start: 0.9383 (tppp) cc_final: 0.9023 (tppp) REVERT: 0 10 GLU cc_start: 0.9613 (pp20) cc_final: 0.9388 (pp20) REVERT: 0 14 LYS cc_start: 0.8828 (ttpp) cc_final: 0.8449 (tptp) REVERT: 0 16 ARG cc_start: 0.8072 (tpm170) cc_final: 0.7732 (tpm170) REVERT: 0 22 TYR cc_start: 0.8603 (m-80) cc_final: 0.8112 (m-80) REVERT: 0 38 MET cc_start: 0.9199 (tpp) cc_final: 0.8212 (tmm) REVERT: 0 58 MET cc_start: 0.8885 (tpp) cc_final: 0.8448 (tpp) REVERT: 0 191 TYR cc_start: 0.8005 (t80) cc_final: 0.7349 (t80) outliers start: 238 outliers final: 144 residues processed: 923 average time/residue: 2.1480 time to fit residues: 2914.4071 Evaluate side-chains 898 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 737 time to evaluate : 8.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 126 VAL Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 94 SER Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 85 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 47 ASP Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 72 LEU Chi-restraints excluded: chain b residue 84 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 59 ASP Chi-restraints excluded: chain k residue 73 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 336 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 36 ILE Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain q residue 76 ASP Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain r residue 26 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 26 SER Chi-restraints excluded: chain s residue 30 LEU Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 47 GLN Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 158 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 6 ILE Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 17 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain u residue 135 LEU Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 414 MET Chi-restraints excluded: chain a residue 552 GLN Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 833 HIS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 1038 ASP Chi-restraints excluded: chain e residue 1161 SER Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1474 MET Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 49 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain w residue 145 TYR Chi-restraints excluded: chain 0 residue 32 ASN Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 1190 optimal weight: 7.9990 chunk 139 optimal weight: 3.9990 chunk 703 optimal weight: 0.9990 chunk 901 optimal weight: 9.9990 chunk 698 optimal weight: 2.9990 chunk 1039 optimal weight: 4.9990 chunk 689 optimal weight: 5.9990 chunk 1229 optimal weight: 10.0000 chunk 769 optimal weight: 10.0000 chunk 749 optimal weight: 0.8980 chunk 567 optimal weight: 4.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN A ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 ASN E 92 GLN ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN M 106 GLN Q 57 GLN q 9 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 90 GLN ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 160 GLN e 226 ASN ** e 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8768 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 160078 Z= 0.216 Angle : 0.579 16.943 233663 Z= 0.304 Chirality : 0.037 0.280 29152 Planarity : 0.004 0.100 16403 Dihedral : 22.464 178.604 65640 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 2.71 % Allowed : 18.23 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % 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: 0.58 (0.09), residues: 9312 helix: 1.64 (0.08), residues: 3980 sheet: 0.13 (0.15), residues: 1161 loop : -0.77 (0.09), residues: 4171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP n 9 HIS 0.007 0.001 HIS R 88 PHE 0.036 0.001 PHE v 150 TYR 0.033 0.001 TYR v 90 ARG 0.013 0.000 ARG g 139 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1007 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 802 time to evaluate : 8.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8107 (ttt90) REVERT: H 44 GLU cc_start: 0.7524 (pm20) cc_final: 0.7243 (pm20) REVERT: H 49 ASN cc_start: 0.8322 (t0) cc_final: 0.7909 (t0) REVERT: I 121 GLU cc_start: 0.8786 (mp0) cc_final: 0.8580 (mp0) REVERT: J 12 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8168 (mtpp) REVERT: N 120 ASN cc_start: 0.8604 (t0) cc_final: 0.8316 (t0) REVERT: R 19 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.7442 (ttp-170) REVERT: S 31 LYS cc_start: 0.9144 (OUTLIER) cc_final: 0.8417 (ttmm) REVERT: S 58 GLU cc_start: 0.7205 (tm-30) cc_final: 0.6954 (tm-30) REVERT: U 27 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7235 (tp30) REVERT: U 79 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8369 (p0) REVERT: b 72 LEU cc_start: 0.9219 (OUTLIER) cc_final: 0.8924 (mt) REVERT: k 289 ASP cc_start: 0.7334 (p0) cc_final: 0.6826 (p0) REVERT: m 95 TRP cc_start: 0.9410 (OUTLIER) cc_final: 0.7647 (t60) REVERT: m 158 ARG cc_start: 0.8541 (OUTLIER) cc_final: 0.7709 (ptt-90) REVERT: n 13 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7506 (mt-10) REVERT: n 133 GLU cc_start: 0.7372 (tp30) cc_final: 0.6986 (tp30) REVERT: n 137 ASP cc_start: 0.7445 (m-30) cc_final: 0.6683 (m-30) REVERT: s 47 GLN cc_start: 0.9212 (OUTLIER) cc_final: 0.8886 (mt0) REVERT: s 52 TYR cc_start: 0.8378 (m-80) cc_final: 0.7979 (m-80) REVERT: s 107 ASP cc_start: 0.8403 (t0) cc_final: 0.8041 (t0) REVERT: u 12 TRP cc_start: 0.8837 (OUTLIER) cc_final: 0.8094 (p90) REVERT: u 16 GLU cc_start: 0.8295 (pm20) cc_final: 0.8012 (pm20) REVERT: a 543 MET cc_start: 0.9070 (ttm) cc_final: 0.8352 (tpp) REVERT: a 589 MET cc_start: 0.9083 (OUTLIER) cc_final: 0.8640 (mmm) REVERT: a 590 MET cc_start: 0.8910 (tmm) cc_final: 0.8524 (tmm) REVERT: a 682 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7840 (ppt90) REVERT: a 699 MET cc_start: 0.7807 (pmm) cc_final: 0.7167 (pmm) REVERT: a 884 MET cc_start: 0.9415 (ptp) cc_final: 0.9137 (ptt) REVERT: e 28 ASN cc_start: 0.8438 (OUTLIER) cc_final: 0.7965 (m-40) REVERT: e 67 MET cc_start: 0.8462 (tpp) cc_final: 0.8104 (mmm) REVERT: e 116 MET cc_start: 0.9294 (mtp) cc_final: 0.9037 (mtt) REVERT: e 137 LEU cc_start: 0.9594 (mt) cc_final: 0.9258 (tp) REVERT: e 1060 MET cc_start: 0.1405 (mmt) cc_final: 0.1096 (mpt) REVERT: e 1068 MET cc_start: 0.1301 (ptt) cc_final: 0.0820 (pp-130) REVERT: e 1093 LEU cc_start: 0.7910 (mt) cc_final: 0.7577 (tp) REVERT: e 1286 MET cc_start: 0.6563 (ptt) cc_final: 0.6238 (ptt) REVERT: e 1299 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8091 (mt) REVERT: e 1432 TYR cc_start: 0.2297 (OUTLIER) cc_final: 0.1029 (p90) REVERT: e 1483 MET cc_start: 0.7942 (tpt) cc_final: 0.7534 (pmt) REVERT: g 4 ARG cc_start: 0.7936 (mmt90) cc_final: 0.7610 (mmt90) REVERT: g 6 GLN cc_start: 0.5553 (mt0) cc_final: 0.4735 (pp30) REVERT: g 67 ARG cc_start: 0.8297 (ttm110) cc_final: 0.7794 (mtp-110) REVERT: g 68 ARG cc_start: 0.7815 (mpp80) cc_final: 0.7347 (mpp80) REVERT: g 96 ARG cc_start: 0.8835 (ttm110) cc_final: 0.7710 (mtp-110) REVERT: g 123 ARG cc_start: 0.8396 (mmp80) cc_final: 0.7975 (mmp80) REVERT: g 128 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9132 (tm) REVERT: g 139 ARG cc_start: 0.8747 (ttm110) cc_final: 0.7960 (mtt-85) REVERT: g 140 GLN cc_start: 0.8687 (tp-100) cc_final: 0.8486 (tp40) REVERT: g 197 MET cc_start: 0.8697 (ppp) cc_final: 0.8212 (ppp) REVERT: v 57 VAL cc_start: 0.9230 (t) cc_final: 0.9029 (p) REVERT: v 125 GLN cc_start: 0.9094 (tp40) cc_final: 0.8580 (tp-100) REVERT: v 136 VAL cc_start: 0.8980 (t) cc_final: 0.8767 (p) REVERT: w 72 PHE cc_start: 0.8492 (t80) cc_final: 0.8204 (OUTLIER) REVERT: w 76 ARG cc_start: 0.8735 (mtm180) cc_final: 0.8315 (ttm170) REVERT: w 157 PHE cc_start: 0.8917 (m-10) cc_final: 0.8295 (m-10) REVERT: w 210 MET cc_start: 0.7532 (mmp) cc_final: 0.6941 (mmp) REVERT: 0 7 LYS cc_start: 0.9419 (tppp) cc_final: 0.9073 (tppp) REVERT: 0 8 LYS cc_start: 0.8887 (mttp) cc_final: 0.8598 (tttp) REVERT: 0 14 LYS cc_start: 0.8729 (ttpp) cc_final: 0.8341 (tptp) REVERT: 0 22 TYR cc_start: 0.8582 (m-80) cc_final: 0.8080 (m-80) REVERT: 0 58 MET cc_start: 0.8951 (tpp) cc_final: 0.8307 (tpp) REVERT: 0 60 ARG cc_start: 0.9200 (mpt-90) cc_final: 0.8801 (mpt-90) REVERT: 0 89 THR cc_start: 0.7431 (OUTLIER) cc_final: 0.7220 (t) REVERT: 0 191 TYR cc_start: 0.8028 (t80) cc_final: 0.7428 (t80) outliers start: 205 outliers final: 125 residues processed: 950 average time/residue: 2.0913 time to fit residues: 2936.9067 Evaluate side-chains 907 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 766 time to evaluate : 8.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 40 GLU Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain E residue 127 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 55 THR Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 97 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 14 LEU Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 72 LEU Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain l residue 299 ILE Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 26 SER Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 47 GLN Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 158 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 113 VAL Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 552 GLN Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 833 HIS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 1161 SER Chi-restraints excluded: chain e residue 1299 LEU Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain g residue 137 VAL Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 138 ILE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 89 THR Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 760 optimal weight: 6.9990 chunk 491 optimal weight: 10.0000 chunk 734 optimal weight: 0.7980 chunk 370 optimal weight: 30.0000 chunk 241 optimal weight: 5.9990 chunk 238 optimal weight: 0.9980 chunk 781 optimal weight: 0.9980 chunk 837 optimal weight: 6.9990 chunk 608 optimal weight: 10.0000 chunk 114 optimal weight: 6.9990 chunk 966 optimal weight: 40.0000 overall best weight: 3.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 92 GLN ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN Q 57 GLN V 92 ASN ** p 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 705 ASN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 160078 Z= 0.237 Angle : 0.579 14.571 233663 Z= 0.304 Chirality : 0.037 0.272 29152 Planarity : 0.004 0.101 16403 Dihedral : 22.412 178.934 65637 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.16 % Favored : 95.82 % Rotamer: Outliers : 2.51 % Allowed : 18.77 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.09), residues: 9312 helix: 1.67 (0.08), residues: 3984 sheet: 0.16 (0.15), residues: 1168 loop : -0.73 (0.09), residues: 4160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP a 659 HIS 0.007 0.001 HIS R 88 PHE 0.037 0.001 PHE v 150 TYR 0.046 0.001 TYR v 90 ARG 0.013 0.000 ARG l 288 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 977 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 787 time to evaluate : 12.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8075 (ttt90) REVERT: B 151 ASP cc_start: 0.8772 (OUTLIER) cc_final: 0.8553 (m-30) REVERT: H 44 GLU cc_start: 0.7525 (pm20) cc_final: 0.7259 (pm20) REVERT: H 49 ASN cc_start: 0.8378 (t0) cc_final: 0.7950 (t0) REVERT: J 12 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8164 (mtpp) REVERT: N 120 ASN cc_start: 0.8581 (t0) cc_final: 0.8305 (t0) REVERT: R 19 ARG cc_start: 0.9230 (OUTLIER) cc_final: 0.7499 (ttp-170) REVERT: S 31 LYS cc_start: 0.9136 (OUTLIER) cc_final: 0.8387 (ttmm) REVERT: U 79 ASP cc_start: 0.8602 (OUTLIER) cc_final: 0.8375 (p0) REVERT: b 100 LYS cc_start: 0.7826 (mppt) cc_final: 0.6730 (tppt) REVERT: j 73 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7534 (tm-30) REVERT: k 289 ASP cc_start: 0.7312 (p0) cc_final: 0.6804 (p0) REVERT: m 95 TRP cc_start: 0.9417 (OUTLIER) cc_final: 0.7657 (t60) REVERT: m 158 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.7726 (ptt-90) REVERT: n 13 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7444 (mt-10) REVERT: n 133 GLU cc_start: 0.7409 (tp30) cc_final: 0.6942 (tp30) REVERT: n 137 ASP cc_start: 0.7472 (m-30) cc_final: 0.6647 (m-30) REVERT: q 153 ASP cc_start: 0.7702 (m-30) cc_final: 0.7353 (m-30) REVERT: r 216 TYR cc_start: 0.8775 (t80) cc_final: 0.8532 (t80) REVERT: s 52 TYR cc_start: 0.8380 (m-80) cc_final: 0.7976 (m-80) REVERT: s 78 GLU cc_start: 0.7947 (pp20) cc_final: 0.7661 (pp20) REVERT: s 79 ILE cc_start: 0.9546 (mm) cc_final: 0.9300 (mm) REVERT: s 108 GLU cc_start: 0.8169 (pp20) cc_final: 0.7762 (pp20) REVERT: u 12 TRP cc_start: 0.8817 (OUTLIER) cc_final: 0.8114 (p90) REVERT: u 16 GLU cc_start: 0.8226 (pm20) cc_final: 0.7986 (pm20) REVERT: a 543 MET cc_start: 0.9051 (ttm) cc_final: 0.8281 (tpp) REVERT: a 589 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8691 (mmm) REVERT: a 590 MET cc_start: 0.8885 (tmm) cc_final: 0.8475 (tmm) REVERT: a 682 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7813 (ppt90) REVERT: a 884 MET cc_start: 0.9410 (ptp) cc_final: 0.9121 (ptt) REVERT: e 28 ASN cc_start: 0.8410 (OUTLIER) cc_final: 0.7943 (m-40) REVERT: e 67 MET cc_start: 0.8460 (tpp) cc_final: 0.8093 (mmm) REVERT: e 116 MET cc_start: 0.9305 (mtp) cc_final: 0.9046 (mtt) REVERT: e 137 LEU cc_start: 0.9578 (mt) cc_final: 0.9243 (tp) REVERT: e 963 MET cc_start: -0.0260 (mmt) cc_final: -0.0461 (mmt) REVERT: e 1060 MET cc_start: 0.1358 (mmt) cc_final: 0.1041 (mpt) REVERT: e 1068 MET cc_start: 0.1197 (ptt) cc_final: 0.0734 (pp-130) REVERT: e 1093 LEU cc_start: 0.7815 (mt) cc_final: 0.7530 (tp) REVERT: e 1286 MET cc_start: 0.6527 (ptt) cc_final: 0.6204 (ptt) REVERT: e 1299 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7897 (mt) REVERT: e 1432 TYR cc_start: 0.2266 (OUTLIER) cc_final: 0.1114 (p90) REVERT: e 1483 MET cc_start: 0.7934 (tpt) cc_final: 0.7521 (pmt) REVERT: g 4 ARG cc_start: 0.7872 (mmt90) cc_final: 0.7592 (mmt90) REVERT: g 6 GLN cc_start: 0.5595 (mt0) cc_final: 0.4730 (pp30) REVERT: g 67 ARG cc_start: 0.8295 (ttm110) cc_final: 0.7790 (mtp-110) REVERT: g 123 ARG cc_start: 0.8359 (mmp80) cc_final: 0.7955 (mmp80) REVERT: g 128 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9238 (mm) REVERT: g 139 ARG cc_start: 0.8747 (ttm110) cc_final: 0.7928 (mtt-85) REVERT: g 197 MET cc_start: 0.8708 (ppp) cc_final: 0.8362 (ppp) REVERT: v 125 GLN cc_start: 0.9095 (tp40) cc_final: 0.8592 (tp-100) REVERT: v 136 VAL cc_start: 0.8967 (t) cc_final: 0.8758 (p) REVERT: w 72 PHE cc_start: 0.8539 (t80) cc_final: 0.7013 (t80) REVERT: w 76 ARG cc_start: 0.8729 (mtm180) cc_final: 0.8192 (mtm180) REVERT: w 140 HIS cc_start: 0.8648 (m-70) cc_final: 0.8308 (m90) REVERT: w 157 PHE cc_start: 0.8931 (m-10) cc_final: 0.8274 (m-10) REVERT: w 210 MET cc_start: 0.7477 (mmp) cc_final: 0.6897 (mmp) REVERT: 0 14 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8398 (tptp) REVERT: 0 22 TYR cc_start: 0.8550 (m-80) cc_final: 0.8044 (m-80) REVERT: 0 58 MET cc_start: 0.8959 (tpp) cc_final: 0.8561 (tpp) REVERT: 0 60 ARG cc_start: 0.9160 (mpt-90) cc_final: 0.8913 (mpt-90) REVERT: 0 191 TYR cc_start: 0.8018 (t80) cc_final: 0.7422 (t80) outliers start: 190 outliers final: 139 residues processed: 922 average time/residue: 2.0971 time to fit residues: 2862.3222 Evaluate side-chains 919 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 764 time to evaluate : 8.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 96 ASP Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 58 ASP Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 83 ILE Chi-restraints excluded: chain j residue 73 GLU Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 59 ASP Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 336 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain l residue 259 ASP Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain n residue 145 LEU Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain r residue 26 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 42 THR Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 158 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 552 GLN Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 658 TRP Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 698 TYR Chi-restraints excluded: chain e residue 833 HIS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 960 LEU Chi-restraints excluded: chain e residue 1161 SER Chi-restraints excluded: chain e residue 1299 LEU Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 150 PHE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 1118 optimal weight: 50.0000 chunk 1178 optimal weight: 50.0000 chunk 1074 optimal weight: 30.0000 chunk 1146 optimal weight: 6.9990 chunk 1177 optimal weight: 7.9990 chunk 689 optimal weight: 3.9990 chunk 499 optimal weight: 10.0000 chunk 899 optimal weight: 6.9990 chunk 351 optimal weight: 10.0000 chunk 1035 optimal weight: 10.0000 chunk 1083 optimal weight: 10.0000 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 137 ASN ** D 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN V 92 ASN ** p 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 90 GLN ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 27 GLN ** e 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 810 GLN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1455 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8817 moved from start: 0.2800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.102 160078 Z= 0.474 Angle : 0.674 18.151 233663 Z= 0.350 Chirality : 0.043 0.342 29152 Planarity : 0.005 0.104 16403 Dihedral : 22.392 179.621 65636 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.41 % Favored : 95.56 % Rotamer: Outliers : 2.58 % Allowed : 19.16 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.07 % 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: 0.48 (0.09), residues: 9312 helix: 1.56 (0.08), residues: 3988 sheet: 0.04 (0.15), residues: 1178 loop : -0.81 (0.09), residues: 4146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP n 9 HIS 0.009 0.001 HIS l 311 PHE 0.037 0.002 PHE w 134 TYR 0.024 0.002 TYR l 194 ARG 0.013 0.001 ARG E 151 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 762 time to evaluate : 8.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8081 (ttt90) REVERT: B 151 ASP cc_start: 0.8787 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: C 120 ASN cc_start: 0.8678 (OUTLIER) cc_final: 0.8377 (p0) REVERT: C 182 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8560 (tp) REVERT: E 92 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.7999 (tt0) REVERT: H 49 ASN cc_start: 0.8412 (t0) cc_final: 0.8008 (t0) REVERT: J 12 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8169 (mtpp) REVERT: N 120 ASN cc_start: 0.8682 (t0) cc_final: 0.8398 (t0) REVERT: R 19 ARG cc_start: 0.9317 (OUTLIER) cc_final: 0.7374 (ttp-170) REVERT: S 31 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8431 (ttmm) REVERT: U 27 GLU cc_start: 0.7536 (tp30) cc_final: 0.7052 (tp30) REVERT: U 79 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8372 (p0) REVERT: V 92 ASN cc_start: 0.8995 (m-40) cc_final: 0.8383 (m110) REVERT: k 289 ASP cc_start: 0.7415 (p0) cc_final: 0.6913 (p0) REVERT: m 95 TRP cc_start: 0.9503 (OUTLIER) cc_final: 0.7777 (t60) REVERT: m 158 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.7728 (ptt-90) REVERT: n 13 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7497 (mt-10) REVERT: n 133 GLU cc_start: 0.7268 (tp30) cc_final: 0.6702 (tp30) REVERT: n 137 ASP cc_start: 0.7431 (m-30) cc_final: 0.6527 (m-30) REVERT: o 68 ASP cc_start: 0.8215 (m-30) cc_final: 0.7923 (m-30) REVERT: q 153 ASP cc_start: 0.7747 (m-30) cc_final: 0.7420 (m-30) REVERT: r 216 TYR cc_start: 0.8834 (t80) cc_final: 0.8566 (t80) REVERT: s 25 GLU cc_start: 0.8321 (pm20) cc_final: 0.8095 (pm20) REVERT: s 52 TYR cc_start: 0.8439 (m-80) cc_final: 0.8066 (m-80) REVERT: s 78 GLU cc_start: 0.8001 (pp20) cc_final: 0.7794 (pp20) REVERT: s 79 ILE cc_start: 0.9553 (mm) cc_final: 0.9317 (mm) REVERT: u 12 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8083 (p90) REVERT: u 16 GLU cc_start: 0.8342 (pm20) cc_final: 0.8039 (pm20) REVERT: u 121 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8282 (ttm) REVERT: a 543 MET cc_start: 0.9072 (ttm) cc_final: 0.8363 (tpp) REVERT: a 589 MET cc_start: 0.9076 (OUTLIER) cc_final: 0.8610 (mmm) REVERT: a 590 MET cc_start: 0.8927 (tmm) cc_final: 0.8432 (tmm) REVERT: a 682 ARG cc_start: 0.8613 (OUTLIER) cc_final: 0.8024 (ppt90) REVERT: a 699 MET cc_start: 0.7929 (pmm) cc_final: 0.7197 (pmm) REVERT: a 884 MET cc_start: 0.9410 (ptp) cc_final: 0.9101 (ptt) REVERT: e 67 MET cc_start: 0.8523 (tpp) cc_final: 0.8143 (mmm) REVERT: e 116 MET cc_start: 0.9350 (mtp) cc_final: 0.9067 (mtt) REVERT: e 137 LEU cc_start: 0.9586 (mt) cc_final: 0.9267 (tp) REVERT: e 1060 MET cc_start: 0.1532 (mmt) cc_final: 0.1201 (mpt) REVERT: e 1068 MET cc_start: 0.1096 (OUTLIER) cc_final: 0.0562 (pp-130) REVERT: e 1086 MET cc_start: 0.4973 (OUTLIER) cc_final: 0.4566 (ppp) REVERT: e 1093 LEU cc_start: 0.7826 (mt) cc_final: 0.7506 (tp) REVERT: e 1135 MET cc_start: 0.2993 (mmm) cc_final: 0.1632 (mmm) REVERT: e 1286 MET cc_start: 0.6552 (ptt) cc_final: 0.6219 (ptt) REVERT: e 1432 TYR cc_start: 0.2373 (OUTLIER) cc_final: 0.1298 (p90) REVERT: e 1483 MET cc_start: 0.8005 (tpt) cc_final: 0.7583 (pmt) REVERT: g 1 MET cc_start: 0.4230 (tpt) cc_final: 0.4029 (tpt) REVERT: g 4 ARG cc_start: 0.7924 (mmt90) cc_final: 0.7658 (mmt90) REVERT: g 6 GLN cc_start: 0.5565 (mt0) cc_final: 0.4724 (pp30) REVERT: g 67 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7741 (mtp-110) REVERT: g 68 ARG cc_start: 0.7829 (mpp80) cc_final: 0.7332 (mpp80) REVERT: g 96 ARG cc_start: 0.8824 (ttm110) cc_final: 0.7937 (mtp-110) REVERT: g 123 ARG cc_start: 0.8363 (mmp80) cc_final: 0.7936 (mmp80) REVERT: g 128 LEU cc_start: 0.9453 (OUTLIER) cc_final: 0.9111 (tm) REVERT: g 139 ARG cc_start: 0.8771 (ttm110) cc_final: 0.7930 (mtt-85) REVERT: g 197 MET cc_start: 0.8795 (ppp) cc_final: 0.8559 (ppp) REVERT: v 125 GLN cc_start: 0.9105 (tp40) cc_final: 0.8600 (tp-100) REVERT: w 45 ARG cc_start: 0.9197 (mmm-85) cc_final: 0.8808 (mtm-85) REVERT: w 72 PHE cc_start: 0.8594 (t80) cc_final: 0.6945 (t80) REVERT: w 76 ARG cc_start: 0.8736 (mtm180) cc_final: 0.8211 (mtm180) REVERT: w 140 HIS cc_start: 0.8693 (m-70) cc_final: 0.8301 (m90) REVERT: w 157 PHE cc_start: 0.8967 (m-10) cc_final: 0.8258 (m-10) REVERT: w 210 MET cc_start: 0.7699 (mmp) cc_final: 0.7125 (mmp) REVERT: 0 8 LYS cc_start: 0.8891 (mttp) cc_final: 0.8563 (tttt) REVERT: 0 14 LYS cc_start: 0.8861 (ttpp) cc_final: 0.8469 (tptp) REVERT: 0 22 TYR cc_start: 0.8521 (m-80) cc_final: 0.8041 (m-80) REVERT: 0 58 MET cc_start: 0.9004 (tpp) cc_final: 0.8400 (tpp) REVERT: 0 60 ARG cc_start: 0.9164 (mpt-90) cc_final: 0.8651 (mpt-90) REVERT: 0 191 TYR cc_start: 0.7984 (t80) cc_final: 0.7334 (t80) outliers start: 195 outliers final: 151 residues processed: 897 average time/residue: 2.0917 time to fit residues: 2756.5987 Evaluate side-chains 916 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 746 time to evaluate : 8.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 120 ASN Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 92 GLN Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 107 VAL Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain N residue 88 ASP Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 102 THR Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 31 ASN Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain V residue 94 ILE Chi-restraints excluded: chain X residue 6 THR Chi-restraints excluded: chain X residue 8 ILE Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 83 ILE Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 84 VAL Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 336 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain n residue 132 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain r residue 26 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 42 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 210 ILE Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 26 SER Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 127 PHE Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 158 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain u residue 121 MET Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 552 GLN Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 833 HIS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 1068 MET Chi-restraints excluded: chain e residue 1086 MET Chi-restraints excluded: chain e residue 1161 SER Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 88 ASN Chi-restraints excluded: chain v residue 150 PHE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain 0 residue 10 GLU Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 1142 optimal weight: 10.0000 chunk 752 optimal weight: 1.9990 chunk 1211 optimal weight: 9.9990 chunk 739 optimal weight: 0.9990 chunk 574 optimal weight: 10.0000 chunk 842 optimal weight: 3.9990 chunk 1271 optimal weight: 9.9990 chunk 1170 optimal weight: 40.0000 chunk 1012 optimal weight: 5.9990 chunk 105 optimal weight: 3.9990 chunk 781 optimal weight: 5.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN A ** F 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 134 GLN Q 57 GLN ** U 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 GLN ** r 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 113 GLN ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e1455 GLN ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 160078 Z= 0.257 Angle : 0.607 18.485 233663 Z= 0.318 Chirality : 0.038 0.321 29152 Planarity : 0.004 0.101 16403 Dihedral : 22.441 179.104 65636 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.27 % Favored : 95.72 % Rotamer: Outliers : 2.22 % Allowed : 19.71 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 9312 helix: 1.62 (0.08), residues: 3987 sheet: 0.09 (0.15), residues: 1152 loop : -0.74 (0.09), residues: 4173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP n 9 HIS 0.007 0.001 HIS w 12 PHE 0.053 0.001 PHE 0 88 TYR 0.041 0.001 TYR v 90 ARG 0.013 0.000 ARG l 288 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18624 Ramachandran restraints generated. 9312 Oldfield, 0 Emsley, 9312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 942 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 774 time to evaluate : 8.333 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8086 (ttt90) REVERT: B 151 ASP cc_start: 0.8741 (OUTLIER) cc_final: 0.8535 (m-30) REVERT: C 182 ILE cc_start: 0.8745 (OUTLIER) cc_final: 0.8476 (tp) REVERT: G 134 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8135 (mp-120) REVERT: H 37 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8809 (mm) REVERT: H 49 ASN cc_start: 0.8404 (t0) cc_final: 0.7972 (t0) REVERT: J 12 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8150 (mtpp) REVERT: N 120 ASN cc_start: 0.8590 (t0) cc_final: 0.8317 (t0) REVERT: R 19 ARG cc_start: 0.9260 (OUTLIER) cc_final: 0.7402 (ttp-170) REVERT: S 31 LYS cc_start: 0.9142 (OUTLIER) cc_final: 0.8385 (ttmm) REVERT: S 58 GLU cc_start: 0.7289 (tm-30) cc_final: 0.6982 (tm-30) REVERT: T 107 GLU cc_start: 0.8727 (pp20) cc_final: 0.8493 (pp20) REVERT: U 27 GLU cc_start: 0.7423 (tp30) cc_final: 0.7168 (tp30) REVERT: U 79 ASP cc_start: 0.8605 (OUTLIER) cc_final: 0.8375 (p0) REVERT: b 100 LYS cc_start: 0.7898 (mppt) cc_final: 0.6730 (tppt) REVERT: k 289 ASP cc_start: 0.7374 (p0) cc_final: 0.6872 (p0) REVERT: m 95 TRP cc_start: 0.9457 (OUTLIER) cc_final: 0.7702 (t60) REVERT: m 158 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.7710 (ptt-90) REVERT: n 13 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7437 (mt-10) REVERT: n 133 GLU cc_start: 0.7341 (tp30) cc_final: 0.6823 (tp30) REVERT: n 137 ASP cc_start: 0.7451 (m-30) cc_final: 0.6484 (m-30) REVERT: q 153 ASP cc_start: 0.7709 (m-30) cc_final: 0.7381 (m-30) REVERT: r 216 TYR cc_start: 0.8800 (t80) cc_final: 0.8532 (t80) REVERT: s 52 TYR cc_start: 0.8379 (m-80) cc_final: 0.8008 (m-80) REVERT: s 78 GLU cc_start: 0.7950 (pp20) cc_final: 0.7735 (pp20) REVERT: s 79 ILE cc_start: 0.9545 (mm) cc_final: 0.9274 (mm) REVERT: u 12 TRP cc_start: 0.8886 (OUTLIER) cc_final: 0.8041 (p90) REVERT: u 16 GLU cc_start: 0.8310 (pm20) cc_final: 0.8012 (pm20) REVERT: a 543 MET cc_start: 0.9055 (ttm) cc_final: 0.8355 (tpp) REVERT: a 589 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8586 (mmm) REVERT: a 590 MET cc_start: 0.8911 (tmm) cc_final: 0.8507 (tmm) REVERT: a 682 ARG cc_start: 0.8612 (OUTLIER) cc_final: 0.7846 (ppt90) REVERT: a 884 MET cc_start: 0.9409 (ptp) cc_final: 0.9132 (ptt) REVERT: e 67 MET cc_start: 0.8492 (tpp) cc_final: 0.8137 (mmm) REVERT: e 116 MET cc_start: 0.9315 (mtp) cc_final: 0.9050 (mtt) REVERT: e 137 LEU cc_start: 0.9576 (mt) cc_final: 0.9250 (tp) REVERT: e 1060 MET cc_start: 0.1441 (mmt) cc_final: 0.1134 (mpt) REVERT: e 1068 MET cc_start: 0.1171 (OUTLIER) cc_final: 0.0606 (pp-130) REVERT: e 1086 MET cc_start: 0.4955 (pp-130) cc_final: 0.4636 (ppp) REVERT: e 1093 LEU cc_start: 0.7853 (mt) cc_final: 0.7524 (tp) REVERT: e 1135 MET cc_start: 0.2934 (mmm) cc_final: 0.1647 (mmm) REVERT: e 1286 MET cc_start: 0.6527 (ptt) cc_final: 0.6203 (ptt) REVERT: e 1432 TYR cc_start: 0.2315 (OUTLIER) cc_final: 0.1273 (p90) REVERT: e 1483 MET cc_start: 0.7979 (tpt) cc_final: 0.7577 (pmt) REVERT: g 4 ARG cc_start: 0.7879 (mmt90) cc_final: 0.7600 (mmt90) REVERT: g 6 GLN cc_start: 0.5605 (mt0) cc_final: 0.4718 (pp30) REVERT: g 67 ARG cc_start: 0.8288 (ttm110) cc_final: 0.7728 (mtp-110) REVERT: g 68 ARG cc_start: 0.7859 (mpp80) cc_final: 0.7388 (mpp80) REVERT: g 96 ARG cc_start: 0.8768 (ttm110) cc_final: 0.8081 (mtp-110) REVERT: g 123 ARG cc_start: 0.8347 (mmp80) cc_final: 0.7898 (mmp80) REVERT: g 128 LEU cc_start: 0.9444 (OUTLIER) cc_final: 0.9105 (tm) REVERT: g 139 ARG cc_start: 0.8756 (ttm110) cc_final: 0.8190 (mtt-85) REVERT: g 140 GLN cc_start: 0.8497 (tp40) cc_final: 0.8227 (mp10) REVERT: g 197 MET cc_start: 0.8770 (ppp) cc_final: 0.8536 (ppp) REVERT: v 88 ASN cc_start: 0.7495 (t0) cc_final: 0.7163 (t0) REVERT: v 125 GLN cc_start: 0.9109 (tp40) cc_final: 0.8607 (tp40) REVERT: w 72 PHE cc_start: 0.8590 (t80) cc_final: 0.7389 (t80) REVERT: w 76 ARG cc_start: 0.8738 (mtm180) cc_final: 0.8233 (mtm180) REVERT: w 140 HIS cc_start: 0.8664 (m-70) cc_final: 0.8373 (m90) REVERT: w 157 PHE cc_start: 0.8948 (m-10) cc_final: 0.8213 (m-10) REVERT: w 210 MET cc_start: 0.7734 (mmp) cc_final: 0.7144 (mmp) REVERT: w 215 ARG cc_start: 0.8966 (mmt180) cc_final: 0.8748 (mmt180) REVERT: 0 8 LYS cc_start: 0.8899 (mttp) cc_final: 0.8480 (tttt) REVERT: 0 14 LYS cc_start: 0.8797 (ttpp) cc_final: 0.8398 (tptp) REVERT: 0 22 TYR cc_start: 0.8542 (m-80) cc_final: 0.8043 (m-80) REVERT: 0 38 MET cc_start: 0.9064 (mpp) cc_final: 0.8394 (mpm) REVERT: 0 58 MET cc_start: 0.8966 (tpp) cc_final: 0.8090 (tpp) REVERT: 0 60 ARG cc_start: 0.9201 (mpt-90) cc_final: 0.8925 (mpt-90) REVERT: 0 191 TYR cc_start: 0.7973 (t80) cc_final: 0.7335 (t80) outliers start: 168 outliers final: 145 residues processed: 897 average time/residue: 2.0992 time to fit residues: 2776.4364 Evaluate side-chains 925 residues out of total 8113 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 763 time to evaluate : 8.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 18 VAL Chi-restraints excluded: chain A residue 24 ARG Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 56 ASP Chi-restraints excluded: chain B residue 129 LEU Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 151 ASP Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain C residue 182 ILE Chi-restraints excluded: chain D residue 100 THR Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 93 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 45 LEU Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 70 THR Chi-restraints excluded: chain F residue 93 GLU Chi-restraints excluded: chain F residue 126 VAL Chi-restraints excluded: chain F residue 160 THR Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 32 LYS Chi-restraints excluded: chain G residue 39 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 134 GLN Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 25 ASN Chi-restraints excluded: chain H residue 37 LEU Chi-restraints excluded: chain H residue 39 ASP Chi-restraints excluded: chain H residue 50 LEU Chi-restraints excluded: chain H residue 54 VAL Chi-restraints excluded: chain I residue 22 ILE Chi-restraints excluded: chain I residue 73 VAL Chi-restraints excluded: chain I residue 88 ARG Chi-restraints excluded: chain I residue 115 THR Chi-restraints excluded: chain J residue 12 LYS Chi-restraints excluded: chain K residue 26 VAL Chi-restraints excluded: chain K residue 67 ILE Chi-restraints excluded: chain K residue 139 ILE Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 11 ASP Chi-restraints excluded: chain L residue 74 TYR Chi-restraints excluded: chain L residue 82 VAL Chi-restraints excluded: chain M residue 10 VAL Chi-restraints excluded: chain M residue 26 VAL Chi-restraints excluded: chain M residue 33 SER Chi-restraints excluded: chain M residue 75 VAL Chi-restraints excluded: chain M residue 86 THR Chi-restraints excluded: chain M residue 88 ASP Chi-restraints excluded: chain M residue 98 THR Chi-restraints excluded: chain M residue 102 GLU Chi-restraints excluded: chain M residue 108 GLU Chi-restraints excluded: chain N residue 121 VAL Chi-restraints excluded: chain P residue 90 VAL Chi-restraints excluded: chain P residue 103 THR Chi-restraints excluded: chain Q residue 9 THR Chi-restraints excluded: chain Q residue 42 LEU Chi-restraints excluded: chain Q residue 104 LEU Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 10 VAL Chi-restraints excluded: chain R residue 19 ARG Chi-restraints excluded: chain R residue 63 THR Chi-restraints excluded: chain R residue 67 SER Chi-restraints excluded: chain S residue 31 LYS Chi-restraints excluded: chain S residue 33 GLU Chi-restraints excluded: chain U residue 79 ASP Chi-restraints excluded: chain V residue 20 MET Chi-restraints excluded: chain V residue 93 ILE Chi-restraints excluded: chain X residue 13 GLU Chi-restraints excluded: chain X residue 55 VAL Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain Z residue 108 THR Chi-restraints excluded: chain b residue 64 THR Chi-restraints excluded: chain b residue 93 LEU Chi-restraints excluded: chain c residue 83 ILE Chi-restraints excluded: chain j residue 202 VAL Chi-restraints excluded: chain k residue 77 THR Chi-restraints excluded: chain k residue 90 VAL Chi-restraints excluded: chain k residue 103 THR Chi-restraints excluded: chain k residue 208 VAL Chi-restraints excluded: chain k residue 336 VAL Chi-restraints excluded: chain l residue 8 VAL Chi-restraints excluded: chain l residue 230 VAL Chi-restraints excluded: chain m residue 95 TRP Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 158 ARG Chi-restraints excluded: chain m residue 163 LEU Chi-restraints excluded: chain m residue 173 VAL Chi-restraints excluded: chain m residue 222 LEU Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain p residue 71 VAL Chi-restraints excluded: chain p residue 158 ASP Chi-restraints excluded: chain p residue 180 VAL Chi-restraints excluded: chain p residue 197 VAL Chi-restraints excluded: chain p residue 207 ASP Chi-restraints excluded: chain q residue 82 VAL Chi-restraints excluded: chain q residue 126 VAL Chi-restraints excluded: chain q residue 146 LEU Chi-restraints excluded: chain r residue 26 VAL Chi-restraints excluded: chain r residue 36 LEU Chi-restraints excluded: chain r residue 42 THR Chi-restraints excluded: chain r residue 53 VAL Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain s residue 11 ASP Chi-restraints excluded: chain s residue 44 THR Chi-restraints excluded: chain s residue 46 VAL Chi-restraints excluded: chain s residue 67 VAL Chi-restraints excluded: chain s residue 88 GLU Chi-restraints excluded: chain s residue 109 HIS Chi-restraints excluded: chain s residue 114 ILE Chi-restraints excluded: chain s residue 131 MET Chi-restraints excluded: chain s residue 158 ASP Chi-restraints excluded: chain t residue 58 VAL Chi-restraints excluded: chain t residue 138 VAL Chi-restraints excluded: chain t residue 162 ASN Chi-restraints excluded: chain u residue 5 SER Chi-restraints excluded: chain u residue 7 VAL Chi-restraints excluded: chain u residue 12 TRP Chi-restraints excluded: chain u residue 15 VAL Chi-restraints excluded: chain u residue 91 CYS Chi-restraints excluded: chain u residue 105 GLN Chi-restraints excluded: chain a residue 9 ASP Chi-restraints excluded: chain a residue 25 ARG Chi-restraints excluded: chain a residue 41 LEU Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain a residue 63 THR Chi-restraints excluded: chain a residue 112 LEU Chi-restraints excluded: chain a residue 121 ASN Chi-restraints excluded: chain a residue 145 VAL Chi-restraints excluded: chain a residue 316 ILE Chi-restraints excluded: chain a residue 552 GLN Chi-restraints excluded: chain a residue 589 MET Chi-restraints excluded: chain a residue 609 ASP Chi-restraints excluded: chain a residue 630 VAL Chi-restraints excluded: chain a residue 658 TRP Chi-restraints excluded: chain a residue 682 ARG Chi-restraints excluded: chain a residue 947 LEU Chi-restraints excluded: chain a residue 1004 ASP Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 401 VAL Chi-restraints excluded: chain e residue 833 HIS Chi-restraints excluded: chain e residue 893 MET Chi-restraints excluded: chain e residue 1068 MET Chi-restraints excluded: chain e residue 1325 LYS Chi-restraints excluded: chain e residue 1367 THR Chi-restraints excluded: chain e residue 1432 TYR Chi-restraints excluded: chain e residue 1439 LEU Chi-restraints excluded: chain e residue 1491 LEU Chi-restraints excluded: chain g residue 128 LEU Chi-restraints excluded: chain v residue 41 ILE Chi-restraints excluded: chain v residue 46 THR Chi-restraints excluded: chain v residue 54 HIS Chi-restraints excluded: chain v residue 66 THR Chi-restraints excluded: chain v residue 150 PHE Chi-restraints excluded: chain w residue 67 ILE Chi-restraints excluded: chain 0 residue 57 THR Chi-restraints excluded: chain 0 residue 186 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1276 random chunks: chunk 620 optimal weight: 10.0000 chunk 804 optimal weight: 7.9990 chunk 1078 optimal weight: 10.0000 chunk 310 optimal weight: 6.9990 chunk 933 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 281 optimal weight: 2.9990 chunk 1013 optimal weight: 8.9990 chunk 424 optimal weight: 50.0000 chunk 1041 optimal weight: 5.9990 chunk 128 optimal weight: 0.9980 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 193 GLN A ** C 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 106 GLN V 92 ASN ** X 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 9 GLN r 113 GLN ** s 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 160 GLN u 27 GLN ** e 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 705 ASN ** e1354 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.070729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.043227 restraints weight = 519008.680| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 1.99 r_work: 0.2533 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2442 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2436 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2436 r_free = 0.2436 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 21 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2435 r_free = 0.2435 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9097 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.399 160078 Z= 0.335 Angle : 0.673 61.852 233663 Z= 0.352 Chirality : 0.040 1.347 29152 Planarity : 0.006 0.243 16403 Dihedral : 22.439 179.067 65636 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.30 % Favored : 95.68 % Rotamer: Outliers : 2.35 % Allowed : 19.51 % Favored : 78.14 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 2.10 % Cis-general : 0.00 % Twisted Proline : 0.30 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.09), residues: 9312 helix: 1.62 (0.08), residues: 3987 sheet: 0.09 (0.15), residues: 1152 loop : -0.74 (0.09), residues: 4173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.161 0.003 TRP H 92 HIS 0.013 0.001 HIS w 12 PHE 0.043 0.001 PHE g 138 TYR 0.049 0.002 TYR v 90 ARG 0.011 0.000 ARG l 288 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49883.31 seconds wall clock time: 867 minutes 17.96 seconds (52037.96 seconds total)