Starting phenix.real_space_refine on Thu Feb 15 11:38:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6y79_10711/02_2024/6y79_10711_updated.pdb" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 Fe 28 7.16 5 Zn 1 6.06 5 P 38 5.49 5 S 306 5.16 5 C 42296 2.51 5 N 10612 2.21 5 O 11892 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 67": "NH1" <-> "NH2" Residue "A ARG 89": "NH1" <-> "NH2" Residue "A ARG 108": "NH1" <-> "NH2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ARG 153": "NH1" <-> "NH2" Residue "A ARG 155": "NH1" <-> "NH2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A ARG 427": "NH1" <-> "NH2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A ARG 528": "NH1" <-> "NH2" Residue "A ARG 610": "NH1" <-> "NH2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "B ARG 113": "NH1" <-> "NH2" Residue "B ARG 130": "NH1" <-> "NH2" Residue "B ARG 134": "NH1" <-> "NH2" Residue "B ARG 149": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 201": "NH1" <-> "NH2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B ARG 226": "NH1" <-> "NH2" Residue "B ARG 240": "NH1" <-> "NH2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "B ARG 258": "NH1" <-> "NH2" Residue "B ARG 259": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B ARG 271": "NH1" <-> "NH2" Residue "B GLU 292": "OE1" <-> "OE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B GLU 303": "OE1" <-> "OE2" Residue "B ARG 367": "NH1" <-> "NH2" Residue "B ARG 388": "NH1" <-> "NH2" Residue "B ARG 402": "NH1" <-> "NH2" Residue "B ARG 409": "NH1" <-> "NH2" Residue "B GLU 422": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 449": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 121": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C GLU 218": "OE1" <-> "OE2" Residue "C ARG 219": "NH1" <-> "NH2" Residue "C ARG 224": "NH1" <-> "NH2" Residue "C ARG 231": "NH1" <-> "NH2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 274": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 466": "NH1" <-> "NH2" Residue "D ARG 32": "NH1" <-> "NH2" Residue "D ARG 37": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "E ARG 48": "NH1" <-> "NH2" Residue "E ARG 51": "NH1" <-> "NH2" Residue "E ARG 85": "NH1" <-> "NH2" Residue "E ARG 91": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 120": "NH1" <-> "NH2" Residue "E ARG 131": "NH1" <-> "NH2" Residue "E GLU 134": "OE1" <-> "OE2" Residue "E PHE 138": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E ARG 150": "NH1" <-> "NH2" Residue "E GLU 178": "OE1" <-> "OE2" Residue "E ARG 201": "NH1" <-> "NH2" Residue "E ARG 208": "NH1" <-> "NH2" Residue "E ARG 216": "NH1" <-> "NH2" Residue "E GLU 367": "OE1" <-> "OE2" Residue "F GLU 72": "OE1" <-> "OE2" Residue "G ARG 43": "NH1" <-> "NH2" Residue "G GLU 52": "OE1" <-> "OE2" Residue "G PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G ARG 223": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G ARG 259": "NH1" <-> "NH2" Residue "G ARG 262": "NH1" <-> "NH2" Residue "H GLU 46": "OE1" <-> "OE2" Residue "H GLU 50": "OE1" <-> "OE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 116": "NH1" <-> "NH2" Residue "H GLU 165": "OE1" <-> "OE2" Residue "H GLU 198": "OE1" <-> "OE2" Residue "H ARG 216": "NH1" <-> "NH2" Residue "H GLU 231": "OE1" <-> "OE2" Residue "I ARG 59": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "J ARG 55": "NH1" <-> "NH2" Residue "J ARG 91": "NH1" <-> "NH2" Residue "J ARG 143": "NH1" <-> "NH2" Residue "J GLU 157": "OE1" <-> "OE2" Residue "J ARG 183": "NH1" <-> "NH2" Residue "K ARG 196": "NH1" <-> "NH2" Residue "K ARG 199": "NH1" <-> "NH2" Residue "L ARG 20": "NH1" <-> "NH2" Residue "L ARG 79": "NH1" <-> "NH2" Residue "M ARG 42": "NH1" <-> "NH2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M ARG 88": "NH1" <-> "NH2" Residue "M ARG 131": "NH1" <-> "NH2" Residue "O ARG 29": "NH1" <-> "NH2" Residue "O GLU 33": "OE1" <-> "OE2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P ARG 30": "NH1" <-> "NH2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P GLU 103": "OE1" <-> "OE2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q GLU 114": "OE1" <-> "OE2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 57": "NH1" <-> "NH2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "S ARG 49": "NH1" <-> "NH2" Residue "S ARG 62": "NH1" <-> "NH2" Residue "S GLU 90": "OE1" <-> "OE2" Residue "S GLU 93": "OE1" <-> "OE2" Residue "S ARG 120": "NH1" <-> "NH2" Residue "S ARG 135": "NH1" <-> "NH2" Residue "S ARG 188": "NH1" <-> "NH2" Residue "U GLU 58": "OE1" <-> "OE2" Residue "U GLU 59": "OE1" <-> "OE2" Residue "U ARG 74": "NH1" <-> "NH2" Residue "U GLU 84": "OE1" <-> "OE2" Residue "U ARG 95": "NH1" <-> "NH2" Residue "U ARG 112": "NH1" <-> "NH2" Residue "U GLU 115": "OE1" <-> "OE2" Residue "U ARG 161": "NH1" <-> "NH2" Residue "U GLU 165": "OE1" <-> "OE2" Residue "W ARG 20": "NH1" <-> "NH2" Residue "W ARG 21": "NH1" <-> "NH2" Residue "W ARG 26": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 60": "NH1" <-> "NH2" Residue "W ARG 66": "NH1" <-> "NH2" Residue "W GLU 77": "OE1" <-> "OE2" Residue "W ARG 83": "NH1" <-> "NH2" Residue "W ARG 84": "NH1" <-> "NH2" Residue "W ARG 91": "NH1" <-> "NH2" Residue "W GLU 92": "OE1" <-> "OE2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "X ARG 76": "NH1" <-> "NH2" Residue "X GLU 112": "OE1" <-> "OE2" Residue "X ARG 118": "NH1" <-> "NH2" Residue "X GLU 124": "OE1" <-> "OE2" Residue "X ARG 166": "NH1" <-> "NH2" Residue "Y ARG 79": "NH1" <-> "NH2" Residue "Y ARG 140": "NH1" <-> "NH2" Residue "Y ARG 159": "NH1" <-> "NH2" Residue "Z PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 77": "NH1" <-> "NH2" Residue "Z ARG 80": "NH1" <-> "NH2" Residue "Z ARG 179": "NH1" <-> "NH2" Residue "a PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a GLU 34": "OE1" <-> "OE2" Residue "a ARG 84": "NH1" <-> "NH2" Residue "a GLU 117": "OE1" <-> "OE2" Residue "a ARG 123": "NH1" <-> "NH2" Residue "a GLU 124": "OE1" <-> "OE2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 16": "NH1" <-> "NH2" Residue "c ARG 23": "NH1" <-> "NH2" Residue "c ARG 26": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d ARG 32": "NH1" <-> "NH2" Residue "d ARG 37": "NH1" <-> "NH2" Residue "d GLU 39": "OE1" <-> "OE2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d GLU 61": "OE1" <-> "OE2" Residue "e ARG 41": "NH1" <-> "NH2" Residue "e GLU 44": "OE1" <-> "OE2" Residue "f ARG 6": "NH1" <-> "NH2" Residue "f ARG 9": "NH1" <-> "NH2" Residue "f ARG 23": "NH1" <-> "NH2" Residue "f ARG 45": "NH1" <-> "NH2" Residue "f ARG 57": "NH1" <-> "NH2" Residue "f ARG 79": "NH1" <-> "NH2" Residue "g ARG 17": "NH1" <-> "NH2" Residue "g ARG 47": "NH1" <-> "NH2" Residue "g ARG 69": "NH1" <-> "NH2" Residue "h ARG 18": "NH1" <-> "NH2" Residue "h ARG 57": "NH1" <-> "NH2" Residue "h ARG 137": "NH1" <-> "NH2" Residue "i TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 55": "NH1" <-> "NH2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "j ARG 34": "NH1" <-> "NH2" Residue "j ARG 39": "NH1" <-> "NH2" Residue "j ARG 50": "NH1" <-> "NH2" Residue "j GLU 75": "OE1" <-> "OE2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 60": "OE1" <-> "OE2" Residue "1 GLU 7": "OE1" <-> "OE2" Residue "1 GLU 61": "OE1" <-> "OE2" Residue "1 GLU 67": "OE1" <-> "OE2" Residue "2 ARG 22": "NH1" <-> "NH2" Residue "2 PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 98": "OE1" <-> "OE2" Residue "2 TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 161": "OE1" <-> "OE2" Residue "4 ARG 162": "NH1" <-> "NH2" Residue "4 GLU 237": "OE1" <-> "OE2" Residue "4 ARG 353": "NH1" <-> "NH2" Residue "4 ARG 405": "NH1" <-> "NH2" Residue "4 ARG 449": "NH1" <-> "NH2" Residue "5 ARG 115": "NH1" <-> "NH2" Residue "5 ARG 175": "NH1" <-> "NH2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 611": "NH1" <-> "NH2" Residue "6 PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 GLU 84": "OE1" <-> "OE2" Residue "6 ARG 92": "NH1" <-> "NH2" Residue "8 ARG 37": "NH1" <-> "NH2" Residue "8 ARG 51": "NH1" <-> "NH2" Residue "8 ARG 65": "NH1" <-> "NH2" Residue "9 ARG 14": "NH1" <-> "NH2" Residue "9 ARG 58": "NH1" <-> "NH2" Residue "9 GLU 59": "OE1" <-> "OE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 65173 Number of models: 1 Model: "" Number of chains: 65 Chain: "A" Number of atoms: 5258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 692, 5258 Classifications: {'peptide': 692} Link IDs: {'PTRANS': 34, 'TRANS': 657} Chain: "B" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3528 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 22, 'TRANS': 433} Chain: "C" Number of atoms: 3426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3426 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 409} Chain breaks: 1 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: "D" Number of atoms: 681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 681 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "E" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2527 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain breaks: 3 Chain: "F" Number of atoms: 990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 990 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "G" Number of atoms: 1978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1978 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 18, 'TRANS': 220} Chain: "H" Number of atoms: 1688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1688 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 18, 'TRANS': 197} Chain: "I" Number of atoms: 1519 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1519 Classifications: {'peptide': 190} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 177} Chain: "J" Number of atoms: 1329 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1329 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain: "K" Number of atoms: 1377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1377 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 14, 'TRANS': 160} Chain: "L" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Chain: "M" Number of atoms: 912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 912 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 9, 'TRANS': 107} Chain: "O" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 591 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "P" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1030 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Q" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 648 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 2, 'TRANS': 82} Chain: "R" Number of atoms: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 884 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 10, 'TRANS': 95} Chain: "S" Number of atoms: 1430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1430 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain breaks: 2 Chain: "U" Number of atoms: 1345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1345 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 10, 'TRANS': 160} Chain: "W" Number of atoms: 974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 974 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 9, 'TRANS': 111} Chain: "X" Number of atoms: 1296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1296 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain: "Y" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1021 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "Z" Number of atoms: 1389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 1389 Classifications: {'peptide': 181} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 160} Chain: "a" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 1030 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 10, 'TRANS': 113} Chain: "b" Number of atoms: 490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 490 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "c" Number of atoms: 353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 353 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain: "d" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 760 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "e" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 436 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 6, 'TRANS': 45} Chain: "f" Number of atoms: 629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 629 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "g" Number of atoms: 617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 617 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 10, 'TRANS': 65} Chain: "h" Number of atoms: 1130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1130 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 10, 'TRANS': 125} Chain: "i" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 4, 'TRANS': 78} Chain: "j" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 724 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 4, 'TRANS': 85} Chain: "n" Number of atoms: 914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 914 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 9, 'TRANS': 104} Chain: "1" Number of atoms: 2627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2627 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 14, 'TRANS': 314} Chain breaks: 1 Chain: "2" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 469, 3774 Classifications: {'peptide': 469} Link IDs: {'PTRANS': 7, 'TRANS': 461} Chain: "3" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 933 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain breaks: 1 Chain: "4" Number of atoms: 3847 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3847 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 14, 'TRANS': 470} Chain: "5" Number of atoms: 5197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 654, 5197 Classifications: {'peptide': 654} Link IDs: {'PTRANS': 15, 'TRANS': 638} Chain: "6" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1415 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "8" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 643 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 4, 'TRANS': 72} Chain: "9" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 4, 'TRANS': 81} Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 20 Unusual residues: {'FES': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 39 Unusual residues: {'FMN': 1, 'SF4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'NDP': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 67 Unusual residues: {'3PE': 1, 'SF4': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 219 Unusual residues: {'3PE': 2, 'LMN': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 21 Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "Q" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'ZMP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "W" Number of atoms: 83 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 83 Unusual residues: {'PLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 86 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "Z" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 76 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 24 Chain: "a" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "i" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "j" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 69 Unusual residues: {'LMN': 1} Classifications: {'undetermined': 1} Chain: "1" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 112 Unusual residues: {'PLC': 2, 'UQ9': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'UQ9:plan-8': 1, 'UQ9:plan-9': 1, 'UQ9:plan-10': 1, 'UQ9:plan-7': 1, 'UQ9:plan-2': 1} Unresolved non-hydrogen planarities: 23 Chain: "2" Number of atoms: 235 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 235 Unusual residues: {'CDL': 1, 'PSC': 1, 'T7X': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 39 Chain: "3" Number of atoms: 92 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 92 Unusual residues: {'3PE': 1, 'T7X': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'T7X:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "4" Number of atoms: 271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 271 Unusual residues: {'3PE': 3, 'CDL': 1, 'T7X': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 43 Planarities with less than four sites: {'T7X:plan-5': 1, 'T7X:plan-4': 1, 'T7X:plan-6': 1} Unresolved non-hydrogen planarities: 9 Chain: "5" Number of atoms: 151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 151 Unusual residues: {'CDL': 1, 'PLC': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 33 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 809 SG CYS A 142 63.577 141.133 156.690 1.00 9.73 S ATOM 749 SG CYS A 133 60.983 143.766 151.243 1.00 21.16 S ATOM 769 SG CYS A 136 65.317 146.702 155.608 1.00 16.96 S ATOM 1163 SG CYS A 186 62.219 142.195 167.738 1.00 10.04 S ATOM 1139 SG CYS A 183 59.500 147.235 165.971 1.00 13.25 S ATOM 1187 SG CYS A 189 64.198 147.127 170.843 1.00 9.38 S ATOM 1511 SG CYS A 233 64.874 145.291 164.396 1.00 25.48 S ATOM 255 SG CYS A 69 59.086 136.486 170.568 1.00 7.43 S ATOM 338 SG CYS A 80 57.980 135.122 167.312 1.00 6.34 S ATOM 363 SG CYS A 83 57.921 129.726 169.420 1.00 8.91 S ATOM 465 SG CYS A 97 58.998 131.455 172.576 1.00 8.64 S ATOM 7999 SG CYS B 384 48.852 138.157 171.150 1.00 23.43 S ATOM 8019 SG CYS B 387 44.347 140.624 170.540 1.00 26.15 S ATOM 7980 SG CYS B 381 48.512 143.113 175.592 1.00 31.34 S ATOM 8350 SG CYS B 427 45.029 138.323 176.090 1.00 33.94 S ATOM 19205 SG CYS H 127 29.787 152.987 177.004 1.00 59.45 S ATOM 19239 SG CYS H 132 26.175 153.425 177.119 1.00 61.22 S ATOM 19508 SG CYS H 168 30.507 148.675 179.677 1.00 61.58 S ATOM 19531 SG CYS H 172 27.619 147.746 180.235 1.00 67.11 S ATOM 21133 SG CYS I 172 69.536 139.912 130.578 1.00 14.37 S ATOM 21107 SG CYS I 169 73.646 144.496 128.056 1.00 25.48 S ATOM 21155 SG CYS I 175 68.829 145.912 132.279 1.00 16.71 S ATOM 20880 SG CYS I 140 74.257 142.037 133.657 1.00 22.33 S ATOM 21185 SG CYS I 179 64.392 149.856 138.713 1.00 18.08 S ATOM 20852 SG CYS I 136 70.752 147.609 138.351 1.00 25.48 S ATOM 20810 SG CYS I 130 69.655 153.357 140.216 1.00 11.49 S ATOM 20829 SG CYS I 133 66.767 148.049 143.266 1.00 15.53 S ATOM 23813 SG CYS K 150 79.386 136.615 122.562 1.00 8.32 S ATOM 23309 SG CYS K 86 76.957 138.526 116.772 1.00 11.54 S ATOM 23303 SG CYS K 85 75.393 133.038 118.768 1.00 12.38 S ATOM 24041 SG CYS K 180 74.909 138.251 122.754 1.00 11.96 S ATOM 25621 SG CYS M 97 54.559 159.058 147.033 1.00 24.81 S ATOM 25816 SG CYS M 125 58.152 158.355 148.450 1.00 22.59 S ATOM 25843 SG CYS M 128 57.888 160.445 146.023 1.00 23.32 S Time building chain proxies: 25.63, per 1000 atoms: 0.39 Number of scatterers: 65173 At special positions: 0 Unit cell: (224.316, 187.488, 225.153, 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 1 29.99 Fe 28 26.01 S 306 16.00 P 38 15.00 O 11892 8.00 N 10612 7.00 C 42296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS U 46 " - pdb=" SG CYS U 78 " distance=2.04 Simple disulfide: pdb=" SG CYS U 56 " - pdb=" SG CYS U 68 " distance=2.04 Simple disulfide: pdb=" SG CYS U 90 " - pdb=" SG CYS U 121 " distance=2.03 Simple disulfide: pdb=" SG CYS U 100 " - pdb=" SG CYS U 111 " distance=2.05 Simple disulfide: pdb=" SG CYS d 51 " - pdb=" SG CYS d 63 " distance=2.04 Simple disulfide: pdb=" SG CYS 8 26 " - pdb=" SG CYS 8 57 " distance=2.05 Simple disulfide: pdb=" SG CYS 8 36 " - pdb=" SG CYS 8 47 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 15 " - pdb=" SG CYS 9 47 " distance=2.04 Simple disulfide: pdb=" SG CYS 9 25 " - pdb=" SG CYS 9 37 " distance=2.05 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 20.92 Conformation dependent library (CDL) restraints added in 8.6 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES A 803 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 80 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 83 " pdb="FE1 FES A 803 " - pdb=" SG CYS A 69 " pdb="FE2 FES A 803 " - pdb=" SG CYS A 97 " pdb=" FES H 301 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 127 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 172 " pdb="FE1 FES H 301 " - pdb=" SG CYS H 132 " pdb="FE2 FES H 301 " - pdb=" SG CYS H 168 " pdb=" SF4 A 801 " pdb="FE3 SF4 A 801 " - pdb=" NE2 HIS A 129 " pdb="FE4 SF4 A 801 " - pdb=" SG CYS A 136 " pdb="FE2 SF4 A 801 " - pdb=" SG CYS A 133 " pdb="FE1 SF4 A 801 " - pdb=" SG CYS A 142 " pdb=" SF4 A 802 " pdb="FE4 SF4 A 802 " - pdb=" SG CYS A 233 " pdb="FE1 SF4 A 802 " - pdb=" SG CYS A 186 " pdb="FE2 SF4 A 802 " - pdb=" SG CYS A 183 " pdb="FE3 SF4 A 802 " - pdb=" SG CYS A 189 " pdb=" SF4 B 501 " pdb="FE4 SF4 B 501 " - pdb=" SG CYS B 427 " pdb="FE3 SF4 B 501 " - pdb=" SG CYS B 381 " pdb="FE2 SF4 B 501 " - pdb=" SG CYS B 387 " pdb="FE1 SF4 B 501 " - pdb=" SG CYS B 384 " pdb=" SF4 I 502 " pdb="FE1 SF4 I 502 " - pdb=" SG CYS I 172 " pdb="FE3 SF4 I 502 " - pdb=" SG CYS I 175 " pdb="FE4 SF4 I 502 " - pdb=" SG CYS I 140 " pdb="FE2 SF4 I 502 " - pdb=" SG CYS I 169 " pdb=" SF4 I 503 " pdb="FE1 SF4 I 503 " - pdb=" SG CYS I 179 " pdb="FE3 SF4 I 503 " - pdb=" SG CYS I 130 " pdb="FE2 SF4 I 503 " - pdb=" SG CYS I 136 " pdb="FE4 SF4 I 503 " - pdb=" SG CYS I 133 " pdb=" SF4 K 301 " pdb="FE1 SF4 K 301 " - pdb=" SG CYS K 150 " pdb="FE3 SF4 K 301 " - pdb=" SG CYS K 85 " pdb="FE4 SF4 K 301 " - pdb=" SG CYS K 180 " pdb="FE2 SF4 K 301 " - pdb=" SG CYS K 86 " Number of angles added : 81 Zn2+ tetrahedral coordination pdb=" ZN M 201 " pdb="ZN ZN M 201 " - pdb=" NE2 HIS M 110 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 128 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 97 " pdb="ZN ZN M 201 " - pdb=" SG CYS M 125 " Number of angles added : 3 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14928 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 306 helices and 31 sheets defined 48.9% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.47 Creating SS restraints... Processing helix chain 'A' and resid 54 through 60 Processing helix chain 'A' and resid 112 through 127 Processing helix chain 'A' and resid 143 through 151 removed outlier: 3.554A pdb=" N MET A 149 " --> pdb=" O GLN A 145 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG A 150 " --> pdb=" O ASP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 188 through 195 Processing helix chain 'A' and resid 208 through 210 No H-bonds generated for 'chain 'A' and resid 208 through 210' Processing helix chain 'A' and resid 295 through 301 removed outlier: 3.632A pdb=" N ALA A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 339 Processing helix chain 'A' and resid 356 through 367 Processing helix chain 'A' and resid 392 through 394 No H-bonds generated for 'chain 'A' and resid 392 through 394' Processing helix chain 'A' and resid 404 through 406 No H-bonds generated for 'chain 'A' and resid 404 through 406' Processing helix chain 'A' and resid 422 through 434 Processing helix chain 'A' and resid 459 through 468 Processing helix chain 'A' and resid 470 through 476 Processing helix chain 'A' and resid 494 through 507 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 578 through 581 No H-bonds generated for 'chain 'A' and resid 578 through 581' Processing helix chain 'A' and resid 622 through 632 removed outlier: 3.604A pdb=" N LEU A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLU A 631 " --> pdb=" O ARG A 627 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N TYR A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 652 Processing helix chain 'A' and resid 668 through 678 removed outlier: 3.659A pdb=" N VAL A 672 " --> pdb=" O GLY A 668 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN A 673 " --> pdb=" O ASP A 669 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLY A 678 " --> pdb=" O HIS A 674 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 716 removed outlier: 3.971A pdb=" N ILE A 715 " --> pdb=" O ALA A 711 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 716 " --> pdb=" O LYS A 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 58 Processing helix chain 'B' and resid 64 through 69 Processing helix chain 'B' and resid 72 through 82 Processing helix chain 'B' and resid 94 through 99 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 138 through 150 Processing helix chain 'B' and resid 165 through 180 Processing helix chain 'B' and resid 207 through 209 No H-bonds generated for 'chain 'B' and resid 207 through 209' Processing helix chain 'B' and resid 211 through 219 Processing helix chain 'B' and resid 237 through 239 No H-bonds generated for 'chain 'B' and resid 237 through 239' Processing helix chain 'B' and resid 247 through 251 Processing helix chain 'B' and resid 253 through 259 Processing helix chain 'B' and resid 261 through 265 Processing helix chain 'B' and resid 299 through 302 No H-bonds generated for 'chain 'B' and resid 299 through 302' Processing helix chain 'B' and resid 313 through 315 No H-bonds generated for 'chain 'B' and resid 313 through 315' Processing helix chain 'B' and resid 342 through 345 No H-bonds generated for 'chain 'B' and resid 342 through 345' Processing helix chain 'B' and resid 365 through 379 Processing helix chain 'B' and resid 385 through 403 removed outlier: 3.991A pdb=" N THR B 392 " --> pdb=" O ARG B 388 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TRP B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG B 400 " --> pdb=" O LYS B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 408 through 421 removed outlier: 4.453A pdb=" N ASP B 412 " --> pdb=" O GLU B 408 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE B 421 " --> pdb=" O LEU B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 443 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 445 through 458 removed outlier: 3.741A pdb=" N ARG B 451 " --> pdb=" O GLU B 447 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 123 through 129 removed outlier: 4.154A pdb=" N GLU C 128 " --> pdb=" O GLU C 124 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N TYR C 129 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 141 Proline residue: C 137 - end of helix removed outlier: 4.087A pdb=" N ASP C 140 " --> pdb=" O LEU C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 162 removed outlier: 3.632A pdb=" N PHE C 154 " --> pdb=" O ASN C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 197 removed outlier: 3.518A pdb=" N THR C 181 " --> pdb=" O PHE C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 220 removed outlier: 4.045A pdb=" N PHE C 216 " --> pdb=" O LYS C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 263 removed outlier: 3.750A pdb=" N TYR C 248 " --> pdb=" O LEU C 244 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLN C 253 " --> pdb=" O MET C 249 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ASP C 256 " --> pdb=" O THR C 252 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASP C 259 " --> pdb=" O GLY C 255 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ILE C 261 " --> pdb=" O ARG C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 274 Processing helix chain 'C' and resid 283 through 288 removed outlier: 3.833A pdb=" N LEU C 287 " --> pdb=" O ALA C 283 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ASN C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 283 through 288' Processing helix chain 'C' and resid 305 through 308 No H-bonds generated for 'chain 'C' and resid 305 through 308' Processing helix chain 'C' and resid 329 through 352 removed outlier: 3.729A pdb=" N ARG C 336 " --> pdb=" O ARG C 332 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ARG C 341 " --> pdb=" O MET C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 374 No H-bonds generated for 'chain 'C' and resid 371 through 374' Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.740A pdb=" N TYR C 388 " --> pdb=" O HIS C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 436 Processing helix chain 'C' and resid 438 through 441 No H-bonds generated for 'chain 'C' and resid 438 through 441' Processing helix chain 'C' and resid 448 through 450 No H-bonds generated for 'chain 'C' and resid 448 through 450' Processing helix chain 'C' and resid 454 through 457 No H-bonds generated for 'chain 'C' and resid 454 through 457' Processing helix chain 'D' and resid 5 through 33 Proline residue: D 10 - end of helix Processing helix chain 'D' and resid 44 through 57 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'E' and resid 64 through 73 removed outlier: 4.195A pdb=" N TYR E 68 " --> pdb=" O PHE E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 93 Processing helix chain 'E' and resid 112 through 118 Processing helix chain 'E' and resid 140 through 144 Processing helix chain 'E' and resid 146 through 158 Processing helix chain 'E' and resid 178 through 193 Processing helix chain 'E' and resid 214 through 217 No H-bonds generated for 'chain 'E' and resid 214 through 217' Processing helix chain 'E' and resid 238 through 250 removed outlier: 3.681A pdb=" N PHE E 250 " --> pdb=" O GLU E 246 " (cutoff:3.500A) Processing helix chain 'E' and resid 252 through 254 No H-bonds generated for 'chain 'E' and resid 252 through 254' Processing helix chain 'E' and resid 269 through 279 Processing helix chain 'E' and resid 291 through 302 Processing helix chain 'E' and resid 311 through 318 removed outlier: 3.951A pdb=" N GLU E 315 " --> pdb=" O PRO E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 369 removed outlier: 4.047A pdb=" N THR E 369 " --> pdb=" O ASN E 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 60 Processing helix chain 'F' and resid 66 through 84 Processing helix chain 'F' and resid 88 through 95 removed outlier: 3.968A pdb=" N ASN F 93 " --> pdb=" O GLU F 89 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 120 removed outlier: 3.849A pdb=" N SER F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU F 119 " --> pdb=" O LYS F 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 81 removed outlier: 3.710A pdb=" N ARG G 63 " --> pdb=" O PRO G 60 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU G 65 " --> pdb=" O ASP G 62 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N GLN G 66 " --> pdb=" O ARG G 63 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N MET G 79 " --> pdb=" O LYS G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 114 removed outlier: 5.126A pdb=" N ILE G 106 " --> pdb=" O SER G 103 " (cutoff:3.500A) Proline residue: G 107 - end of helix removed outlier: 4.179A pdb=" N THR G 110 " --> pdb=" O PRO G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 186 removed outlier: 3.522A pdb=" N TYR G 186 " --> pdb=" O ALA G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 264 through 266 No H-bonds generated for 'chain 'G' and resid 264 through 266' Processing helix chain 'H' and resid 49 through 61 removed outlier: 3.676A pdb=" N ALA H 60 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS H 61 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 68 through 81 removed outlier: 4.422A pdb=" N MET H 72 " --> pdb=" O ALA H 69 " (cutoff:3.500A) Proline residue: H 73 - end of helix Processing helix chain 'H' and resid 87 through 96 Processing helix chain 'H' and resid 101 through 110 removed outlier: 3.520A pdb=" N VAL H 107 " --> pdb=" O ARG H 103 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 133 No H-bonds generated for 'chain 'H' and resid 130 through 133' Processing helix chain 'H' and resid 137 through 147 removed outlier: 3.795A pdb=" N THR H 147 " --> pdb=" O ALA H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 190 through 202 removed outlier: 4.023A pdb=" N VAL H 194 " --> pdb=" O PRO H 190 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS H 195 " --> pdb=" O GLU H 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 70 through 78 Processing helix chain 'I' and resid 81 through 95 removed outlier: 3.757A pdb=" N VAL I 90 " --> pdb=" O GLY I 86 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N PHE I 95 " --> pdb=" O LEU I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 135 through 139 Processing helix chain 'I' and resid 174 through 178 Processing helix chain 'I' and resid 198 through 200 No H-bonds generated for 'chain 'I' and resid 198 through 200' Processing helix chain 'I' and resid 204 through 213 Processing helix chain 'I' and resid 215 through 225 removed outlier: 3.677A pdb=" N TYR I 220 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA I 224 " --> pdb=" O TYR I 220 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 49 Processing helix chain 'J' and resid 67 through 89 Processing helix chain 'J' and resid 94 through 110 Processing helix chain 'J' and resid 115 through 134 Processing helix chain 'J' and resid 172 through 178 Processing helix chain 'J' and resid 190 through 193 No H-bonds generated for 'chain 'J' and resid 190 through 193' Processing helix chain 'K' and resid 56 through 74 Processing helix chain 'K' and resid 85 through 91 Processing helix chain 'K' and resid 101 through 103 No H-bonds generated for 'chain 'K' and resid 101 through 103' Processing helix chain 'K' and resid 128 through 137 removed outlier: 3.650A pdb=" N GLN K 137 " --> pdb=" O GLN K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 155 through 157 No H-bonds generated for 'chain 'K' and resid 155 through 157' Processing helix chain 'K' and resid 184 through 199 Processing helix chain 'K' and resid 206 through 208 No H-bonds generated for 'chain 'K' and resid 206 through 208' Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'L' and resid 23 through 47 Processing helix chain 'L' and resid 51 through 80 removed outlier: 3.693A pdb=" N ILE L 61 " --> pdb=" O ILE L 57 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU L 80 " --> pdb=" O SER L 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 35 No H-bonds generated for 'chain 'M' and resid 33 through 35' Processing helix chain 'M' and resid 53 through 59 Processing helix chain 'M' and resid 78 through 81 No H-bonds generated for 'chain 'M' and resid 78 through 81' Processing helix chain 'O' and resid 30 through 40 Processing helix chain 'O' and resid 66 through 78 removed outlier: 4.353A pdb=" N VAL O 70 " --> pdb=" O SER O 66 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL O 74 " --> pdb=" O VAL O 70 " (cutoff:3.500A) Processing helix chain 'O' and resid 95 through 101 Processing helix chain 'P' and resid 18 through 34 Processing helix chain 'P' and resid 36 through 42 Processing helix chain 'P' and resid 49 through 63 removed outlier: 4.472A pdb=" N HIS P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) Processing helix chain 'P' and resid 69 through 87 Processing helix chain 'P' and resid 93 through 96 No H-bonds generated for 'chain 'P' and resid 93 through 96' Processing helix chain 'P' and resid 115 through 119 Processing helix chain 'Q' and resid 52 through 65 removed outlier: 3.637A pdb=" N ALA Q 61 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 109 through 112 No H-bonds generated for 'chain 'Q' and resid 109 through 112' Processing helix chain 'Q' and resid 118 through 126 Processing helix chain 'R' and resid 10 through 29 removed outlier: 3.777A pdb=" N ASN R 28 " --> pdb=" O LYS R 24 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TRP R 29 " --> pdb=" O LEU R 25 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 49 Processing helix chain 'R' and resid 57 through 72 Processing helix chain 'S' and resid 53 through 64 Processing helix chain 'S' and resid 91 through 99 Processing helix chain 'S' and resid 105 through 110 removed outlier: 3.547A pdb=" N LEU S 109 " --> pdb=" O ILE S 105 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU S 110 " --> pdb=" O LEU S 106 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 105 through 110' Processing helix chain 'S' and resid 114 through 136 removed outlier: 3.614A pdb=" N GLY S 133 " --> pdb=" O TYR S 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 165 through 168 No H-bonds generated for 'chain 'S' and resid 165 through 168' Processing helix chain 'S' and resid 172 through 186 Processing helix chain 'S' and resid 191 through 206 Processing helix chain 'S' and resid 208 through 212 Processing helix chain 'S' and resid 215 through 228 removed outlier: 3.793A pdb=" N ASP S 219 " --> pdb=" O GLU S 215 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA S 220 " --> pdb=" O ASN S 216 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 237 No H-bonds generated for 'chain 'S' and resid 234 through 237' Processing helix chain 'U' and resid 32 through 37 Processing helix chain 'U' and resid 39 through 45 Processing helix chain 'U' and resid 47 through 59 Processing helix chain 'U' and resid 66 through 102 removed outlier: 3.660A pdb=" N LEU U 69 " --> pdb=" O ILE U 66 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N LYS U 70 " --> pdb=" O ASP U 67 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLU U 71 " --> pdb=" O CYS U 68 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG U 73 " --> pdb=" O LYS U 70 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N VAL U 75 " --> pdb=" O GLY U 72 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N CYS U 78 " --> pdb=" O VAL U 75 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLU U 84 " --> pdb=" O SER U 81 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS U 88 " --> pdb=" O ASP U 85 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N SER U 89 " --> pdb=" O ILE U 86 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS U 90 " --> pdb=" O ASN U 87 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU U 91 " --> pdb=" O LYS U 88 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N ASP U 92 " --> pdb=" O SER U 89 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU U 93 " --> pdb=" O CYS U 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE U 94 " --> pdb=" O LEU U 91 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TRP U 98 " --> pdb=" O ARG U 95 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN U 99 " --> pdb=" O LEU U 96 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU U 102 " --> pdb=" O GLN U 99 " (cutoff:3.500A) Processing helix chain 'U' and resid 104 through 106 No H-bonds generated for 'chain 'U' and resid 104 through 106' Processing helix chain 'U' and resid 108 through 110 No H-bonds generated for 'chain 'U' and resid 108 through 110' Processing helix chain 'U' and resid 112 through 125 removed outlier: 3.863A pdb=" N LEU U 117 " --> pdb=" O LYS U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 142 through 144 No H-bonds generated for 'chain 'U' and resid 142 through 144' Processing helix chain 'U' and resid 157 through 169 Processing helix chain 'W' and resid 30 through 95 Proline residue: W 71 - end of helix removed outlier: 3.725A pdb=" N GLU W 76 " --> pdb=" O LEU W 72 " (cutoff:3.500A) Processing helix chain 'X' and resid 28 through 33 Processing helix chain 'X' and resid 37 through 60 removed outlier: 3.558A pdb=" N LEU X 50 " --> pdb=" O ALA X 46 " (cutoff:3.500A) Proline residue: X 51 - end of helix Processing helix chain 'X' and resid 72 through 99 removed outlier: 3.770A pdb=" N VAL X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG X 97 " --> pdb=" O ARG X 93 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE X 98 " --> pdb=" O SER X 94 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 120 removed outlier: 3.836A pdb=" N LYS X 109 " --> pdb=" O ALA X 105 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LYS X 110 " --> pdb=" O ARG X 106 " (cutoff:3.500A) Processing helix chain 'X' and resid 133 through 142 Processing helix chain 'Y' and resid 42 through 44 No H-bonds generated for 'chain 'Y' and resid 42 through 44' Processing helix chain 'Y' and resid 50 through 55 Processing helix chain 'Y' and resid 115 through 124 Processing helix chain 'Y' and resid 145 through 148 removed outlier: 3.694A pdb=" N PHE Y 148 " --> pdb=" O ALA Y 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 145 through 148' Processing helix chain 'Z' and resid 20 through 27 removed outlier: 3.893A pdb=" N LEU Z 27 " --> pdb=" O LYS Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 64 through 67 No H-bonds generated for 'chain 'Z' and resid 64 through 67' Processing helix chain 'Z' and resid 74 through 77 No H-bonds generated for 'chain 'Z' and resid 74 through 77' Processing helix chain 'Z' and resid 91 through 99 Processing helix chain 'Z' and resid 111 through 123 removed outlier: 4.250A pdb=" N LYS Z 116 " --> pdb=" O GLU Z 112 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN Z 120 " --> pdb=" O LYS Z 116 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ILE Z 121 " --> pdb=" O ALA Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 128 through 134 Processing helix chain 'Z' and resid 137 through 140 No H-bonds generated for 'chain 'Z' and resid 137 through 140' Processing helix chain 'a' and resid 28 through 32 Processing helix chain 'a' and resid 74 through 76 No H-bonds generated for 'chain 'a' and resid 74 through 76' Processing helix chain 'a' and resid 90 through 112 removed outlier: 3.513A pdb=" N THR a 112 " --> pdb=" O SER a 108 " (cutoff:3.500A) Processing helix chain 'a' and resid 126 through 130 Processing helix chain 'a' and resid 138 through 140 No H-bonds generated for 'chain 'a' and resid 138 through 140' Processing helix chain 'b' and resid 3 through 24 Processing helix chain 'b' and resid 34 through 64 removed outlier: 3.711A pdb=" N LYS b 64 " --> pdb=" O VAL b 60 " (cutoff:3.500A) Processing helix chain 'c' and resid 23 through 26 No H-bonds generated for 'chain 'c' and resid 23 through 26' Processing helix chain 'c' and resid 34 through 48 removed outlier: 4.015A pdb=" N VAL c 39 " --> pdb=" O GLY c 35 " (cutoff:3.500A) Processing helix chain 'd' and resid 20 through 55 Processing helix chain 'd' and resid 58 through 62 removed outlier: 4.067A pdb=" N ASP d 62 " --> pdb=" O HIS d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 73 Processing helix chain 'd' and resid 83 through 86 No H-bonds generated for 'chain 'd' and resid 83 through 86' Processing helix chain 'e' and resid 21 through 49 removed outlier: 3.646A pdb=" N LYS e 28 " --> pdb=" O ARG e 24 " (cutoff:3.500A) Proline residue: e 47 - end of helix Processing helix chain 'f' and resid 20 through 36 removed outlier: 6.748A pdb=" N GLY f 31 " --> pdb=" O LYS f 27 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ALA f 32 " --> pdb=" O ASN f 28 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS f 35 " --> pdb=" O GLY f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 84 Processing helix chain 'g' and resid 12 through 22 Processing helix chain 'g' and resid 24 through 42 removed outlier: 3.785A pdb=" N GLY g 36 " --> pdb=" O ILE g 32 " (cutoff:3.500A) Proline residue: g 37 - end of helix Processing helix chain 'g' and resid 44 through 50 Processing helix chain 'h' and resid 5 through 15 Processing helix chain 'h' and resid 17 through 24 Processing helix chain 'h' and resid 70 through 72 No H-bonds generated for 'chain 'h' and resid 70 through 72' Processing helix chain 'h' and resid 75 through 81 removed outlier: 3.924A pdb=" N TRP h 80 " --> pdb=" O GLY h 76 " (cutoff:3.500A) Processing helix chain 'i' and resid 26 through 47 removed outlier: 3.656A pdb=" N PHE i 32 " --> pdb=" O LEU i 28 " (cutoff:3.500A) Processing helix chain 'i' and resid 61 through 77 Processing helix chain 'j' and resid 30 through 40 Processing helix chain 'j' and resid 42 through 44 No H-bonds generated for 'chain 'j' and resid 42 through 44' Processing helix chain 'j' and resid 50 through 60 Processing helix chain 'j' and resid 62 through 73 Processing helix chain 'n' and resid 19 through 45 removed outlier: 3.960A pdb=" N ALA n 43 " --> pdb=" O SER n 39 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LYS n 44 " --> pdb=" O SER n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 60 through 88 removed outlier: 3.759A pdb=" N ASN n 64 " --> pdb=" O GLU n 60 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLU n 65 " --> pdb=" O ASP n 61 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE n 69 " --> pdb=" O GLU n 65 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LYS n 87 " --> pdb=" O MET n 83 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG n 88 " --> pdb=" O HIS n 84 " (cutoff:3.500A) Processing helix chain 'n' and resid 93 through 96 No H-bonds generated for 'chain 'n' and resid 93 through 96' Processing helix chain '1' and resid 2 through 33 removed outlier: 3.920A pdb=" N ALA 1 20 " --> pdb=" O LEU 1 16 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR 1 23 " --> pdb=" O VAL 1 19 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) Processing helix chain '1' and resid 49 through 59 removed outlier: 3.696A pdb=" N LEU 1 59 " --> pdb=" O VAL 1 55 " (cutoff:3.500A) Processing helix chain '1' and resid 70 through 88 Proline residue: 1 77 - end of helix removed outlier: 4.126A pdb=" N GLY 1 87 " --> pdb=" O THR 1 83 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N TRP 1 88 " --> pdb=" O ALA 1 84 " (cutoff:3.500A) Processing helix chain '1' and resid 105 through 125 removed outlier: 3.587A pdb=" N SER 1 114 " --> pdb=" O LEU 1 110 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY 1 116 " --> pdb=" O ILE 1 112 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N VAL 1 117 " --> pdb=" O GLY 1 113 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE 1 118 " --> pdb=" O SER 1 114 " (cutoff:3.500A) removed outlier: 5.057A pdb=" N GLY 1 119 " --> pdb=" O LEU 1 115 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER 1 120 " --> pdb=" O GLY 1 116 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N SER 1 123 " --> pdb=" O GLY 1 119 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N TRP 1 125 " --> pdb=" O LEU 1 121 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 158 removed outlier: 3.820A pdb=" N GLY 1 135 " --> pdb=" O TYR 1 131 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N SER 1 136 " --> pdb=" O SER 1 132 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 1 149 " --> pdb=" O SER 1 145 " (cutoff:3.500A) Processing helix chain '1' and resid 166 through 174 removed outlier: 3.586A pdb=" N ARG 1 174 " --> pdb=" O ILE 1 170 " (cutoff:3.500A) Processing helix chain '1' and resid 178 through 181 No H-bonds generated for 'chain '1' and resid 178 through 181' Processing helix chain '1' and resid 183 through 196 Processing helix chain '1' and resid 222 through 245 removed outlier: 3.690A pdb=" N PHE 1 227 " --> pdb=" O PRO 1 223 " (cutoff:3.500A) Processing helix chain '1' and resid 257 through 262 Processing helix chain '1' and resid 268 through 298 Processing helix chain '1' and resid 305 through 314 Processing helix chain '1' and resid 316 through 333 Proline residue: 1 328 - end of helix Processing helix chain '2' and resid 2 through 15 removed outlier: 3.796A pdb=" N THR 2 11 " --> pdb=" O ILE 2 7 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET 2 15 " --> pdb=" O THR 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 18 through 45 removed outlier: 3.744A pdb=" N ASN 2 21 " --> pdb=" O LEU 2 18 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N ARG 2 22 " --> pdb=" O SER 2 19 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU 2 38 " --> pdb=" O VAL 2 35 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASP 2 39 " --> pdb=" O LEU 2 36 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N SER 2 40 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N PHE 2 41 " --> pdb=" O LEU 2 38 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU 2 42 " --> pdb=" O ASP 2 39 " (cutoff:3.500A) Processing helix chain '2' and resid 47 through 49 No H-bonds generated for 'chain '2' and resid 47 through 49' Processing helix chain '2' and resid 63 through 84 Processing helix chain '2' and resid 91 through 96 removed outlier: 3.885A pdb=" N THR 2 95 " --> pdb=" O ASN 2 91 " (cutoff:3.500A) Processing helix chain '2' and resid 103 through 118 removed outlier: 3.671A pdb=" N ILE 2 117 " --> pdb=" O GLY 2 113 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N VAL 2 118 " --> pdb=" O ALA 2 114 " (cutoff:3.500A) Processing helix chain '2' and resid 123 through 141 Processing helix chain '2' and resid 148 through 178 removed outlier: 3.678A pdb=" N LEU 2 164 " --> pdb=" O MET 2 160 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE 2 168 " --> pdb=" O LEU 2 164 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL 2 178 " --> pdb=" O THR 2 174 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 194 No H-bonds generated for 'chain '2' and resid 191 through 194' Processing helix chain '2' and resid 198 through 209 Processing helix chain '2' and resid 215 through 217 No H-bonds generated for 'chain '2' and resid 215 through 217' Processing helix chain '2' and resid 219 through 227 Processing helix chain '2' and resid 233 through 236 No H-bonds generated for 'chain '2' and resid 233 through 236' Processing helix chain '2' and resid 239 through 250 removed outlier: 3.532A pdb=" N LEU 2 250 " --> pdb=" O SER 2 246 " (cutoff:3.500A) Processing helix chain '2' and resid 258 through 272 Processing helix chain '2' and resid 281 through 301 removed outlier: 3.625A pdb=" N SER 2 288 " --> pdb=" O LEU 2 284 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY 2 289 " --> pdb=" O LEU 2 285 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET 2 296 " --> pdb=" O ASN 2 292 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU 2 299 " --> pdb=" O TYR 2 295 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU 2 301 " --> pdb=" O MET 2 297 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 333 removed outlier: 3.648A pdb=" N ILE 2 327 " --> pdb=" O ILE 2 323 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N TYR 2 332 " --> pdb=" O ILE 2 328 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR 2 333 " --> pdb=" O PHE 2 329 " (cutoff:3.500A) Processing helix chain '2' and resid 347 through 350 removed outlier: 3.526A pdb=" N LEU 2 350 " --> pdb=" O VAL 2 347 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 347 through 350' Processing helix chain '2' and resid 358 through 372 Processing helix chain '2' and resid 378 through 393 removed outlier: 3.543A pdb=" N GLY 2 382 " --> pdb=" O LEU 2 378 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASN 2 392 " --> pdb=" O MET 2 388 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN 2 393 " --> pdb=" O SER 2 389 " (cutoff:3.500A) Processing helix chain '2' and resid 396 through 420 removed outlier: 3.523A pdb=" N ILE 2 400 " --> pdb=" O TYR 2 396 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LEU 2 411 " --> pdb=" O LEU 2 407 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR 2 412 " --> pdb=" O ILE 2 408 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 2 416 " --> pdb=" O TYR 2 412 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LEU 2 417 " --> pdb=" O TYR 2 413 " (cutoff:3.500A) Processing helix chain '2' and resid 437 through 452 removed outlier: 3.852A pdb=" N ILE 2 442 " --> pdb=" O VAL 2 438 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU 2 443 " --> pdb=" O LEU 2 439 " (cutoff:3.500A) Processing helix chain '2' and resid 454 through 467 removed outlier: 3.611A pdb=" N ASN 2 457 " --> pdb=" O PHE 2 454 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N SER 2 458 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) Processing helix chain '3' and resid 5 through 25 Proline residue: 3 12 - end of helix Processing helix chain '3' and resid 54 through 70 removed outlier: 4.085A pdb=" N ALA 3 60 " --> pdb=" O PHE 3 56 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LEU 3 64 " --> pdb=" O ALA 3 60 " (cutoff:3.500A) Proline residue: 3 65 - end of helix Processing helix chain '3' and resid 73 through 78 removed outlier: 3.863A pdb=" N MET 3 78 " --> pdb=" O LEU 3 74 " (cutoff:3.500A) Processing helix chain '3' and resid 87 through 107 removed outlier: 3.599A pdb=" N GLY 3 101 " --> pdb=" O ILE 3 97 " (cutoff:3.500A) Processing helix chain '4' and resid 3 through 20 removed outlier: 3.520A pdb=" N LEU 4 7 " --> pdb=" O LEU 4 3 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N TYR 4 12 " --> pdb=" O LEU 4 8 " (cutoff:3.500A) Processing helix chain '4' and resid 25 through 44 Processing helix chain '4' and resid 83 through 102 removed outlier: 3.841A pdb=" N PHE 4 88 " --> pdb=" O LEU 4 84 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU 4 95 " --> pdb=" O LEU 4 91 " (cutoff:3.500A) Proline residue: 4 97 - end of helix Processing helix chain '4' and resid 111 through 128 Processing helix chain '4' and resid 134 through 154 removed outlier: 3.735A pdb=" N LEU 4 140 " --> pdb=" O SER 4 136 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N THR 4 144 " --> pdb=" O LEU 4 140 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N LEU 4 145 " --> pdb=" O PHE 4 141 " (cutoff:3.500A) Proline residue: 4 146 - end of helix Processing helix chain '4' and resid 160 through 188 removed outlier: 4.124A pdb=" N THR 4 171 " --> pdb=" O VAL 4 167 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE 4 177 " --> pdb=" O SER 4 173 " (cutoff:3.500A) Processing helix chain '4' and resid 204 through 221 removed outlier: 4.035A pdb=" N LEU 4 212 " --> pdb=" O THR 4 208 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLY 4 213 " --> pdb=" O ILE 4 209 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU 4 214 " --> pdb=" O ILE 4 210 " (cutoff:3.500A) Processing helix chain '4' and resid 225 through 227 No H-bonds generated for 'chain '4' and resid 225 through 227' Processing helix chain '4' and resid 230 through 236 Processing helix chain '4' and resid 240 through 261 removed outlier: 5.597A pdb=" N LEU 4 251 " --> pdb=" O ALA 4 247 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N LYS 4 252 " --> pdb=" O GLY 4 248 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU 4 259 " --> pdb=" O LEU 4 255 " (cutoff:3.500A) Processing helix chain '4' and resid 267 through 291 removed outlier: 4.106A pdb=" N LEU 4 272 " --> pdb=" O GLU 4 268 " (cutoff:3.500A) Proline residue: 4 275 - end of helix removed outlier: 3.575A pdb=" N LEU 4 287 " --> pdb=" O LEU 4 283 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR 4 288 " --> pdb=" O THR 4 284 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 319 removed outlier: 3.862A pdb=" N LEU 4 315 " --> pdb=" O GLY 4 311 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY 4 316 " --> pdb=" O ILE 4 312 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N SER 4 319 " --> pdb=" O LEU 4 315 " (cutoff:3.500A) Processing helix chain '4' and resid 322 through 347 Proline residue: 4 340 - end of helix Processing helix chain '4' and resid 351 through 354 No H-bonds generated for 'chain '4' and resid 351 through 354' Processing helix chain '4' and resid 359 through 361 No H-bonds generated for 'chain '4' and resid 359 through 361' Processing helix chain '4' and resid 370 through 384 Processing helix chain '4' and resid 391 through 405 Processing helix chain '4' and resid 407 through 432 removed outlier: 4.297A pdb=" N ILE 4 415 " --> pdb=" O GLY 4 411 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N SER 4 416 " --> pdb=" O ILE 4 412 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N VAL 4 417 " --> pdb=" O SER 4 413 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU 4 418 " --> pdb=" O CYS 4 414 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA 4 421 " --> pdb=" O VAL 4 417 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N TYR 4 423 " --> pdb=" O LEU 4 419 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN 4 424 " --> pdb=" O ALA 4 420 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS 4 430 " --> pdb=" O LYS 4 426 " (cutoff:3.500A) Processing helix chain '4' and resid 448 through 466 removed outlier: 3.805A pdb=" N THR 4 461 " --> pdb=" O LEU 4 457 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE 4 464 " --> pdb=" O SER 4 460 " (cutoff:3.500A) Processing helix chain '4' and resid 468 through 471 removed outlier: 4.040A pdb=" N MET 4 471 " --> pdb=" O PRO 4 468 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 468 through 471' Processing helix chain '4' and resid 476 through 480 removed outlier: 3.885A pdb=" N ASN 4 480 " --> pdb=" O TYR 4 476 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 476 through 480' Processing helix chain '5' and resid 4 through 21 removed outlier: 3.557A pdb=" N ILE 5 8 " --> pdb=" O ALA 5 4 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE 5 9 " --> pdb=" O ILE 5 5 " (cutoff:3.500A) Proline residue: 5 12 - end of helix Proline residue: 5 19 - end of helix Processing helix chain '5' and resid 23 through 26 No H-bonds generated for 'chain '5' and resid 23 through 26' Processing helix chain '5' and resid 28 through 55 removed outlier: 4.013A pdb=" N ARG 5 33 " --> pdb=" O VAL 5 29 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 5 55 " --> pdb=" O TYR 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 106 removed outlier: 3.701A pdb=" N ALA 5 91 " --> pdb=" O THR 5 87 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY 5 105 " --> pdb=" O ILE 5 101 " (cutoff:3.500A) Processing helix chain '5' and resid 113 through 132 Processing helix chain '5' and resid 136 through 154 removed outlier: 3.827A pdb=" N GLY 5 147 " --> pdb=" O TRP 5 143 " (cutoff:3.500A) Processing helix chain '5' and resid 161 through 191 Processing helix chain '5' and resid 197 through 202 Processing helix chain '5' and resid 209 through 226 Processing helix chain '5' and resid 230 through 239 removed outlier: 4.072A pdb=" N HIS 5 233 " --> pdb=" O PHE 5 230 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N ASN 5 234 " --> pdb=" O GLY 5 231 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N TRP 5 235 " --> pdb=" O LEU 5 232 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N THR 5 237 " --> pdb=" O ASN 5 234 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU 5 238 " --> pdb=" O TRP 5 235 " (cutoff:3.500A) Processing helix chain '5' and resid 244 through 250 Processing helix chain '5' and resid 254 through 265 removed outlier: 4.329A pdb=" N GLY 5 259 " --> pdb=" O LEU 5 255 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE 5 260 " --> pdb=" O VAL 5 256 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU 5 263 " --> pdb=" O GLY 5 259 " (cutoff:3.500A) Processing helix chain '5' and resid 267 through 270 No H-bonds generated for 'chain '5' and resid 267 through 270' Processing helix chain '5' and resid 275 through 297 removed outlier: 3.926A pdb=" N LEU 5 289 " --> pdb=" O ALA 5 285 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N CYS 5 297 " --> pdb=" O LEU 5 293 " (cutoff:3.500A) Processing helix chain '5' and resid 301 through 321 removed outlier: 3.776A pdb=" N GLN 5 312 " --> pdb=" O SER 5 308 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N GLY 5 314 " --> pdb=" O MET 5 310 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N MET 5 315 " --> pdb=" O SER 5 311 " (cutoff:3.500A) Processing helix chain '5' and resid 325 through 352 removed outlier: 3.658A pdb=" N ALA 5 336 " --> pdb=" O LEU 5 332 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N PHE 5 337 " --> pdb=" O LEU 5 333 " (cutoff:3.500A) Processing helix chain '5' and resid 360 through 362 No H-bonds generated for 'chain '5' and resid 360 through 362' Processing helix chain '5' and resid 371 through 384 Processing helix chain '5' and resid 391 through 404 removed outlier: 4.673A pdb=" N ILE 5 398 " --> pdb=" O TYR 5 394 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE 5 399 " --> pdb=" O THR 5 395 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE 5 400 " --> pdb=" O LYS 5 396 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR 5 404 " --> pdb=" O ILE 5 400 " (cutoff:3.500A) Processing helix chain '5' and resid 410 through 437 removed outlier: 4.040A pdb=" N ALA 5 418 " --> pdb=" O TYR 5 415 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU 5 424 " --> pdb=" O SER 5 421 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N TYR 5 428 " --> pdb=" O THR 5 425 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N LEU 5 435 " --> pdb=" O ILE 5 432 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N THR 5 436 " --> pdb=" O LEU 5 433 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 450 Processing helix chain '5' and resid 456 through 480 Proline residue: 5 461 - end of helix removed outlier: 6.234A pdb=" N GLY 5 473 " --> pdb=" O ALA 5 469 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N TRP 5 474 " --> pdb=" O MET 5 470 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N ASP 5 478 " --> pdb=" O TRP 5 474 " (cutoff:3.500A) removed outlier: 4.966A pdb=" N ILE 5 479 " --> pdb=" O ILE 5 475 " (cutoff:3.500A) Processing helix chain '5' and resid 499 through 502 No H-bonds generated for 'chain '5' and resid 499 through 502' Processing helix chain '5' and resid 508 through 531 Proline residue: 5 514 - end of helix removed outlier: 3.574A pdb=" N SER 5 522 " --> pdb=" O ALA 5 518 " (cutoff:3.500A) Processing helix chain '5' and resid 541 through 551 Processing helix chain '5' and resid 556 through 563 removed outlier: 3.662A pdb=" N PHE 5 563 " --> pdb=" O ILE 5 559 " (cutoff:3.500A) Processing helix chain '5' and resid 565 through 578 Processing helix chain '5' and resid 589 through 607 removed outlier: 3.650A pdb=" N ASN 5 593 " --> pdb=" O PRO 5 589 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARG 5 594 " --> pdb=" O VAL 5 590 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N SER 5 607 " --> pdb=" O VAL 5 603 " (cutoff:3.500A) Processing helix chain '5' and resid 614 through 637 removed outlier: 3.511A pdb=" N LEU 5 622 " --> pdb=" O SER 5 618 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR 5 624 " --> pdb=" O LEU 5 620 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LEU 5 629 " --> pdb=" O ILE 5 625 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N VAL 5 637 " --> pdb=" O LEU 5 633 " (cutoff:3.500A) Processing helix chain '5' and resid 640 through 654 Proline residue: 5 644 - end of helix Processing helix chain '6' and resid 8 through 24 Processing helix chain '6' and resid 29 through 50 Processing helix chain '6' and resid 53 through 62 removed outlier: 3.888A pdb=" N LEU 6 57 " --> pdb=" O GLY 6 53 " (cutoff:3.500A) Processing helix chain '6' and resid 67 through 77 removed outlier: 3.919A pdb=" N LEU 6 77 " --> pdb=" O PHE 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 87 through 90 No H-bonds generated for 'chain '6' and resid 87 through 90' Processing helix chain '6' and resid 94 through 110 Processing helix chain '6' and resid 118 through 123 Processing helix chain '6' and resid 146 through 153 Processing helix chain '6' and resid 159 through 179 Proline residue: 6 176 - end of helix Processing helix chain '8' and resid 10 through 16 Processing helix chain '8' and resid 27 through 39 removed outlier: 4.310A pdb=" N VAL 8 31 " --> pdb=" O ALA 8 28 " (cutoff:3.500A) Proline residue: 8 32 - end of helix Processing helix chain '8' and resid 49 through 79 Processing helix chain '9' and resid 16 through 27 Processing helix chain '9' and resid 34 through 49 removed outlier: 3.651A pdb=" N LEU 9 38 " --> pdb=" O ALA 9 35 " (cutoff:3.500A) Proline residue: 9 39 - end of helix removed outlier: 4.140A pdb=" N GLU 9 46 " --> pdb=" O ASP 9 43 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N HIS 9 49 " --> pdb=" O GLU 9 46 " (cutoff:3.500A) Processing helix chain '9' and resid 51 through 64 removed outlier: 3.760A pdb=" N VAL 9 63 " --> pdb=" O GLU 9 59 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 36 through 41 Processing sheet with id= B, first strand: chain 'A' and resid 176 through 178 Processing sheet with id= C, first strand: chain 'A' and resid 253 through 255 Processing sheet with id= D, first strand: chain 'A' and resid 312 through 315 Processing sheet with id= E, first strand: chain 'A' and resid 346 through 350 removed outlier: 6.186A pdb=" N MET A 549 " --> pdb=" O LYS A 347 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL A 349 " --> pdb=" O MET A 549 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N TRP A 551 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N PHE A 568 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 552 " --> pdb=" O PHE A 568 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N VAL A 570 " --> pdb=" O LEU A 552 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL A 585 " --> pdb=" O TYR A 571 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N GLY A 573 " --> pdb=" O VAL A 585 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU A 587 " --> pdb=" O GLY A 573 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'A' and resid 438 through 442 removed outlier: 3.711A pdb=" N ALA A 440 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU A 481 " --> pdb=" O LEU A 411 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N VAL A 413 " --> pdb=" O LEU A 481 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ILE A 483 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 597 through 600 Processing sheet with id= H, first strand: chain 'B' and resid 242 through 246 removed outlier: 7.319A pdb=" N TYR B 114 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N THR B 245 " --> pdb=" O TYR B 114 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N VAL B 116 " --> pdb=" O THR B 245 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA B 155 " --> pdb=" O LEU B 115 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N VAL B 117 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N TYR B 157 " --> pdb=" O VAL B 117 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ALA B 119 " --> pdb=" O TYR B 157 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TYR B 159 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ASP B 196 " --> pdb=" O ALA B 156 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N ILE B 158 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N TYR B 198 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N ILE B 160 " --> pdb=" O TYR B 198 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N HIS B 200 " --> pdb=" O ILE B 160 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 288 through 293 removed outlier: 3.659A pdb=" N VAL B 358 " --> pdb=" O SER B 281 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY B 318 " --> pdb=" O ILE B 359 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 83 through 87 removed outlier: 3.505A pdb=" N ARG C 99 " --> pdb=" O HIS C 115 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N SER C 105 " --> pdb=" O ILE C 109 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ILE C 109 " --> pdb=" O SER C 105 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 397 through 405 Processing sheet with id= L, first strand: chain 'E' and resid 31 through 33 Processing sheet with id= M, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.628A pdb=" N ILE E 199 " --> pdb=" O PHE E 259 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N LEU E 261 " --> pdb=" O ILE E 199 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N ARG E 201 " --> pdb=" O LEU E 261 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N VAL E 125 " --> pdb=" O ILE E 164 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N VAL E 166 " --> pdb=" O VAL E 125 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASN E 127 " --> pdb=" O VAL E 166 " (cutoff:3.500A) removed outlier: 9.079A pdb=" N ALA E 168 " --> pdb=" O ASN E 127 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N THR E 79 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N VAL E 58 " --> pdb=" O THR E 79 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL E 81 " --> pdb=" O VAL E 58 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 204 through 206 Processing sheet with id= O, first strand: chain 'G' and resid 122 through 130 removed outlier: 6.792A pdb=" N ASN G 143 " --> pdb=" O ILE G 124 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ILE G 126 " --> pdb=" O VAL G 141 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL G 141 " --> pdb=" O ILE G 126 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA G 128 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N GLU G 139 " --> pdb=" O ALA G 128 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N LEU G 96 " --> pdb=" O ARG G 152 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR G 158 " --> pdb=" O VAL G 100 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'G' and resid 220 through 225 removed outlier: 3.534A pdb=" N ARG G 230 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 122 through 127 Processing sheet with id= R, first strand: chain 'H' and resid 177 through 179 Processing sheet with id= S, first strand: chain 'I' and resid 118 through 120 Processing sheet with id= T, first strand: chain 'I' and resid 145 through 151 removed outlier: 5.833A pdb=" N GLU I 150 " --> pdb=" O THR I 159 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N THR I 159 " --> pdb=" O GLU I 150 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'K' and resid 78 through 80 removed outlier: 6.123A pdb=" N ILE K 116 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N TRP K 143 " --> pdb=" O MET K 117 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N VAL K 119 " --> pdb=" O TRP K 143 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ILE K 145 " --> pdb=" O VAL K 119 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL K 175 " --> pdb=" O SER K 146 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 20 through 22 Processing sheet with id= W, first strand: chain 'M' and resid 88 through 90 Processing sheet with id= X, first strand: chain 'M' and resid 94 through 97 Processing sheet with id= Y, first strand: chain 'Y' and resid 128 through 132 removed outlier: 4.509A pdb=" N GLN Y 62 " --> pdb=" O GLN Y 132 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'f' and resid 41 through 46 Processing sheet with id= AA, first strand: chain 'h' and resid 44 through 47 Processing sheet with id= AB, first strand: chain '2' and resid 52 through 54 Processing sheet with id= AC, first strand: chain '4' and resid 57 through 59 Processing sheet with id= AD, first strand: chain '5' and resid 61 through 63 Processing sheet with id= AE, first strand: chain '5' and resid 66 through 69 removed outlier: 6.689A pdb=" N ILE 5 75 " --> pdb=" O TYR 5 67 " (cutoff:3.500A) 2548 hydrogen bonds defined for protein. 7233 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 20.83 Time building geometry restraints manager: 23.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.39: 26407 1.39 - 1.62: 39691 1.62 - 1.85: 515 1.85 - 2.08: 4 2.08 - 2.31: 80 Bond restraints: 66697 Sorted by residual: bond pdb=" N PRO K 78 " pdb=" CA PRO K 78 " ideal model delta sigma weight residual 1.469 1.698 -0.229 1.28e-02 6.10e+03 3.21e+02 bond pdb=" C3 UQ9 1 402 " pdb=" C4 UQ9 1 402 " ideal model delta sigma weight residual 1.340 1.518 -0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C MET M 74 " pdb=" O MET M 74 " ideal model delta sigma weight residual 1.233 1.190 0.043 4.80e-03 4.34e+04 7.85e+01 bond pdb=" C5N NDP E 401 " pdb=" C6N NDP E 401 " ideal model delta sigma weight residual 1.337 1.548 -0.211 2.40e-02 1.74e+03 7.75e+01 bond pdb=" C1 UQ9 1 402 " pdb=" C6 UQ9 1 402 " ideal model delta sigma weight residual 1.345 1.520 -0.175 2.00e-02 2.50e+03 7.69e+01 ... (remaining 66692 not shown) Histogram of bond angle deviations from ideal: 70.80 - 87.93: 75 87.93 - 105.07: 1604 105.07 - 122.20: 77930 122.20 - 139.33: 10708 139.33 - 156.47: 2 Bond angle restraints: 90319 Sorted by residual: angle pdb=" C TRP K 77 " pdb=" N PRO K 78 " pdb=" CA PRO K 78 " ideal model delta sigma weight residual 119.84 139.80 -19.96 1.25e+00 6.40e-01 2.55e+02 angle pdb=" S1 FES H 301 " pdb="FE2 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 89.48 14.85 1.14e+00 7.69e-01 1.70e+02 angle pdb=" S1 FES H 301 " pdb="FE1 FES H 301 " pdb=" S2 FES H 301 " ideal model delta sigma weight residual 104.33 90.07 14.26 1.20e+00 6.94e-01 1.41e+02 angle pdb=" S1 FES A 803 " pdb="FE2 FES A 803 " pdb=" S2 FES A 803 " ideal model delta sigma weight residual 104.33 91.23 13.10 1.14e+00 7.69e-01 1.32e+02 angle pdb="FE1 FES A 803 " pdb=" S2 FES A 803 " pdb="FE2 FES A 803 " ideal model delta sigma weight residual 75.66 88.18 -12.52 1.14e+00 7.69e-01 1.21e+02 ... (remaining 90314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 39439 35.81 - 71.62: 842 71.62 - 107.42: 107 107.42 - 143.23: 32 143.23 - 179.04: 7 Dihedral angle restraints: 40427 sinusoidal: 17180 harmonic: 23247 Sorted by residual: dihedral pdb=" CA LEU 5 554 " pdb=" C LEU 5 554 " pdb=" N VAL 5 555 " pdb=" CA VAL 5 555 " ideal model delta harmonic sigma weight residual -180.00 -127.70 -52.30 0 5.00e+00 4.00e-02 1.09e+02 dihedral pdb=" CA ILE H 29 " pdb=" C ILE H 29 " pdb=" N VAL H 30 " pdb=" CA VAL H 30 " ideal model delta harmonic sigma weight residual -180.00 -134.71 -45.29 0 5.00e+00 4.00e-02 8.20e+01 dihedral pdb=" CA ASN H 174 " pdb=" C ASN H 174 " pdb=" N ALA H 175 " pdb=" CA ALA H 175 " ideal model delta harmonic sigma weight residual 180.00 -138.98 -41.02 0 5.00e+00 4.00e-02 6.73e+01 ... (remaining 40424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 4.245: 10013 4.245 - 8.491: 2 8.491 - 12.736: 0 12.736 - 16.981: 0 16.981 - 21.227: 20 Chirality restraints: 10035 Sorted by residual: chirality pdb="FE1 SF4 I 502 " pdb=" S2 SF4 I 502 " pdb=" S3 SF4 I 502 " pdb=" S4 SF4 I 502 " both_signs ideal model delta sigma weight residual False -10.55 10.67 -21.23 2.00e-01 2.50e+01 1.13e+04 chirality pdb="FE1 SF4 A 801 " pdb=" S2 SF4 A 801 " pdb=" S3 SF4 A 801 " pdb=" S4 SF4 A 801 " both_signs ideal model delta sigma weight residual False -10.55 10.56 -21.12 2.00e-01 2.50e+01 1.11e+04 chirality pdb="FE2 SF4 K 301 " pdb=" S1 SF4 K 301 " pdb=" S3 SF4 K 301 " pdb=" S4 SF4 K 301 " both_signs ideal model delta sigma weight residual False 10.55 -10.49 21.05 2.00e-01 2.50e+01 1.11e+04 ... (remaining 10032 not shown) Planarity restraints: 11276 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C17 T7X 2 504 " 0.231 2.00e-02 2.50e+03 2.39e-01 5.69e+02 pdb=" C18 T7X 2 504 " -0.213 2.00e-02 2.50e+03 pdb=" C19 T7X 2 504 " -0.263 2.00e-02 2.50e+03 pdb=" C20 T7X 2 504 " 0.245 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 165 " -0.924 9.50e-02 1.11e+02 4.14e-01 1.04e+02 pdb=" NE ARG A 165 " 0.055 2.00e-02 2.50e+03 pdb=" CZ ARG A 165 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG A 165 " -0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A 165 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG K 199 " 0.868 9.50e-02 1.11e+02 3.89e-01 9.18e+01 pdb=" NE ARG K 199 " -0.053 2.00e-02 2.50e+03 pdb=" CZ ARG K 199 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG K 199 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG K 199 " 0.023 2.00e-02 2.50e+03 ... (remaining 11273 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 9466 2.76 - 3.29: 62731 3.29 - 3.83: 111439 3.83 - 4.36: 136782 4.36 - 4.90: 226965 Nonbonded interactions: 547383 Sorted by model distance: nonbonded pdb=" O ILE 5 400 " pdb=" OG1 THR 5 403 " model vdw 2.220 2.440 nonbonded pdb=" OG1 THR E 198 " pdb=" O THR E 254 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR U 40 " pdb=" O GLU W 61 " model vdw 2.234 2.440 nonbonded pdb=" OH TYR 5 374 " pdb=" OH TYR 5 438 " model vdw 2.234 2.440 nonbonded pdb=" O PHE a 104 " pdb=" OG SER a 108 " model vdw 2.257 2.440 ... (remaining 547378 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=0.70 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 15.520 Check model and map are aligned: 0.720 Set scattering table: 0.470 Process input model: 153.270 Find NCS groups from input model: 2.330 Set up NCS constraints: 0.240 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:13.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 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 : 0.012 0.253 66697 Z= 0.773 Angle : 1.533 35.196 90319 Z= 0.784 Chirality : 0.938 21.227 10035 Planarity : 0.012 0.414 11276 Dihedral : 15.797 179.040 25472 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.48 % Favored : 94.42 % Rotamer: Outliers : 0.37 % Allowed : 4.39 % Favored : 95.24 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.77 % Twisted General : 0.27 % 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: -3.60 (0.07), residues: 7887 helix: -2.23 (0.06), residues: 4042 sheet: -1.34 (0.24), residues: 396 loop : -2.62 (0.09), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP B 263 HIS 0.016 0.003 HIS 4 235 PHE 0.050 0.004 PHE O 80 TYR 0.064 0.004 TYR I 103 ARG 0.040 0.001 ARG E 216 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2093 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 2068 time to evaluate : 5.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 106 TRP cc_start: 0.7739 (p-90) cc_final: 0.7520 (p-90) REVERT: B 159 TYR cc_start: 0.7218 (t80) cc_final: 0.6847 (t80) REVERT: B 298 LEU cc_start: 0.7107 (tp) cc_final: 0.6831 (tp) REVERT: B 313 TRP cc_start: 0.7423 (t-100) cc_final: 0.6219 (m100) REVERT: B 459 VAL cc_start: 0.6120 (OUTLIER) cc_final: 0.5869 (t) REVERT: C 80 ILE cc_start: 0.8185 (tp) cc_final: 0.7909 (pp) REVERT: E 331 ASN cc_start: 0.7047 (m-40) cc_final: 0.6606 (t0) REVERT: F 41 ASN cc_start: 0.7216 (t0) cc_final: 0.6960 (t0) REVERT: J 113 LYS cc_start: 0.7095 (mmtp) cc_final: 0.6864 (mptp) REVERT: L 85 ASN cc_start: 0.8205 (m-40) cc_final: 0.7959 (m-40) REVERT: M 66 GLN cc_start: 0.6591 (mm110) cc_final: 0.6342 (mp10) REVERT: P 85 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7161 (mt-10) REVERT: Q 56 GLN cc_start: 0.6705 (tp40) cc_final: 0.6410 (tp40) REVERT: R 27 ARG cc_start: 0.7551 (tpt90) cc_final: 0.7027 (tpm170) REVERT: S 85 GLU cc_start: 0.6278 (pm20) cc_final: 0.5850 (mm-30) REVERT: W 38 CYS cc_start: 0.7861 (m) cc_final: 0.7593 (m) REVERT: a 95 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8046 (pttp) REVERT: a 113 TYR cc_start: 0.7497 (m-80) cc_final: 0.7214 (m-10) REVERT: a 124 GLU cc_start: 0.6776 (pm20) cc_final: 0.6450 (pm20) REVERT: e 43 LYS cc_start: 0.8369 (tttp) cc_final: 0.7876 (mptt) REVERT: h 13 TRP cc_start: 0.6093 (t60) cc_final: 0.5282 (m100) REVERT: h 133 VAL cc_start: 0.7894 (t) cc_final: 0.7471 (t) REVERT: n 48 THR cc_start: 0.8271 (m) cc_final: 0.8062 (t) REVERT: 2 406 SER cc_start: 0.8907 (t) cc_final: 0.8489 (m) REVERT: 2 462 ASP cc_start: 0.7918 (m-30) cc_final: 0.7692 (m-30) REVERT: 4 159 ASP cc_start: 0.7097 (t70) cc_final: 0.6605 (t0) REVERT: 5 98 MET cc_start: 0.8128 (mmp) cc_final: 0.7669 (mmt) REVERT: 5 528 LEU cc_start: 0.8864 (tt) cc_final: 0.8588 (tp) REVERT: 6 114 ASN cc_start: 0.7264 (m-40) cc_final: 0.6567 (t0) REVERT: 8 66 VAL cc_start: 0.8062 (t) cc_final: 0.7766 (m) outliers start: 25 outliers final: 14 residues processed: 2084 average time/residue: 1.4270 time to fit residues: 3838.5023 Evaluate side-chains 1196 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1181 time to evaluate : 5.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain G residue 77 TYR Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain L residue 51 SER Chi-restraints excluded: chain O residue 88 GLU Chi-restraints excluded: chain R residue 28 ASN Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain a residue 82 PRO Chi-restraints excluded: chain 1 residue 155 ILE Chi-restraints excluded: chain 4 residue 280 ILE Chi-restraints excluded: chain 6 residue 111 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 658 optimal weight: 3.9990 chunk 591 optimal weight: 0.4980 chunk 328 optimal weight: 5.9990 chunk 201 optimal weight: 5.9990 chunk 398 optimal weight: 2.9990 chunk 315 optimal weight: 9.9990 chunk 611 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 chunk 371 optimal weight: 6.9990 chunk 455 optimal weight: 0.0470 chunk 708 optimal weight: 1.9990 overall best weight: 1.3082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 171 ASN A 185 HIS A 398 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 HIS C 57 HIS C 120 HIS D 33 ASN D 60 GLN D 64 GLN E 62 ASN E 170 ASN F 24 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 85 ASN ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN H 91 ASN H 125 GLN H 145 GLN H 146 ASN I 210 ASN J 48 ASN K 73 GLN K 100 GLN L 18 ASN M 93 ASN M 102 HIS M 116 ASN Q 48 HIS R 38 GLN R 50 ASN R 105 ASN ** S 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 113 ASN S 201 GLN S 211 ASN U 97 HIS U 169 ASN X 161 HIS Y 42 HIS Y 109 GLN Y 132 GLN Z 38 ASN Z 72 ASN a 49 GLN a 61 GLN a 73 ASN b 22 ASN c 20 ASN d 4 HIS d 65 ASN d 88 ASN e 7 ASN g 3 ASN h 23 GLN h 25 ASN h 50 HIS i 78 HIS n 47 HIS n 95 HIS 1 310 ASN ** 2 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 185 HIS ** 2 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 227 ASN 2 393 ASN 2 469 ASN ** 3 22 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 109 ASN 4 153 HIS ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 424 GLN 4 444 ASN 5 326 ASN 5 335 HIS 5 411 ASN 5 496 ASN 5 617 ASN 6 136 GLN 8 16 HIS Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.277 66697 Z= 0.534 Angle : 1.529 50.928 90319 Z= 0.968 Chirality : 0.286 6.612 10035 Planarity : 0.006 0.075 11276 Dihedral : 15.022 178.805 10546 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.12 % Favored : 95.85 % Rotamer: Outliers : 4.23 % Allowed : 16.54 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.09), residues: 7887 helix: -0.56 (0.08), residues: 4034 sheet: -0.81 (0.25), residues: 383 loop : -2.11 (0.09), residues: 3470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 5 143 HIS 0.013 0.001 HIS D 78 PHE 0.022 0.002 PHE C 139 TYR 0.029 0.002 TYR 1 244 ARG 0.010 0.001 ARG U 161 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1631 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 289 poor density : 1342 time to evaluate : 5.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8169 (mmt) cc_final: 0.7828 (tpt) REVERT: A 549 MET cc_start: 0.6186 (OUTLIER) cc_final: 0.5712 (ttp) REVERT: B 106 TRP cc_start: 0.7795 (p-90) cc_final: 0.7464 (p-90) REVERT: B 131 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6565 (mm-30) REVERT: B 159 TYR cc_start: 0.7362 (t80) cc_final: 0.6983 (t80) REVERT: B 291 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6421 (tm-30) REVERT: B 332 ASN cc_start: 0.7572 (p0) cc_final: 0.7319 (p0) REVERT: C 80 ILE cc_start: 0.8088 (tp) cc_final: 0.7881 (pp) REVERT: C 188 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.6664 (tpt) REVERT: C 285 ASP cc_start: 0.7058 (t0) cc_final: 0.6794 (t0) REVERT: E 201 ARG cc_start: 0.6551 (mpp80) cc_final: 0.6069 (tpp80) REVERT: E 314 VAL cc_start: 0.4554 (OUTLIER) cc_final: 0.4343 (m) REVERT: E 331 ASN cc_start: 0.7147 (m-40) cc_final: 0.6666 (t0) REVERT: F 68 ARG cc_start: 0.7582 (OUTLIER) cc_final: 0.7176 (ttt180) REVERT: G 134 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7836 (mtp180) REVERT: I 82 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7635 (pp20) REVERT: J 170 ARG cc_start: 0.8382 (OUTLIER) cc_final: 0.7660 (ttm170) REVERT: K 91 MET cc_start: 0.6878 (OUTLIER) cc_final: 0.6256 (mtp) REVERT: K 165 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8517 (mtt180) REVERT: M 53 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7653 (mptm) REVERT: M 66 GLN cc_start: 0.6699 (mm110) cc_final: 0.6469 (mp10) REVERT: P 85 GLU cc_start: 0.7525 (mt-10) cc_final: 0.7199 (mt-10) REVERT: Q 56 GLN cc_start: 0.6566 (tp40) cc_final: 0.6184 (tp40) REVERT: Q 95 VAL cc_start: 0.8438 (p) cc_final: 0.8186 (m) REVERT: Q 97 MET cc_start: 0.7578 (OUTLIER) cc_final: 0.7113 (tpt) REVERT: R 27 ARG cc_start: 0.7578 (tpt90) cc_final: 0.7077 (tpm170) REVERT: R 43 ILE cc_start: 0.8762 (pt) cc_final: 0.8541 (pt) REVERT: S 85 GLU cc_start: 0.6206 (pm20) cc_final: 0.5874 (mm-30) REVERT: S 201 GLN cc_start: 0.8176 (tp40) cc_final: 0.7960 (tp-100) REVERT: X 75 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8516 (mp) REVERT: a 95 LYS cc_start: 0.8407 (ttpt) cc_final: 0.8052 (pttp) REVERT: d 80 GLN cc_start: 0.8429 (mt0) cc_final: 0.8170 (mp10) REVERT: e 43 LYS cc_start: 0.8244 (tttp) cc_final: 0.7865 (mptt) REVERT: h 13 TRP cc_start: 0.6203 (t60) cc_final: 0.5394 (t-100) REVERT: h 74 GLU cc_start: 0.7073 (OUTLIER) cc_final: 0.6845 (tt0) REVERT: i 31 LEU cc_start: 0.8403 (mp) cc_final: 0.7885 (mt) REVERT: n 48 THR cc_start: 0.7997 (m) cc_final: 0.7712 (t) REVERT: 1 33 MET cc_start: 0.8344 (mtt) cc_final: 0.7971 (mtt) REVERT: 1 64 LEU cc_start: 0.6122 (tp) cc_final: 0.5824 (mm) REVERT: 1 150 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8646 (mt) REVERT: 3 71 SER cc_start: 0.8433 (t) cc_final: 0.8230 (t) REVERT: 4 159 ASP cc_start: 0.7257 (t70) cc_final: 0.6724 (t0) REVERT: 5 98 MET cc_start: 0.8294 (mmp) cc_final: 0.7875 (mmt) REVERT: 5 303 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7844 (ttm170) REVERT: 5 409 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.7957 (pp) REVERT: 5 507 THR cc_start: 0.8181 (m) cc_final: 0.7922 (p) REVERT: 5 524 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8626 (tp) REVERT: 6 30 MET cc_start: 0.7627 (OUTLIER) cc_final: 0.7324 (ttp) REVERT: 6 87 VAL cc_start: 0.7622 (p) cc_final: 0.7416 (p) REVERT: 6 91 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7337 (mt) REVERT: 6 114 ASN cc_start: 0.7524 (m-40) cc_final: 0.6844 (t0) REVERT: 6 119 ILE cc_start: 0.7714 (OUTLIER) cc_final: 0.7294 (tp) REVERT: 8 56 MET cc_start: 0.6396 (tpp) cc_final: 0.6006 (tpp) REVERT: 8 64 ARG cc_start: 0.7564 (ptm-80) cc_final: 0.7285 (ppt170) outliers start: 289 outliers final: 79 residues processed: 1515 average time/residue: 1.3365 time to fit residues: 2672.4617 Evaluate side-chains 1175 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1075 time to evaluate : 5.530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 377 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 549 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain C residue 108 GLU Chi-restraints excluded: chain C residue 188 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain E residue 122 SER Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 314 VAL Chi-restraints excluded: chain F residue 58 GLN Chi-restraints excluded: chain F residue 68 ARG Chi-restraints excluded: chain F residue 139 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 164 SER Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 170 ARG Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 MET Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 65 SER Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain U residue 39 SER Chi-restraints excluded: chain X residue 42 VAL Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain b residue 7 LEU Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain f residue 6 ARG Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain 1 residue 10 ILE Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 2 residue 96 LEU Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 303 ARG Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 546 VAL Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 6 residue 30 MET Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 111 ILE Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 393 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 589 optimal weight: 0.9980 chunk 482 optimal weight: 10.0000 chunk 195 optimal weight: 9.9990 chunk 709 optimal weight: 8.9990 chunk 766 optimal weight: 9.9990 chunk 631 optimal weight: 5.9990 chunk 703 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 569 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN A 367 ASN ** B 272 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 456 HIS C 288 ASN C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN E 181 HIS E 317 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN G 208 HIS H 133 GLN H 145 GLN J 48 ASN K 200 ASN M 38 GLN M 41 ASN M 93 ASN P 63 HIS P 72 GLN Q 48 HIS R 38 GLN U 87 ASN U 127 ASN Y 132 GLN Y 146 ASN c 20 ASN d 88 ASN g 3 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 60 GLN h 50 HIS n 47 HIS ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 173 ASN ** 2 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 469 ASN 3 22 ASN 3 109 ASN 4 128 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 136 GLN 8 16 HIS Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.3433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 66697 Z= 0.549 Angle : 1.524 50.619 90319 Z= 0.966 Chirality : 0.287 6.472 10035 Planarity : 0.005 0.076 11276 Dihedral : 13.787 179.023 10525 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.65 % Favored : 95.32 % Rotamer: Outliers : 5.30 % Allowed : 18.85 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.09), residues: 7887 helix: 0.13 (0.08), residues: 4102 sheet: -0.62 (0.26), residues: 384 loop : -1.85 (0.10), residues: 3401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 143 HIS 0.011 0.001 HIS 4 197 PHE 0.037 0.002 PHE G 189 TYR 0.030 0.002 TYR I 171 ARG 0.010 0.001 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1551 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 362 poor density : 1189 time to evaluate : 6.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 149 MET cc_start: 0.8128 (OUTLIER) cc_final: 0.7803 (tpt) REVERT: A 478 LYS cc_start: 0.7405 (OUTLIER) cc_final: 0.7128 (ptmt) REVERT: B 72 ASP cc_start: 0.5444 (p0) cc_final: 0.5210 (p0) REVERT: B 106 TRP cc_start: 0.7794 (p-90) cc_final: 0.7377 (p-90) REVERT: B 146 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7791 (mt) REVERT: B 183 LEU cc_start: 0.5810 (OUTLIER) cc_final: 0.5511 (mm) REVERT: B 291 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6449 (tm-30) REVERT: E 213 PHE cc_start: 0.6701 (t80) cc_final: 0.6396 (m-80) REVERT: E 304 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.5098 (mm) REVERT: E 333 LEU cc_start: 0.7099 (OUTLIER) cc_final: 0.6807 (pp) REVERT: F 41 ASN cc_start: 0.7183 (t0) cc_final: 0.6568 (t0) REVERT: G 134 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.7830 (mtp180) REVERT: I 82 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7957 (pm20) REVERT: J 58 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6705 (pp) REVERT: J 144 LYS cc_start: 0.8050 (mmtm) cc_final: 0.7826 (mppt) REVERT: K 64 LEU cc_start: 0.7776 (OUTLIER) cc_final: 0.7501 (tm) REVERT: K 91 MET cc_start: 0.6972 (OUTLIER) cc_final: 0.6439 (mtp) REVERT: M 53 LYS cc_start: 0.8506 (OUTLIER) cc_final: 0.7635 (mptm) REVERT: M 66 GLN cc_start: 0.6758 (mm110) cc_final: 0.6491 (mp10) REVERT: P 62 ARG cc_start: 0.7451 (ttm-80) cc_final: 0.7167 (tpp80) REVERT: Q 56 GLN cc_start: 0.6626 (tp40) cc_final: 0.6104 (tp40) REVERT: Q 97 MET cc_start: 0.7344 (OUTLIER) cc_final: 0.6824 (tpt) REVERT: R 18 MET cc_start: 0.7270 (ttm) cc_final: 0.7017 (mtm) REVERT: S 85 GLU cc_start: 0.6262 (pm20) cc_final: 0.5904 (mm-30) REVERT: S 201 GLN cc_start: 0.8192 (tp40) cc_final: 0.7945 (mm-40) REVERT: U 54 MET cc_start: 0.8411 (mmt) cc_final: 0.8165 (mmt) REVERT: U 73 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7610 (mtt90) REVERT: Y 133 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7443 (mp0) REVERT: a 95 LYS cc_start: 0.8309 (ttpt) cc_final: 0.7848 (pttp) REVERT: a 124 GLU cc_start: 0.7280 (pm20) cc_final: 0.6857 (pm20) REVERT: d 33 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7336 (mp0) REVERT: d 39 GLU cc_start: 0.6575 (mp0) cc_final: 0.6192 (mp0) REVERT: d 80 GLN cc_start: 0.8564 (mt0) cc_final: 0.8350 (mp10) REVERT: f 74 LYS cc_start: 0.7341 (mmmm) cc_final: 0.7120 (mmmt) REVERT: h 13 TRP cc_start: 0.6283 (t60) cc_final: 0.5489 (t-100) REVERT: h 41 TYR cc_start: 0.7916 (OUTLIER) cc_final: 0.6692 (t80) REVERT: h 59 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.8444 (mtt180) REVERT: h 126 LYS cc_start: 0.8460 (mppt) cc_final: 0.8038 (mmtm) REVERT: j 26 LEU cc_start: 0.9155 (OUTLIER) cc_final: 0.8932 (tp) REVERT: 1 64 LEU cc_start: 0.5483 (tp) cc_final: 0.5172 (mm) REVERT: 1 231 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6957 (tt0) REVERT: 2 273 VAL cc_start: 0.8845 (OUTLIER) cc_final: 0.8545 (t) REVERT: 2 364 MET cc_start: 0.8747 (OUTLIER) cc_final: 0.8472 (ttm) REVERT: 4 159 ASP cc_start: 0.7193 (t70) cc_final: 0.6522 (t0) REVERT: 5 61 ASN cc_start: 0.8319 (OUTLIER) cc_final: 0.8056 (p0) REVERT: 5 98 MET cc_start: 0.8356 (mmp) cc_final: 0.8153 (mmt) REVERT: 5 269 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8234 (pt) REVERT: 5 303 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8022 (ttm170) REVERT: 5 409 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7859 (pp) REVERT: 6 59 TYR cc_start: 0.7799 (m-10) cc_final: 0.7453 (m-80) REVERT: 6 114 ASN cc_start: 0.7403 (m-40) cc_final: 0.6800 (t0) REVERT: 6 119 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7310 (tp) REVERT: 8 14 LYS cc_start: 0.7957 (mtpp) cc_final: 0.7552 (mmtt) REVERT: 9 8 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8617 (mt) REVERT: 9 18 GLU cc_start: 0.8248 (mp0) cc_final: 0.7998 (mp0) REVERT: 9 58 ARG cc_start: 0.7143 (mmt90) cc_final: 0.6923 (mmt-90) outliers start: 362 outliers final: 135 residues processed: 1420 average time/residue: 1.3294 time to fit residues: 2494.4413 Evaluate side-chains 1216 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 1052 time to evaluate : 5.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 ASP Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 219 LYS Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 302 ASP Chi-restraints excluded: chain A residue 305 LYS Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 163 GLU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 306 CYS Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 468 MET Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 85 ASN Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 154 ASP Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 91 MET Chi-restraints excluded: chain K residue 134 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 41 ASN Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 53 LYS Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 74 VAL Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 76 VAL Chi-restraints excluded: chain h residue 41 TYR Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 59 ARG Chi-restraints excluded: chain h residue 71 SER Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain j residue 26 LEU Chi-restraints excluded: chain j residue 50 ARG Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain j residue 61 VAL Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain 1 residue 15 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 150 LEU Chi-restraints excluded: chain 1 residue 167 THR Chi-restraints excluded: chain 1 residue 228 PHE Chi-restraints excluded: chain 1 residue 231 GLU Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 221 LEU Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 340 GLN Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 364 MET Chi-restraints excluded: chain 2 residue 426 ASN Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 2 residue 438 VAL Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 317 VAL Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 417 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 61 ASN Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 269 ILE Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 303 ARG Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 513 LEU Chi-restraints excluded: chain 5 residue 527 VAL Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 546 VAL Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 616 MET Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 18 LEU Chi-restraints excluded: chain 6 residue 33 ILE Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 8 residue 39 LYS Chi-restraints excluded: chain 9 residue 8 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 701 optimal weight: 2.9990 chunk 533 optimal weight: 4.9990 chunk 368 optimal weight: 7.9990 chunk 78 optimal weight: 10.0000 chunk 338 optimal weight: 0.9990 chunk 476 optimal weight: 7.9990 chunk 712 optimal weight: 0.8980 chunk 753 optimal weight: 0.1980 chunk 372 optimal weight: 3.9990 chunk 674 optimal weight: 4.9990 chunk 203 optimal weight: 5.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 62 ASN E 269 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN H 65 GLN H 133 GLN H 159 ASN J 48 ASN K 200 ASN L 18 ASN M 93 ASN M 116 ASN Q 48 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN c 18 GLN c 20 ASN d 88 ASN f 11 HIS ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 47 HIS ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 61 ASN 4 128 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 100 HIS ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 331 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 450 ASN 6 136 GLN 8 10 GLN 8 16 HIS Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 66697 Z= 0.508 Angle : 1.492 50.665 90319 Z= 0.954 Chirality : 0.285 6.399 10035 Planarity : 0.005 0.076 11276 Dihedral : 13.089 177.473 10520 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.08 % Favored : 95.89 % Rotamer: Outliers : 4.71 % Allowed : 20.80 % Favored : 74.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.09), residues: 7887 helix: 0.57 (0.08), residues: 4075 sheet: -0.56 (0.25), residues: 417 loop : -1.70 (0.10), residues: 3395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 70 HIS 0.007 0.001 HIS 4 197 PHE 0.024 0.002 PHE f 25 TYR 0.024 0.002 TYR 1 244 ARG 0.013 0.001 ARG g 67 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1439 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 322 poor density : 1117 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 72 ASP cc_start: 0.5391 (p0) cc_final: 0.5176 (p0) REVERT: B 106 TRP cc_start: 0.7799 (p-90) cc_final: 0.7352 (p-90) REVERT: B 146 LEU cc_start: 0.8041 (OUTLIER) cc_final: 0.7797 (mt) REVERT: B 183 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5583 (mm) REVERT: B 291 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6464 (tm-30) REVERT: C 48 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7681 (m-70) REVERT: C 188 MET cc_start: 0.7764 (tpt) cc_final: 0.6988 (tpt) REVERT: C 348 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7355 (tt0) REVERT: E 201 ARG cc_start: 0.6286 (ttm110) cc_final: 0.5602 (tpp80) REVERT: E 213 PHE cc_start: 0.6471 (t80) cc_final: 0.6241 (m-80) REVERT: F 41 ASN cc_start: 0.7170 (t0) cc_final: 0.6607 (t0) REVERT: F 126 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7790 (pp) REVERT: F 129 LYS cc_start: 0.7976 (mptt) cc_final: 0.7664 (ttpp) REVERT: G 134 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8050 (mtp180) REVERT: H 141 MET cc_start: 0.7791 (ttm) cc_final: 0.6986 (tpt) REVERT: H 205 MET cc_start: 0.5882 (mmt) cc_final: 0.5663 (ppp) REVERT: I 82 GLU cc_start: 0.8244 (OUTLIER) cc_final: 0.7331 (pp20) REVERT: I 146 THR cc_start: 0.9137 (OUTLIER) cc_final: 0.8837 (m) REVERT: I 186 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.8418 (mt-10) REVERT: J 58 LEU cc_start: 0.7281 (OUTLIER) cc_final: 0.6778 (pp) REVERT: K 165 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8620 (mpt180) REVERT: M 66 GLN cc_start: 0.6717 (mm110) cc_final: 0.6480 (mp10) REVERT: P 85 GLU cc_start: 0.7709 (mt-10) cc_final: 0.7365 (tt0) REVERT: Q 56 GLN cc_start: 0.6473 (tp40) cc_final: 0.6067 (tp40) REVERT: Q 97 MET cc_start: 0.7284 (OUTLIER) cc_final: 0.6790 (tpt) REVERT: Q 102 GLU cc_start: 0.7904 (tp30) cc_final: 0.7522 (tp30) REVERT: S 85 GLU cc_start: 0.6234 (pm20) cc_final: 0.5899 (mm-30) REVERT: S 201 GLN cc_start: 0.8128 (tp40) cc_final: 0.7846 (mm-40) REVERT: U 73 ARG cc_start: 0.7991 (OUTLIER) cc_final: 0.7611 (mtt90) REVERT: U 158 LYS cc_start: 0.8389 (mmtp) cc_final: 0.8158 (mmtm) REVERT: X 75 LEU cc_start: 0.8780 (OUTLIER) cc_final: 0.8437 (mp) REVERT: Y 51 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7036 (pt0) REVERT: Z 45 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7392 (mtp180) REVERT: a 74 ASP cc_start: 0.8011 (t70) cc_final: 0.7420 (t0) REVERT: a 95 LYS cc_start: 0.8288 (ttpt) cc_final: 0.7840 (pttp) REVERT: a 103 ILE cc_start: 0.8469 (mt) cc_final: 0.8063 (mm) REVERT: a 123 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.6116 (ptt90) REVERT: a 124 GLU cc_start: 0.7214 (pm20) cc_final: 0.6716 (mp0) REVERT: d 33 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: d 39 GLU cc_start: 0.6556 (mp0) cc_final: 0.6172 (mp0) REVERT: g 49 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7818 (ttmt) REVERT: g 60 GLN cc_start: 0.7830 (mt0) cc_final: 0.7604 (mt0) REVERT: h 13 TRP cc_start: 0.6225 (t60) cc_final: 0.5450 (t-100) REVERT: 1 64 LEU cc_start: 0.5493 (tp) cc_final: 0.5172 (mm) REVERT: 1 231 GLU cc_start: 0.7464 (OUTLIER) cc_final: 0.7100 (tt0) REVERT: 2 137 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8845 (tp) REVERT: 2 296 MET cc_start: 0.8033 (OUTLIER) cc_final: 0.7222 (mmt) REVERT: 4 11 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8339 (mp) REVERT: 4 159 ASP cc_start: 0.7142 (t70) cc_final: 0.6461 (t0) REVERT: 4 227 ILE cc_start: 0.7999 (mp) cc_final: 0.7748 (mm) REVERT: 5 63 GLU cc_start: 0.7738 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: 5 409 ILE cc_start: 0.8252 (OUTLIER) cc_final: 0.7883 (pp) REVERT: 5 511 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8347 (ttpp) REVERT: 6 30 MET cc_start: 0.7463 (ttp) cc_final: 0.7199 (ttp) REVERT: 6 59 TYR cc_start: 0.7900 (m-10) cc_final: 0.7553 (m-80) REVERT: 6 114 ASN cc_start: 0.7336 (m-40) cc_final: 0.6856 (t0) REVERT: 6 119 ILE cc_start: 0.7695 (pp) cc_final: 0.7337 (tp) REVERT: 8 14 LYS cc_start: 0.7898 (mtpp) cc_final: 0.7527 (mmmt) REVERT: 9 18 GLU cc_start: 0.8261 (mp0) cc_final: 0.7993 (mp0) REVERT: 9 58 ARG cc_start: 0.7178 (mmt90) cc_final: 0.6917 (mmm-85) outliers start: 322 outliers final: 130 residues processed: 1332 average time/residue: 1.3275 time to fit residues: 2354.9521 Evaluate side-chains 1170 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 157 poor density : 1013 time to evaluate : 5.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 286 GLU Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 669 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain C residue 46 GLU Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 147 MET Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 288 ASN Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 37 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain Y residue 51 GLU Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 143 PHE Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain g residue 49 LYS Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 231 GLU Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 195 LEU Chi-restraints excluded: chain 2 residue 219 LYS Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 327 ILE Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 426 ASN Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 511 LYS Chi-restraints excluded: chain 5 residue 527 VAL Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 546 VAL Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 58 LEU Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 98 LEU Chi-restraints excluded: chain 8 residue 39 LYS Chi-restraints excluded: chain 9 residue 9 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 627 optimal weight: 7.9990 chunk 427 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 561 optimal weight: 6.9990 chunk 311 optimal weight: 0.7980 chunk 643 optimal weight: 2.9990 chunk 521 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 384 optimal weight: 10.0000 chunk 676 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** A 222 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 62 ASN E 317 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN J 48 ASN K 200 ASN M 93 ASN ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 ASN Y 132 GLN Y 146 ASN c 18 GLN c 20 ASN d 27 GLN d 88 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 47 HIS ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 385 ASN 4 128 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 331 HIS 6 136 GLN 8 10 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 66697 Z= 0.515 Angle : 1.492 50.589 90319 Z= 0.954 Chirality : 0.286 6.411 10035 Planarity : 0.005 0.064 11276 Dihedral : 12.608 176.789 10520 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.65 % Favored : 95.33 % Rotamer: Outliers : 5.34 % Allowed : 20.93 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.09), residues: 7887 helix: 0.77 (0.08), residues: 4082 sheet: -0.50 (0.25), residues: 419 loop : -1.58 (0.10), residues: 3386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP e 10 HIS 0.008 0.001 HIS 2 320 PHE 0.029 0.002 PHE f 25 TYR 0.028 0.002 TYR 6 130 ARG 0.009 0.001 ARG P 62 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1448 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 365 poor density : 1083 time to evaluate : 5.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ARG cc_start: 0.7857 (ttt-90) cc_final: 0.7625 (ttp-170) REVERT: A 283 ARG cc_start: 0.8983 (OUTLIER) cc_final: 0.8617 (ptm-80) REVERT: A 359 MET cc_start: 0.7117 (mtm) cc_final: 0.6863 (mtm) REVERT: A 594 GLU cc_start: 0.7812 (mp0) cc_final: 0.7444 (mp0) REVERT: B 72 ASP cc_start: 0.5429 (p0) cc_final: 0.5224 (p0) REVERT: B 106 TRP cc_start: 0.7800 (p-90) cc_final: 0.7287 (p-90) REVERT: B 183 LEU cc_start: 0.6124 (OUTLIER) cc_final: 0.5685 (mm) REVERT: B 416 GLU cc_start: 0.8071 (OUTLIER) cc_final: 0.7810 (mm-30) REVERT: C 48 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7758 (m-70) REVERT: C 188 MET cc_start: 0.7813 (tpt) cc_final: 0.7064 (tpt) REVERT: C 348 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7381 (tt0) REVERT: E 201 ARG cc_start: 0.6341 (ttm110) cc_final: 0.5617 (tpp80) REVERT: E 213 PHE cc_start: 0.6335 (t80) cc_final: 0.6117 (m-80) REVERT: E 304 ILE cc_start: 0.5553 (OUTLIER) cc_final: 0.5228 (mm) REVERT: F 41 ASN cc_start: 0.7210 (t0) cc_final: 0.6713 (t0) REVERT: F 63 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8124 (mttm) REVERT: F 126 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7786 (pp) REVERT: F 129 LYS cc_start: 0.8068 (mptt) cc_final: 0.7797 (ttpp) REVERT: G 134 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8036 (mtp180) REVERT: H 141 MET cc_start: 0.7783 (ttm) cc_final: 0.7321 (tpt) REVERT: H 205 MET cc_start: 0.5954 (mmt) cc_final: 0.5743 (ppp) REVERT: I 82 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.7985 (pm20) REVERT: I 186 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8397 (mt-10) REVERT: J 58 LEU cc_start: 0.7301 (OUTLIER) cc_final: 0.6826 (pp) REVERT: J 149 GLN cc_start: 0.8532 (OUTLIER) cc_final: 0.8052 (mm110) REVERT: K 64 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7605 (tm) REVERT: K 165 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8543 (mpt180) REVERT: M 66 GLN cc_start: 0.6731 (mm110) cc_final: 0.6472 (mp10) REVERT: P 85 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7326 (tt0) REVERT: Q 56 GLN cc_start: 0.6512 (tp40) cc_final: 0.6106 (tp40) REVERT: Q 97 MET cc_start: 0.7240 (OUTLIER) cc_final: 0.6738 (tpt) REVERT: Q 102 GLU cc_start: 0.7860 (tp30) cc_final: 0.7470 (tp30) REVERT: R 35 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8287 (tt) REVERT: R 65 GLU cc_start: 0.7186 (tm-30) cc_final: 0.6838 (pp20) REVERT: S 85 GLU cc_start: 0.6203 (pm20) cc_final: 0.5909 (mm-30) REVERT: S 201 GLN cc_start: 0.8113 (tp40) cc_final: 0.7891 (mm-40) REVERT: U 73 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7634 (mtt90) REVERT: U 127 ASN cc_start: 0.7301 (t0) cc_final: 0.7043 (t0) REVERT: W 88 GLN cc_start: 0.8529 (tp40) cc_final: 0.8280 (tp-100) REVERT: W 92 GLU cc_start: 0.6987 (pt0) cc_final: 0.6751 (mt-10) REVERT: Y 51 GLU cc_start: 0.7528 (OUTLIER) cc_final: 0.7114 (pt0) REVERT: Z 45 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7645 (mtp180) REVERT: Z 54 GLU cc_start: 0.6945 (mm-30) cc_final: 0.6632 (mm-30) REVERT: a 103 ILE cc_start: 0.8468 (mt) cc_final: 0.8085 (mm) REVERT: a 123 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.6005 (ptt90) REVERT: a 124 GLU cc_start: 0.7243 (pm20) cc_final: 0.6758 (mp0) REVERT: d 33 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: d 39 GLU cc_start: 0.6590 (mp0) cc_final: 0.6206 (mp0) REVERT: f 7 GLU cc_start: 0.6453 (OUTLIER) cc_final: 0.5957 (pm20) REVERT: g 49 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7836 (ttmt) REVERT: g 60 GLN cc_start: 0.7853 (mt0) cc_final: 0.7638 (mt0) REVERT: h 13 TRP cc_start: 0.6172 (t60) cc_final: 0.5413 (t-100) REVERT: h 41 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.6981 (t80) REVERT: 1 64 LEU cc_start: 0.5194 (tp) cc_final: 0.4932 (mm) REVERT: 2 137 ILE cc_start: 0.9105 (OUTLIER) cc_final: 0.8882 (tp) REVERT: 2 296 MET cc_start: 0.8090 (OUTLIER) cc_final: 0.7311 (mmt) REVERT: 4 11 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8338 (mp) REVERT: 4 34 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8695 (mm) REVERT: 4 159 ASP cc_start: 0.7127 (t70) cc_final: 0.6408 (t0) REVERT: 5 62 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8697 (pt) REVERT: 5 63 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7141 (mm-30) REVERT: 5 107 MET cc_start: 0.9057 (OUTLIER) cc_final: 0.7755 (mmm) REVERT: 5 269 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8139 (pt) REVERT: 5 302 LYS cc_start: 0.8404 (OUTLIER) cc_final: 0.7860 (mttt) REVERT: 5 303 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7978 (ttm170) REVERT: 5 396 LYS cc_start: 0.8713 (OUTLIER) cc_final: 0.8286 (tttm) REVERT: 5 409 ILE cc_start: 0.8263 (OUTLIER) cc_final: 0.7891 (pp) REVERT: 5 507 THR cc_start: 0.7850 (m) cc_final: 0.7319 (p) REVERT: 5 511 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8352 (ttpp) REVERT: 5 524 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8541 (tp) REVERT: 6 59 TYR cc_start: 0.7891 (m-10) cc_final: 0.7675 (m-80) REVERT: 6 114 ASN cc_start: 0.7382 (m-40) cc_final: 0.6976 (t0) REVERT: 6 119 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7322 (tp) REVERT: 8 14 LYS cc_start: 0.7873 (mtpp) cc_final: 0.7478 (mmmt) REVERT: 9 58 ARG cc_start: 0.7065 (mmt90) cc_final: 0.6856 (mmm-85) outliers start: 365 outliers final: 165 residues processed: 1326 average time/residue: 1.3178 time to fit residues: 2317.5211 Evaluate side-chains 1220 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1015 time to evaluate : 5.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 457 MET Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 81 ILE Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 116 THR Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 82 GLU Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 94 THR Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 89 LYS Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain X residue 119 LYS Chi-restraints excluded: chain Y residue 51 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 70 SER Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain a residue 143 PHE Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain c residue 20 ASN Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 38 LEU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain g residue 49 LYS Chi-restraints excluded: chain h residue 41 TYR Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain n residue 96 SER Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 167 THR Chi-restraints excluded: chain 1 residue 246 LEU Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 133 GLN Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 327 ILE Chi-restraints excluded: chain 2 residue 340 GLN Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 426 ASN Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 21 GLN Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 417 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 463 ILE Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 5 residue 61 ASN Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 107 MET Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 269 ILE Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 302 LYS Chi-restraints excluded: chain 5 residue 303 ARG Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 396 LYS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 511 LYS Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 527 VAL Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 546 VAL Chi-restraints excluded: chain 5 residue 548 SER Chi-restraints excluded: chain 5 residue 616 MET Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 58 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 8 residue 39 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 253 optimal weight: 5.9990 chunk 678 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 442 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 754 optimal weight: 6.9990 chunk 626 optimal weight: 9.9990 chunk 349 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 249 optimal weight: 0.8980 chunk 396 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN A 222 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 62 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN K 200 ASN L 18 ASN M 93 ASN ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN a 146 GLN c 18 GLN c 20 ASN d 88 ASN ** g 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN ** 4 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 136 GLN 8 10 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 66697 Z= 0.500 Angle : 1.482 50.644 90319 Z= 0.950 Chirality : 0.285 6.421 10035 Planarity : 0.004 0.068 11276 Dihedral : 12.229 175.594 10520 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.34 % Favored : 95.65 % Rotamer: Outliers : 5.01 % Allowed : 21.91 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.09), residues: 7887 helix: 0.95 (0.08), residues: 4085 sheet: -0.48 (0.25), residues: 419 loop : -1.49 (0.10), residues: 3383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP e 10 HIS 0.006 0.001 HIS 4 197 PHE 0.020 0.001 PHE M 114 TYR 0.024 0.001 TYR a 96 ARG 0.012 0.000 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 342 poor density : 1070 time to evaluate : 5.602 Fit side-chains REVERT: A 359 MET cc_start: 0.7089 (mtm) cc_final: 0.6878 (mtm) REVERT: A 595 LYS cc_start: 0.8770 (OUTLIER) cc_final: 0.8563 (pttt) REVERT: B 56 ARG cc_start: 0.5880 (mmm160) cc_final: 0.5651 (mpt90) REVERT: B 106 TRP cc_start: 0.7776 (p-90) cc_final: 0.7257 (p-90) REVERT: B 129 ASP cc_start: 0.6618 (m-30) cc_final: 0.6295 (m-30) REVERT: B 183 LEU cc_start: 0.6403 (OUTLIER) cc_final: 0.5821 (mm) REVERT: B 291 GLU cc_start: 0.6858 (OUTLIER) cc_final: 0.6372 (tm-30) REVERT: B 402 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7397 (ttm-80) REVERT: B 413 MET cc_start: 0.7260 (ttt) cc_final: 0.7045 (ttt) REVERT: B 416 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7815 (mm-30) REVERT: C 188 MET cc_start: 0.7896 (tpt) cc_final: 0.7134 (tpt) REVERT: C 260 GLU cc_start: 0.7706 (tt0) cc_final: 0.7468 (tt0) REVERT: C 348 GLU cc_start: 0.7630 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: E 201 ARG cc_start: 0.6323 (ttm110) cc_final: 0.5618 (tpp80) REVERT: E 213 PHE cc_start: 0.6340 (OUTLIER) cc_final: 0.6001 (m-80) REVERT: E 304 ILE cc_start: 0.5678 (OUTLIER) cc_final: 0.5400 (mm) REVERT: E 333 LEU cc_start: 0.7311 (OUTLIER) cc_final: 0.6851 (pp) REVERT: F 41 ASN cc_start: 0.7155 (t0) cc_final: 0.6660 (t0) REVERT: F 63 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8156 (mttm) REVERT: F 117 MET cc_start: 0.7754 (mmp) cc_final: 0.7533 (mmp) REVERT: F 126 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7762 (pp) REVERT: F 129 LYS cc_start: 0.8090 (mptt) cc_final: 0.7791 (ttpp) REVERT: G 134 ARG cc_start: 0.8631 (OUTLIER) cc_final: 0.8064 (mtp180) REVERT: G 173 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.6952 (pt0) REVERT: H 141 MET cc_start: 0.7811 (ttm) cc_final: 0.7430 (tpt) REVERT: H 205 MET cc_start: 0.6019 (mmt) cc_final: 0.5788 (ppp) REVERT: I 146 THR cc_start: 0.9165 (OUTLIER) cc_final: 0.8851 (m) REVERT: I 186 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8368 (mt-10) REVERT: J 58 LEU cc_start: 0.7246 (OUTLIER) cc_final: 0.6811 (pp) REVERT: J 149 GLN cc_start: 0.8461 (OUTLIER) cc_final: 0.8066 (mm110) REVERT: K 64 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7700 (tm) REVERT: K 165 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8539 (mpt180) REVERT: M 66 GLN cc_start: 0.6744 (mm110) cc_final: 0.6512 (mp10) REVERT: P 85 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7428 (tt0) REVERT: Q 56 GLN cc_start: 0.6523 (tp40) cc_final: 0.6118 (tp40) REVERT: Q 97 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6696 (tpt) REVERT: Q 102 GLU cc_start: 0.7847 (tp30) cc_final: 0.7476 (tp30) REVERT: R 18 MET cc_start: 0.7292 (ttm) cc_final: 0.6960 (mtm) REVERT: R 35 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8278 (tt) REVERT: R 65 GLU cc_start: 0.7238 (tm-30) cc_final: 0.6816 (pp20) REVERT: S 85 GLU cc_start: 0.6203 (pm20) cc_final: 0.5947 (mm-30) REVERT: U 73 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.7670 (mtt90) REVERT: U 127 ASN cc_start: 0.7313 (t0) cc_final: 0.7104 (t0) REVERT: W 88 GLN cc_start: 0.8530 (tp40) cc_final: 0.8256 (tp-100) REVERT: W 96 MET cc_start: 0.6103 (mmm) cc_final: 0.5791 (tmm) REVERT: Y 51 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7145 (pt0) REVERT: Y 133 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.7467 (mp0) REVERT: Z 45 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7422 (mtp180) REVERT: Z 54 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6743 (mm-30) REVERT: a 95 LYS cc_start: 0.8303 (ttpp) cc_final: 0.7901 (tttp) REVERT: a 103 ILE cc_start: 0.8389 (mt) cc_final: 0.8032 (mm) REVERT: a 124 GLU cc_start: 0.7251 (pm20) cc_final: 0.6781 (mp0) REVERT: c 17 TYR cc_start: 0.8313 (m-80) cc_final: 0.8090 (m-10) REVERT: d 33 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.7272 (mp0) REVERT: d 39 GLU cc_start: 0.6580 (mp0) cc_final: 0.6177 (mp0) REVERT: f 7 GLU cc_start: 0.6452 (OUTLIER) cc_final: 0.5917 (pm20) REVERT: g 60 GLN cc_start: 0.7827 (mt0) cc_final: 0.7625 (mt0) REVERT: h 13 TRP cc_start: 0.6181 (t60) cc_final: 0.5409 (t-100) REVERT: h 41 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7707 (t80) REVERT: 1 6 VAL cc_start: 0.8850 (p) cc_final: 0.8601 (t) REVERT: 1 10 ILE cc_start: 0.8133 (OUTLIER) cc_final: 0.7930 (mp) REVERT: 1 64 LEU cc_start: 0.5209 (tp) cc_final: 0.4960 (mm) REVERT: 1 296 VAL cc_start: 0.9137 (OUTLIER) cc_final: 0.8864 (t) REVERT: 1 321 PHE cc_start: 0.8274 (m-80) cc_final: 0.7890 (m-80) REVERT: 2 131 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7435 (mp0) REVERT: 2 137 ILE cc_start: 0.9092 (OUTLIER) cc_final: 0.8876 (tp) REVERT: 2 296 MET cc_start: 0.8077 (OUTLIER) cc_final: 0.7247 (mmt) REVERT: 3 92 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8790 (mp) REVERT: 4 11 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8404 (mp) REVERT: 4 34 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8681 (mm) REVERT: 4 159 ASP cc_start: 0.7107 (t70) cc_final: 0.6379 (t0) REVERT: 5 62 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8721 (pt) REVERT: 5 63 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7162 (mm-30) REVERT: 5 302 LYS cc_start: 0.8342 (OUTLIER) cc_final: 0.7812 (mttt) REVERT: 5 303 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7928 (ttm170) REVERT: 5 409 ILE cc_start: 0.8203 (OUTLIER) cc_final: 0.7829 (pp) REVERT: 5 507 THR cc_start: 0.7782 (m) cc_final: 0.7198 (p) REVERT: 5 524 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8539 (tp) REVERT: 6 94 LEU cc_start: 0.8634 (OUTLIER) cc_final: 0.8398 (mm) REVERT: 6 110 MET cc_start: 0.7468 (tpt) cc_final: 0.7051 (tpt) REVERT: 6 119 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7428 (tp) REVERT: 8 14 LYS cc_start: 0.7828 (mtpp) cc_final: 0.7454 (mmmt) outliers start: 342 outliers final: 158 residues processed: 1312 average time/residue: 1.3212 time to fit residues: 2290.0526 Evaluate side-chains 1213 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1011 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 261 ILE Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain F residue 131 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain I residue 186 GLU Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 93 ASP Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain J residue 149 GLN Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain O residue 36 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 81 SER Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain Y residue 51 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 75 ASP Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 112 THR Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain h residue 41 TYR Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain 1 residue 10 ILE Chi-restraints excluded: chain 1 residue 15 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 167 THR Chi-restraints excluded: chain 1 residue 246 LEU Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 131 GLU Chi-restraints excluded: chain 2 residue 133 GLN Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 327 ILE Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 21 GLN Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 61 ASN Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 302 LYS Chi-restraints excluded: chain 5 residue 303 ARG Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 546 VAL Chi-restraints excluded: chain 5 residue 616 MET Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 58 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 94 LEU Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 8 residue 39 LYS Chi-restraints excluded: chain 9 residue 9 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 727 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 429 optimal weight: 6.9990 chunk 551 optimal weight: 0.9980 chunk 427 optimal weight: 4.9990 chunk 635 optimal weight: 10.0000 chunk 421 optimal weight: 4.9990 chunk 751 optimal weight: 0.8980 chunk 470 optimal weight: 9.9990 chunk 458 optimal weight: 7.9990 chunk 347 optimal weight: 5.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN D 29 HIS D 33 ASN E 62 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN M 85 GLN R 69 HIS S 201 GLN ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 ASN Y 132 GLN Y 146 ASN c 18 GLN c 20 ASN d 88 ASN g 21 HIS ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 114 ASN 6 120 ASN 6 136 GLN 8 10 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 66697 Z= 0.529 Angle : 1.499 50.595 90319 Z= 0.956 Chirality : 0.286 6.426 10035 Planarity : 0.005 0.057 11276 Dihedral : 12.161 179.979 10520 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 4.89 % Allowed : 22.56 % Favored : 72.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.09), residues: 7887 helix: 0.97 (0.08), residues: 4063 sheet: -0.45 (0.25), residues: 426 loop : -1.46 (0.10), residues: 3398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP e 10 HIS 0.008 0.001 HIS 8 49 PHE 0.025 0.002 PHE f 25 TYR 0.029 0.002 TYR 5 48 ARG 0.017 0.001 ARG g 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1395 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 334 poor density : 1061 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.7745 (mtpm) REVERT: A 283 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8639 (ptm-80) REVERT: A 293 ILE cc_start: 0.8739 (tt) cc_final: 0.8479 (tt) REVERT: A 359 MET cc_start: 0.7051 (mtm) cc_final: 0.6832 (mtm) REVERT: A 595 LYS cc_start: 0.8779 (OUTLIER) cc_final: 0.8551 (pttt) REVERT: B 106 TRP cc_start: 0.7801 (p-90) cc_final: 0.7272 (p-90) REVERT: B 183 LEU cc_start: 0.6430 (OUTLIER) cc_final: 0.5920 (mm) REVERT: B 291 GLU cc_start: 0.6785 (OUTLIER) cc_final: 0.6243 (tm-30) REVERT: B 402 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7418 (ttm-80) REVERT: B 416 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7789 (mm-30) REVERT: C 188 MET cc_start: 0.7920 (tpt) cc_final: 0.7207 (tpt) REVERT: C 348 GLU cc_start: 0.7656 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: E 201 ARG cc_start: 0.6348 (ttm110) cc_final: 0.5676 (tpp80) REVERT: E 304 ILE cc_start: 0.5785 (OUTLIER) cc_final: 0.5380 (mt) REVERT: E 333 LEU cc_start: 0.7316 (OUTLIER) cc_final: 0.6841 (pp) REVERT: F 41 ASN cc_start: 0.7206 (t0) cc_final: 0.6749 (t0) REVERT: F 63 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.8162 (mttm) REVERT: F 126 LEU cc_start: 0.8106 (OUTLIER) cc_final: 0.7872 (pp) REVERT: F 129 LYS cc_start: 0.8148 (mptt) cc_final: 0.7886 (ttpp) REVERT: G 37 GLU cc_start: 0.7565 (OUTLIER) cc_final: 0.6963 (mp0) REVERT: G 134 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8053 (mtp180) REVERT: G 173 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7053 (pt0) REVERT: H 141 MET cc_start: 0.7861 (ttm) cc_final: 0.7449 (tpt) REVERT: H 205 MET cc_start: 0.6014 (mmt) cc_final: 0.5696 (ppp) REVERT: K 64 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7783 (tm) REVERT: K 165 ARG cc_start: 0.8985 (OUTLIER) cc_final: 0.8509 (mpt180) REVERT: M 66 GLN cc_start: 0.6713 (mm110) cc_final: 0.6453 (mp10) REVERT: P 85 GLU cc_start: 0.7821 (mt-10) cc_final: 0.7381 (tt0) REVERT: Q 56 GLN cc_start: 0.6554 (tp40) cc_final: 0.6200 (tp40) REVERT: Q 97 MET cc_start: 0.7237 (OUTLIER) cc_final: 0.6673 (tpt) REVERT: Q 102 GLU cc_start: 0.7841 (tp30) cc_final: 0.7455 (tp30) REVERT: R 18 MET cc_start: 0.7408 (ttm) cc_final: 0.7161 (mtm) REVERT: R 35 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8301 (tt) REVERT: S 85 GLU cc_start: 0.6221 (pm20) cc_final: 0.5935 (mm-30) REVERT: S 201 GLN cc_start: 0.8223 (tp40) cc_final: 0.7812 (tp-100) REVERT: U 18 MET cc_start: 0.6913 (mmt) cc_final: 0.6643 (mmp) REVERT: U 73 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7636 (mtt90) REVERT: Y 51 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.7158 (pt0) REVERT: Y 133 GLU cc_start: 0.7991 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: Z 45 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.6539 (mtp180) REVERT: Z 54 GLU cc_start: 0.7101 (mm-30) cc_final: 0.6843 (mm-30) REVERT: a 74 ASP cc_start: 0.8076 (t70) cc_final: 0.7499 (t0) REVERT: a 78 ASP cc_start: 0.7873 (t0) cc_final: 0.7642 (t0) REVERT: a 103 ILE cc_start: 0.8457 (mt) cc_final: 0.8099 (mm) REVERT: a 123 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.6138 (ptt90) REVERT: a 124 GLU cc_start: 0.7291 (pm20) cc_final: 0.6806 (mp0) REVERT: c 17 TYR cc_start: 0.8376 (m-80) cc_final: 0.8127 (m-10) REVERT: d 33 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: f 7 GLU cc_start: 0.6467 (OUTLIER) cc_final: 0.5918 (pm20) REVERT: g 49 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7825 (ttmt) REVERT: h 13 TRP cc_start: 0.6151 (t60) cc_final: 0.5380 (t-100) REVERT: h 54 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7660 (mt) REVERT: h 123 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8745 (pp) REVERT: 1 321 PHE cc_start: 0.8311 (m-80) cc_final: 0.7948 (m-80) REVERT: 2 131 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7376 (mp0) REVERT: 2 137 ILE cc_start: 0.9134 (OUTLIER) cc_final: 0.8904 (tp) REVERT: 2 258 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8549 (tp) REVERT: 2 296 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7304 (mmt) REVERT: 4 11 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8404 (mp) REVERT: 4 34 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8702 (mm) REVERT: 4 159 ASP cc_start: 0.7119 (t70) cc_final: 0.6352 (t0) REVERT: 4 297 ASP cc_start: 0.8212 (t0) cc_final: 0.7940 (t0) REVERT: 5 62 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8770 (pt) REVERT: 5 269 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8207 (pt) REVERT: 5 302 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7910 (mttt) REVERT: 5 303 ARG cc_start: 0.8321 (OUTLIER) cc_final: 0.8020 (ttm170) REVERT: 5 396 LYS cc_start: 0.8712 (OUTLIER) cc_final: 0.8274 (tttm) REVERT: 5 409 ILE cc_start: 0.8261 (OUTLIER) cc_final: 0.7883 (pp) REVERT: 5 524 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8563 (tp) REVERT: 5 530 GLU cc_start: 0.7807 (tp30) cc_final: 0.6639 (tp30) REVERT: 6 94 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8424 (mm) REVERT: 6 110 MET cc_start: 0.7473 (tpt) cc_final: 0.7190 (tpt) REVERT: 6 119 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7461 (tp) REVERT: 8 14 LYS cc_start: 0.7824 (mtpp) cc_final: 0.7446 (mmmt) outliers start: 334 outliers final: 185 residues processed: 1293 average time/residue: 1.3307 time to fit residues: 2272.7831 Evaluate side-chains 1235 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1006 time to evaluate : 5.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LYS Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 310 THR Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 595 LYS Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 212 THR Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 416 GLU Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain G residue 37 GLU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain G residue 260 ASP Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 117 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain K residue 197 LYS Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 57 ILE Chi-restraints excluded: chain M residue 25 ASN Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain M residue 74 MET Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain Q residue 85 LEU Chi-restraints excluded: chain Q residue 97 MET Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 24 ASP Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 85 ASP Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 121 CYS Chi-restraints excluded: chain U residue 140 GLU Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain W residue 86 ILE Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain Y residue 51 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 112 THR Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 76 VAL Chi-restraints excluded: chain g residue 49 LYS Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 123 LEU Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 14 SER Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain n residue 86 LEU Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 15 VAL Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 98 THR Chi-restraints excluded: chain 1 residue 167 THR Chi-restraints excluded: chain 1 residue 228 PHE Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 1 residue 316 LEU Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 131 GLU Chi-restraints excluded: chain 2 residue 133 GLN Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 258 LEU Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 327 ILE Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 21 GLN Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 110 ASN Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 417 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 5 residue 61 ASN Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 249 LEU Chi-restraints excluded: chain 5 residue 269 ILE Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 302 LYS Chi-restraints excluded: chain 5 residue 303 ARG Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 359 ASP Chi-restraints excluded: chain 5 residue 396 LYS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 527 VAL Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 546 VAL Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 616 MET Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 58 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 94 LEU Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 9 residue 9 THR Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 465 optimal weight: 9.9990 chunk 300 optimal weight: 0.8980 chunk 449 optimal weight: 10.0000 chunk 226 optimal weight: 1.9990 chunk 147 optimal weight: 0.8980 chunk 145 optimal weight: 4.9990 chunk 477 optimal weight: 7.9990 chunk 512 optimal weight: 1.9990 chunk 371 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 590 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 405 GLN C 48 HIS C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN D 64 GLN E 62 ASN E 181 HIS ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN L 18 ASN R 69 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 127 ASN Y 132 GLN Y 146 ASN c 18 GLN c 20 ASN d 88 ASN g 60 GLN ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN 5 113 GLN ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 120 ASN 6 136 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.4606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 66697 Z= 0.498 Angle : 1.483 50.540 90319 Z= 0.950 Chirality : 0.285 6.379 10035 Planarity : 0.004 0.062 11276 Dihedral : 11.851 177.861 10520 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 11.24 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.37 % Favored : 95.61 % Rotamer: Outliers : 4.33 % Allowed : 23.74 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.09), residues: 7887 helix: 1.11 (0.08), residues: 4066 sheet: -0.40 (0.25), residues: 405 loop : -1.38 (0.10), residues: 3416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 9 19 HIS 0.008 0.001 HIS E 181 PHE 0.023 0.001 PHE f 25 TYR 0.023 0.001 TYR a 96 ARG 0.017 0.000 ARG g 67 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1340 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1044 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 HIS cc_start: 0.7194 (m-70) cc_final: 0.6953 (m90) REVERT: A 359 MET cc_start: 0.7060 (mtm) cc_final: 0.6845 (mtm) REVERT: B 106 TRP cc_start: 0.7806 (p-90) cc_final: 0.7285 (p-90) REVERT: B 183 LEU cc_start: 0.6420 (OUTLIER) cc_final: 0.6041 (mm) REVERT: B 291 GLU cc_start: 0.6662 (OUTLIER) cc_final: 0.6286 (tm-30) REVERT: B 402 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7358 (ttm-80) REVERT: C 188 MET cc_start: 0.7885 (tpt) cc_final: 0.7210 (tpt) REVERT: C 348 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7398 (tt0) REVERT: E 201 ARG cc_start: 0.6361 (ttm110) cc_final: 0.5907 (tpp80) REVERT: E 304 ILE cc_start: 0.5703 (OUTLIER) cc_final: 0.5314 (mt) REVERT: E 333 LEU cc_start: 0.7290 (OUTLIER) cc_final: 0.6824 (pp) REVERT: E 368 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.7823 (ttmm) REVERT: F 41 ASN cc_start: 0.7183 (t0) cc_final: 0.6716 (t0) REVERT: F 63 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8147 (mttm) REVERT: F 126 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7787 (pp) REVERT: F 129 LYS cc_start: 0.8154 (mptt) cc_final: 0.7864 (ttpp) REVERT: G 134 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8069 (mtp180) REVERT: G 173 GLU cc_start: 0.7302 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: H 141 MET cc_start: 0.7822 (ttm) cc_final: 0.7455 (tpt) REVERT: I 146 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8859 (m) REVERT: K 64 LEU cc_start: 0.8008 (OUTLIER) cc_final: 0.7753 (tm) REVERT: M 66 GLN cc_start: 0.6691 (mm110) cc_final: 0.6420 (mp10) REVERT: O 88 GLU cc_start: 0.7090 (mp0) cc_final: 0.6885 (mp0) REVERT: P 85 GLU cc_start: 0.7710 (mt-10) cc_final: 0.7333 (tt0) REVERT: Q 56 GLN cc_start: 0.6538 (tp40) cc_final: 0.6206 (tp40) REVERT: Q 102 GLU cc_start: 0.7810 (tp30) cc_final: 0.7439 (tp30) REVERT: R 18 MET cc_start: 0.7301 (ttm) cc_final: 0.7047 (mtm) REVERT: R 35 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8281 (tt) REVERT: R 65 GLU cc_start: 0.7363 (tm-30) cc_final: 0.6793 (pp20) REVERT: S 85 GLU cc_start: 0.6249 (pm20) cc_final: 0.5992 (mm-30) REVERT: U 18 MET cc_start: 0.6830 (mmt) cc_final: 0.6600 (mmp) REVERT: U 73 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7684 (mtt90) REVERT: Y 51 GLU cc_start: 0.7555 (OUTLIER) cc_final: 0.7159 (pt0) REVERT: Y 96 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7527 (mt) REVERT: Y 133 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7491 (mp0) REVERT: Z 45 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.6271 (mtp180) REVERT: Z 54 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6785 (mm-30) REVERT: a 74 ASP cc_start: 0.8030 (t70) cc_final: 0.7429 (t0) REVERT: a 123 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.6221 (ptt90) REVERT: a 124 GLU cc_start: 0.7267 (pm20) cc_final: 0.6781 (mp0) REVERT: a 133 GLU cc_start: 0.7085 (mp0) cc_final: 0.6761 (mp0) REVERT: c 17 TYR cc_start: 0.8353 (m-80) cc_final: 0.8121 (m-10) REVERT: d 33 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: f 7 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.5896 (pm20) REVERT: g 49 LYS cc_start: 0.8384 (OUTLIER) cc_final: 0.7825 (ttmt) REVERT: h 13 TRP cc_start: 0.6154 (t60) cc_final: 0.5393 (t-100) REVERT: h 54 ILE cc_start: 0.7816 (OUTLIER) cc_final: 0.7582 (mt) REVERT: 1 321 PHE cc_start: 0.8282 (m-80) cc_final: 0.7952 (m-80) REVERT: 2 131 GLU cc_start: 0.8136 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: 2 137 ILE cc_start: 0.9088 (OUTLIER) cc_final: 0.8888 (tp) REVERT: 2 296 MET cc_start: 0.8037 (OUTLIER) cc_final: 0.7202 (mmt) REVERT: 3 92 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8819 (mp) REVERT: 4 11 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8458 (mp) REVERT: 4 34 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8677 (mm) REVERT: 4 227 ILE cc_start: 0.8140 (mp) cc_final: 0.7851 (mm) REVERT: 5 62 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8742 (pt) REVERT: 5 396 LYS cc_start: 0.8683 (OUTLIER) cc_final: 0.8249 (tttm) REVERT: 5 409 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7825 (pp) REVERT: 5 524 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8544 (tp) REVERT: 6 58 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8614 (mp) REVERT: 6 110 MET cc_start: 0.7478 (tpt) cc_final: 0.7195 (tpt) REVERT: 6 119 ILE cc_start: 0.7717 (OUTLIER) cc_final: 0.7452 (tp) REVERT: 8 14 LYS cc_start: 0.7834 (mtpp) cc_final: 0.7435 (mmtt) REVERT: 8 25 ARG cc_start: 0.5712 (OUTLIER) cc_final: 0.5439 (ttm110) outliers start: 296 outliers final: 158 residues processed: 1244 average time/residue: 1.3447 time to fit residues: 2214.3870 Evaluate side-chains 1195 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 1000 time to evaluate : 5.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 257 LEU Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 469 LYS Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain K residue 64 LEU Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 54 LEU Chi-restraints excluded: chain M residue 29 ILE Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 46 ILE Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 121 CYS Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain Y residue 51 GLU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 75 ASP Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 112 THR Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 38 MET Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 76 VAL Chi-restraints excluded: chain g residue 49 LYS Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 66 LYS Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 149 ILE Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 131 GLU Chi-restraints excluded: chain 2 residue 133 GLN Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 21 GLN Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 246 LEU Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 5 residue 62 LEU Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 396 LYS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 616 MET Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 58 LEU Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 8 residue 25 ARG Chi-restraints excluded: chain 9 residue 9 THR Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 683 optimal weight: 5.9990 chunk 720 optimal weight: 0.0670 chunk 657 optimal weight: 7.9990 chunk 700 optimal weight: 4.9990 chunk 421 optimal weight: 0.8980 chunk 305 optimal weight: 10.0000 chunk 550 optimal weight: 9.9990 chunk 214 optimal weight: 10.0000 chunk 633 optimal weight: 3.9990 chunk 662 optimal weight: 2.9990 chunk 698 optimal weight: 2.9990 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 62 ASN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 158 HIS K 200 ASN R 69 HIS S 113 ASN ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 ASN Y 132 GLN Y 146 ASN c 18 GLN c 20 ASN d 88 ASN ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 128 ASN ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 120 ASN 6 136 GLN 6 183 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.243 66697 Z= 0.519 Angle : 1.495 50.647 90319 Z= 0.954 Chirality : 0.286 6.396 10035 Planarity : 0.004 0.061 11276 Dihedral : 11.800 178.538 10520 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.84 % Favored : 95.14 % Rotamer: Outliers : 3.92 % Allowed : 24.71 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.09), residues: 7887 helix: 1.12 (0.08), residues: 4043 sheet: -0.41 (0.25), residues: 420 loop : -1.36 (0.10), residues: 3424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP e 10 HIS 0.007 0.001 HIS 2 320 PHE 0.037 0.002 PHE n 37 TYR 0.023 0.002 TYR a 96 ARG 0.018 0.001 ARG g 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1029 time to evaluate : 5.810 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 HIS cc_start: 0.7234 (m-70) cc_final: 0.6982 (m90) REVERT: A 246 ARG cc_start: 0.7977 (mmt90) cc_final: 0.7748 (mmt-90) REVERT: A 283 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8561 (ptm-80) REVERT: A 504 PHE cc_start: 0.6857 (t80) cc_final: 0.6632 (t80) REVERT: A 513 ASN cc_start: 0.6819 (OUTLIER) cc_final: 0.6420 (p0) REVERT: B 106 TRP cc_start: 0.7815 (p-90) cc_final: 0.7286 (p-90) REVERT: B 183 LEU cc_start: 0.6492 (OUTLIER) cc_final: 0.6014 (mm) REVERT: B 291 GLU cc_start: 0.6623 (OUTLIER) cc_final: 0.6242 (tm-30) REVERT: B 402 ARG cc_start: 0.8402 (OUTLIER) cc_final: 0.7322 (ttm-80) REVERT: C 48 HIS cc_start: 0.8225 (OUTLIER) cc_final: 0.7480 (m90) REVERT: C 188 MET cc_start: 0.7907 (tpt) cc_final: 0.7319 (tpt) REVERT: C 348 GLU cc_start: 0.7649 (OUTLIER) cc_final: 0.7384 (tt0) REVERT: C 354 MET cc_start: 0.8846 (tpt) cc_final: 0.8642 (tpt) REVERT: E 201 ARG cc_start: 0.6324 (ttm110) cc_final: 0.5675 (tpp80) REVERT: E 304 ILE cc_start: 0.5799 (OUTLIER) cc_final: 0.5411 (mt) REVERT: E 333 LEU cc_start: 0.7357 (OUTLIER) cc_final: 0.6959 (pp) REVERT: E 368 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.7903 (ttmm) REVERT: F 41 ASN cc_start: 0.7224 (t0) cc_final: 0.6768 (t0) REVERT: F 63 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (mttm) REVERT: F 126 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7900 (pp) REVERT: F 129 LYS cc_start: 0.8196 (mptt) cc_final: 0.7914 (ttpp) REVERT: G 134 ARG cc_start: 0.8681 (OUTLIER) cc_final: 0.8082 (mtp180) REVERT: G 173 GLU cc_start: 0.7339 (OUTLIER) cc_final: 0.7093 (pt0) REVERT: H 141 MET cc_start: 0.7774 (ttm) cc_final: 0.7366 (tpt) REVERT: I 146 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8854 (m) REVERT: K 165 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.7105 (mtt180) REVERT: M 66 GLN cc_start: 0.6696 (mm110) cc_final: 0.6467 (mp10) REVERT: O 88 GLU cc_start: 0.7029 (mp0) cc_final: 0.6803 (mp0) REVERT: P 10 GLU cc_start: 0.7464 (tt0) cc_final: 0.7193 (tt0) REVERT: P 85 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7346 (tt0) REVERT: Q 56 GLN cc_start: 0.6556 (tp40) cc_final: 0.6234 (tp40) REVERT: Q 102 GLU cc_start: 0.7848 (tp30) cc_final: 0.7451 (tp30) REVERT: R 18 MET cc_start: 0.7359 (ttm) cc_final: 0.7088 (mtm) REVERT: R 35 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8283 (tt) REVERT: R 65 GLU cc_start: 0.7396 (tm-30) cc_final: 0.6827 (pp20) REVERT: U 18 MET cc_start: 0.6887 (mmt) cc_final: 0.6659 (mmp) REVERT: U 73 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7660 (mtt90) REVERT: W 96 MET cc_start: 0.6202 (mmm) cc_final: 0.5968 (mmm) REVERT: Y 96 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7602 (mt) REVERT: Y 133 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: Z 45 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.6419 (mtp180) REVERT: Z 54 GLU cc_start: 0.7072 (mm-30) cc_final: 0.6840 (mm-30) REVERT: a 74 ASP cc_start: 0.8064 (t70) cc_final: 0.7491 (t0) REVERT: a 78 ASP cc_start: 0.7937 (t0) cc_final: 0.7702 (t0) REVERT: a 123 ARG cc_start: 0.8400 (OUTLIER) cc_final: 0.6264 (ptt90) REVERT: c 17 TYR cc_start: 0.8409 (m-80) cc_final: 0.8168 (m-10) REVERT: d 33 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7257 (mp0) REVERT: f 7 GLU cc_start: 0.6483 (OUTLIER) cc_final: 0.5926 (pm20) REVERT: g 49 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.7787 (ttmt) REVERT: h 13 TRP cc_start: 0.6176 (t60) cc_final: 0.5420 (t-100) REVERT: h 54 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7601 (mt) REVERT: h 123 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8756 (pp) REVERT: 1 296 VAL cc_start: 0.9220 (OUTLIER) cc_final: 0.8941 (t) REVERT: 1 321 PHE cc_start: 0.8288 (m-80) cc_final: 0.7978 (m-80) REVERT: 2 131 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: 2 137 ILE cc_start: 0.9117 (OUTLIER) cc_final: 0.8901 (tp) REVERT: 2 296 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7374 (mmt) REVERT: 3 92 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8827 (mp) REVERT: 4 11 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8481 (mp) REVERT: 4 34 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8681 (mm) REVERT: 5 63 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7260 (mm-30) REVERT: 5 396 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8253 (tttm) REVERT: 5 409 ILE cc_start: 0.8234 (OUTLIER) cc_final: 0.7864 (pp) REVERT: 5 524 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8559 (tp) REVERT: 5 530 GLU cc_start: 0.7973 (tp30) cc_final: 0.6621 (tp30) REVERT: 6 58 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8653 (mp) REVERT: 6 94 LEU cc_start: 0.8782 (mm) cc_final: 0.8461 (mt) REVERT: 6 119 ILE cc_start: 0.7737 (OUTLIER) cc_final: 0.7483 (tp) REVERT: 8 14 LYS cc_start: 0.7832 (mtpp) cc_final: 0.7429 (mmtt) REVERT: 8 25 ARG cc_start: 0.5766 (OUTLIER) cc_final: 0.5529 (ttm110) outliers start: 268 outliers final: 158 residues processed: 1219 average time/residue: 1.3928 time to fit residues: 2245.6220 Evaluate side-chains 1192 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 993 time to evaluate : 5.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain H residue 28 HIS Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain Q residue 53 ASP Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain S residue 94 ILE Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 187 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 121 CYS Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 96 ILE Chi-restraints excluded: chain Y residue 116 GLU Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 112 THR Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 76 VAL Chi-restraints excluded: chain g residue 49 LYS Chi-restraints excluded: chain h residue 54 ILE Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 123 LEU Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 66 LYS Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 167 THR Chi-restraints excluded: chain 1 residue 228 PHE Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 1 residue 316 LEU Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 47 LEU Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 131 GLU Chi-restraints excluded: chain 2 residue 133 GLN Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 328 ILE Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 3 THR Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 21 GLN Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 110 ASN Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 5 residue 63 GLU Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 277 LEU Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 323 SER Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 396 LYS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 58 LEU Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 8 residue 25 ARG Chi-restraints excluded: chain 9 residue 9 THR Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 460 optimal weight: 7.9990 chunk 740 optimal weight: 3.9990 chunk 452 optimal weight: 0.8980 chunk 351 optimal weight: 7.9990 chunk 514 optimal weight: 5.9990 chunk 777 optimal weight: 1.9990 chunk 715 optimal weight: 0.8980 chunk 618 optimal weight: 1.9990 chunk 64 optimal weight: 7.9990 chunk 477 optimal weight: 6.9990 chunk 379 optimal weight: 7.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 673 GLN A 725 GLN ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 62 ASN E 181 HIS E 317 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 200 ASN R 69 HIS ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN Z 130 GLN c 18 GLN c 20 ASN d 88 ASN ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 278 GLN 4 128 ASN 4 235 HIS ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 617 ASN 6 120 ASN 6 136 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.244 66697 Z= 0.511 Angle : 1.496 50.616 90319 Z= 0.955 Chirality : 0.285 6.387 10035 Planarity : 0.004 0.064 11276 Dihedral : 11.666 178.290 10520 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.59 % Favored : 95.40 % Rotamer: Outliers : 3.50 % Allowed : 25.26 % Favored : 71.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.09), residues: 7887 helix: 1.13 (0.08), residues: 4046 sheet: -0.45 (0.26), residues: 410 loop : -1.32 (0.10), residues: 3431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP 9 19 HIS 0.007 0.001 HIS 4 441 PHE 0.021 0.001 PHE 3 94 TYR 0.024 0.002 TYR a 96 ARG 0.018 0.000 ARG g 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15774 Ramachandran restraints generated. 7887 Oldfield, 0 Emsley, 7887 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1034 time to evaluate : 5.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 PHE cc_start: 0.6860 (t80) cc_final: 0.6604 (t80) REVERT: A 513 ASN cc_start: 0.6814 (OUTLIER) cc_final: 0.6495 (p0) REVERT: B 106 TRP cc_start: 0.7790 (p-90) cc_final: 0.7196 (p-90) REVERT: B 183 LEU cc_start: 0.6547 (OUTLIER) cc_final: 0.6102 (mm) REVERT: B 291 GLU cc_start: 0.6599 (OUTLIER) cc_final: 0.6298 (tm-30) REVERT: B 402 ARG cc_start: 0.8406 (OUTLIER) cc_final: 0.7271 (ttm-80) REVERT: B 416 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7405 (mt-10) REVERT: C 48 HIS cc_start: 0.8255 (OUTLIER) cc_final: 0.7489 (m90) REVERT: C 188 MET cc_start: 0.7891 (tpt) cc_final: 0.7319 (tpt) REVERT: C 348 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7397 (tt0) REVERT: E 131 ARG cc_start: 0.5880 (tpp80) cc_final: 0.5629 (tpp80) REVERT: E 304 ILE cc_start: 0.5737 (OUTLIER) cc_final: 0.5370 (mt) REVERT: E 333 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.6993 (pp) REVERT: E 368 LYS cc_start: 0.8523 (OUTLIER) cc_final: 0.7900 (ttmm) REVERT: F 41 ASN cc_start: 0.7189 (t0) cc_final: 0.6755 (t0) REVERT: F 63 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8132 (mttm) REVERT: F 126 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7902 (pp) REVERT: F 129 LYS cc_start: 0.8207 (mptt) cc_final: 0.7925 (ttpp) REVERT: G 134 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8070 (mtp180) REVERT: G 173 GLU cc_start: 0.7359 (OUTLIER) cc_final: 0.7106 (pt0) REVERT: H 90 MET cc_start: 0.6978 (mtt) cc_final: 0.6641 (mtt) REVERT: H 141 MET cc_start: 0.7772 (ttm) cc_final: 0.7388 (tpt) REVERT: I 146 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8855 (m) REVERT: J 58 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.6860 (mt) REVERT: K 165 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7199 (mtt180) REVERT: M 66 GLN cc_start: 0.6702 (mm110) cc_final: 0.6486 (mp10) REVERT: P 10 GLU cc_start: 0.7446 (tt0) cc_final: 0.7178 (tt0) REVERT: P 85 GLU cc_start: 0.7727 (mt-10) cc_final: 0.7331 (tt0) REVERT: Q 56 GLN cc_start: 0.6549 (tp40) cc_final: 0.6206 (tp40) REVERT: Q 102 GLU cc_start: 0.7862 (tp30) cc_final: 0.7484 (tp30) REVERT: R 18 MET cc_start: 0.7431 (ttm) cc_final: 0.7167 (mtm) REVERT: R 35 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8284 (tt) REVERT: R 65 GLU cc_start: 0.7385 (tm-30) cc_final: 0.6826 (pp20) REVERT: U 73 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7659 (mtt90) REVERT: Y 133 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7474 (mp0) REVERT: Z 45 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.6281 (mtp180) REVERT: Z 54 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6869 (mm-30) REVERT: a 74 ASP cc_start: 0.8058 (t70) cc_final: 0.7479 (t0) REVERT: a 78 ASP cc_start: 0.7915 (t0) cc_final: 0.7693 (t0) REVERT: a 123 ARG cc_start: 0.8373 (OUTLIER) cc_final: 0.6316 (ptt90) REVERT: a 133 GLU cc_start: 0.7065 (mp0) cc_final: 0.6738 (mp0) REVERT: c 17 TYR cc_start: 0.8422 (m-80) cc_final: 0.8122 (m-80) REVERT: d 33 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: f 7 GLU cc_start: 0.6438 (OUTLIER) cc_final: 0.5985 (pm20) REVERT: g 49 LYS cc_start: 0.8365 (OUTLIER) cc_final: 0.7799 (ttmt) REVERT: h 13 TRP cc_start: 0.6206 (t60) cc_final: 0.5369 (t-100) REVERT: 1 296 VAL cc_start: 0.9217 (OUTLIER) cc_final: 0.8942 (t) REVERT: 1 321 PHE cc_start: 0.8287 (m-80) cc_final: 0.7983 (m-80) REVERT: 2 131 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7447 (mp0) REVERT: 2 137 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8909 (tp) REVERT: 2 296 MET cc_start: 0.8065 (OUTLIER) cc_final: 0.7266 (mmt) REVERT: 3 92 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8823 (mp) REVERT: 4 11 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8496 (mp) REVERT: 4 34 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8679 (mm) REVERT: 5 290 SER cc_start: 0.8626 (OUTLIER) cc_final: 0.8272 (p) REVERT: 5 303 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.7970 (ttm170) REVERT: 5 396 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8234 (tttm) REVERT: 5 409 ILE cc_start: 0.8246 (OUTLIER) cc_final: 0.7896 (pp) REVERT: 5 524 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8518 (tp) REVERT: 5 530 GLU cc_start: 0.7942 (tp30) cc_final: 0.6672 (tp30) REVERT: 6 94 LEU cc_start: 0.8750 (mm) cc_final: 0.8438 (mt) REVERT: 6 119 ILE cc_start: 0.7775 (OUTLIER) cc_final: 0.7469 (tp) REVERT: 8 14 LYS cc_start: 0.7826 (mtpp) cc_final: 0.7407 (mmtt) REVERT: 8 25 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.5515 (ttm110) outliers start: 239 outliers final: 156 residues processed: 1204 average time/residue: 1.4536 time to fit residues: 2344.2413 Evaluate side-chains 1185 residues out of total 6833 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 991 time to evaluate : 5.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 178 THR Chi-restraints excluded: chain A residue 229 VAL Chi-restraints excluded: chain A residue 322 ASN Chi-restraints excluded: chain A residue 349 VAL Chi-restraints excluded: chain A residue 375 THR Chi-restraints excluded: chain A residue 406 ASP Chi-restraints excluded: chain A residue 470 PHE Chi-restraints excluded: chain A residue 513 ASN Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 537 THR Chi-restraints excluded: chain A residue 657 VAL Chi-restraints excluded: chain B residue 183 LEU Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 291 GLU Chi-restraints excluded: chain B residue 347 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 402 ARG Chi-restraints excluded: chain B residue 431 ASP Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain C residue 48 HIS Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 71 ILE Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 220 VAL Chi-restraints excluded: chain C residue 235 VAL Chi-restraints excluded: chain C residue 348 GLU Chi-restraints excluded: chain C residue 353 ASP Chi-restraints excluded: chain C residue 374 MET Chi-restraints excluded: chain C residue 414 VAL Chi-restraints excluded: chain C residue 417 ASP Chi-restraints excluded: chain C residue 456 THR Chi-restraints excluded: chain C residue 458 ASP Chi-restraints excluded: chain C residue 465 ASP Chi-restraints excluded: chain D residue 14 ILE Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 125 VAL Chi-restraints excluded: chain E residue 137 ASN Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 213 PHE Chi-restraints excluded: chain E residue 304 ILE Chi-restraints excluded: chain E residue 333 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain F residue 63 LYS Chi-restraints excluded: chain F residue 64 ASP Chi-restraints excluded: chain F residue 110 GLU Chi-restraints excluded: chain F residue 126 LEU Chi-restraints excluded: chain G residue 42 ILE Chi-restraints excluded: chain G residue 126 ILE Chi-restraints excluded: chain G residue 134 ARG Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 217 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 119 MET Chi-restraints excluded: chain H residue 235 VAL Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 146 THR Chi-restraints excluded: chain I residue 156 SER Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain J residue 96 ASN Chi-restraints excluded: chain K residue 85 CYS Chi-restraints excluded: chain K residue 88 VAL Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 163 VAL Chi-restraints excluded: chain K residue 165 ARG Chi-restraints excluded: chain L residue 11 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 29 LEU Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 27 ASN Chi-restraints excluded: chain M residue 31 ILE Chi-restraints excluded: chain M residue 52 SER Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain O residue 74 VAL Chi-restraints excluded: chain O residue 93 LYS Chi-restraints excluded: chain O residue 96 ASN Chi-restraints excluded: chain P residue 6 THR Chi-restraints excluded: chain P residue 38 THR Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain S residue 115 HIS Chi-restraints excluded: chain S residue 154 ILE Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 165 VAL Chi-restraints excluded: chain S residue 175 SER Chi-restraints excluded: chain S residue 203 VAL Chi-restraints excluded: chain U residue 4 GLU Chi-restraints excluded: chain U residue 66 ILE Chi-restraints excluded: chain U residue 73 ARG Chi-restraints excluded: chain U residue 87 ASN Chi-restraints excluded: chain U residue 99 GLN Chi-restraints excluded: chain U residue 121 CYS Chi-restraints excluded: chain W residue 85 SER Chi-restraints excluded: chain X residue 8 VAL Chi-restraints excluded: chain X residue 10 THR Chi-restraints excluded: chain X residue 18 ASP Chi-restraints excluded: chain X residue 21 LEU Chi-restraints excluded: chain X residue 50 LEU Chi-restraints excluded: chain X residue 71 SER Chi-restraints excluded: chain X residue 75 LEU Chi-restraints excluded: chain X residue 101 VAL Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 116 GLU Chi-restraints excluded: chain Y residue 133 GLU Chi-restraints excluded: chain Z residue 35 SER Chi-restraints excluded: chain Z residue 45 ARG Chi-restraints excluded: chain a residue 44 ASP Chi-restraints excluded: chain a residue 81 SER Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 91 GLN Chi-restraints excluded: chain a residue 112 THR Chi-restraints excluded: chain a residue 123 ARG Chi-restraints excluded: chain b residue 61 LEU Chi-restraints excluded: chain d residue 33 GLU Chi-restraints excluded: chain d residue 63 CYS Chi-restraints excluded: chain e residue 20 SER Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain f residue 7 GLU Chi-restraints excluded: chain f residue 44 VAL Chi-restraints excluded: chain f residue 76 VAL Chi-restraints excluded: chain g residue 49 LYS Chi-restraints excluded: chain h residue 81 LEU Chi-restraints excluded: chain h residue 92 THR Chi-restraints excluded: chain h residue 133 VAL Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 66 LYS Chi-restraints excluded: chain j residue 55 SER Chi-restraints excluded: chain 1 residue 42 VAL Chi-restraints excluded: chain 1 residue 86 ILE Chi-restraints excluded: chain 1 residue 167 THR Chi-restraints excluded: chain 1 residue 228 PHE Chi-restraints excluded: chain 1 residue 247 LEU Chi-restraints excluded: chain 1 residue 296 VAL Chi-restraints excluded: chain 1 residue 309 ILE Chi-restraints excluded: chain 1 residue 339 THR Chi-restraints excluded: chain 2 residue 10 ILE Chi-restraints excluded: chain 2 residue 63 SER Chi-restraints excluded: chain 2 residue 131 GLU Chi-restraints excluded: chain 2 residue 133 GLN Chi-restraints excluded: chain 2 residue 137 ILE Chi-restraints excluded: chain 2 residue 171 SER Chi-restraints excluded: chain 2 residue 272 SER Chi-restraints excluded: chain 2 residue 273 VAL Chi-restraints excluded: chain 2 residue 296 MET Chi-restraints excluded: chain 2 residue 350 LEU Chi-restraints excluded: chain 2 residue 434 THR Chi-restraints excluded: chain 3 residue 92 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 21 GLN Chi-restraints excluded: chain 4 residue 34 LEU Chi-restraints excluded: chain 4 residue 37 LEU Chi-restraints excluded: chain 4 residue 62 SER Chi-restraints excluded: chain 4 residue 94 LEU Chi-restraints excluded: chain 4 residue 205 ASP Chi-restraints excluded: chain 4 residue 229 VAL Chi-restraints excluded: chain 4 residue 258 ILE Chi-restraints excluded: chain 4 residue 338 VAL Chi-restraints excluded: chain 4 residue 418 LEU Chi-restraints excluded: chain 4 residue 478 THR Chi-restraints excluded: chain 5 residue 31 VAL Chi-restraints excluded: chain 5 residue 103 SER Chi-restraints excluded: chain 5 residue 161 LEU Chi-restraints excluded: chain 5 residue 277 LEU Chi-restraints excluded: chain 5 residue 290 SER Chi-restraints excluded: chain 5 residue 303 ARG Chi-restraints excluded: chain 5 residue 351 HIS Chi-restraints excluded: chain 5 residue 396 LYS Chi-restraints excluded: chain 5 residue 409 ILE Chi-restraints excluded: chain 5 residue 425 THR Chi-restraints excluded: chain 5 residue 455 ASN Chi-restraints excluded: chain 5 residue 483 VAL Chi-restraints excluded: chain 5 residue 524 LEU Chi-restraints excluded: chain 5 residue 527 VAL Chi-restraints excluded: chain 5 residue 543 ILE Chi-restraints excluded: chain 5 residue 554 LEU Chi-restraints excluded: chain 5 residue 648 SER Chi-restraints excluded: chain 6 residue 75 ILE Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 91 ILE Chi-restraints excluded: chain 6 residue 119 ILE Chi-restraints excluded: chain 8 residue 25 ARG Chi-restraints excluded: chain 8 residue 30 LEU Chi-restraints excluded: chain 9 residue 9 THR Chi-restraints excluded: chain 9 residue 13 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 780 random chunks: chunk 491 optimal weight: 0.0570 chunk 659 optimal weight: 1.9990 chunk 189 optimal weight: 9.9990 chunk 570 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 171 optimal weight: 0.3980 chunk 619 optimal weight: 3.9990 chunk 259 optimal weight: 7.9990 chunk 636 optimal weight: 6.9990 chunk 78 optimal weight: 20.0000 chunk 114 optimal weight: 0.0980 overall best weight: 1.3102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 171 ASN ** A 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 337 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 283 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 288 ASN C 349 GLN ** C 367 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 ASN E 62 ASN E 317 GLN ** F 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 HIS K 51 GLN K 200 ASN L 18 ASN R 38 GLN ** R 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 69 HIS S 113 ASN ** S 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 132 GLN Y 146 ASN c 20 ASN d 88 ASN f 24 GLN g 60 GLN ** 2 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 278 GLN 4 128 ASN ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 638 ASN 6 120 ASN 6 136 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.153477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.118813 restraints weight = 84952.283| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.54 r_work: 0.3206 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.70 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3085 r_free = 0.3085 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3085 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.245 66697 Z= 0.498 Angle : 1.488 50.607 90319 Z= 0.952 Chirality : 0.285 6.366 10035 Planarity : 0.004 0.070 11276 Dihedral : 11.467 178.502 10520 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.62 % Favored : 95.37 % Rotamer: Outliers : 3.29 % Allowed : 25.64 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.26 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.09), residues: 7887 helix: 1.20 (0.08), residues: 4041 sheet: -0.44 (0.26), residues: 412 loop : -1.27 (0.10), residues: 3434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP e 10 HIS 0.006 0.001 HIS 4 197 PHE 0.040 0.001 PHE n 37 TYR 0.026 0.001 TYR 9 44 ARG 0.018 0.000 ARG g 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 32641.67 seconds wall clock time: 562 minutes 49.02 seconds (33769.02 seconds total)