Starting phenix.real_space_refine on Tue Feb 20 23:52:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7z_6057/02_2024/3j7z_6057_updated.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 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: 5 Type Number sf(0) Gaussians P 2974 5.49 5 S 90 5.16 5 C 45332 2.51 5 N 16874 2.21 5 O 25430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 GLU 31": "OE1" <-> "OE2" Residue "1 GLU 34": "OE1" <-> "OE2" Residue "1 PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 43": "NH1" <-> "NH2" Residue "2 ARG 3": "NH1" <-> "NH2" Residue "2 ARG 12": "NH1" <-> "NH2" Residue "2 ARG 14": "NH1" <-> "NH2" Residue "2 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 19": "NH1" <-> "NH2" Residue "2 ARG 21": "NH1" <-> "NH2" Residue "2 ARG 33": "NH1" <-> "NH2" Residue "2 ARG 41": "NH1" <-> "NH2" Residue "3 ARG 12": "NH1" <-> "NH2" Residue "3 ARG 29": "NH1" <-> "NH2" Residue "3 ARG 39": "NH1" <-> "NH2" Residue "3 ARG 41": "NH1" <-> "NH2" Residue "4 ARG 24": "NH1" <-> "NH2" Residue "5 GLU 17": "OE1" <-> "OE2" Residue "5 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ASP 124": "OD1" <-> "OD2" Residue "6 ASP 5": "OD1" <-> "OD2" Residue "6 GLU 9": "OE1" <-> "OE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 144": "OE1" <-> "OE2" Residue "C ARG 166": "NH1" <-> "NH2" Residue "C ARG 176": "NH1" <-> "NH2" Residue "C ARG 181": "NH1" <-> "NH2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "C ARG 188": "NH1" <-> "NH2" Residue "C GLU 198": "OE1" <-> "OE2" Residue "C ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C GLU 235": "OE1" <-> "OE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 17": "OE1" <-> "OE2" Residue "D GLU 30": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D GLU 64": "OE1" <-> "OE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D GLU 81": "OE1" <-> "OE2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 86": "OE1" <-> "OE2" Residue "D GLU 89": "OE1" <-> "OE2" Residue "D GLU 168": "OE1" <-> "OE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D GLU 183": "OE1" <-> "OE2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E GLU 152": "OE1" <-> "OE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 10": "OE1" <-> "OE2" Residue "F GLU 31": "OE1" <-> "OE2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F ARG 91": "NH1" <-> "NH2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F GLU 97": "OE1" <-> "OE2" Residue "F ARG 101": "NH1" <-> "NH2" Residue "F ARG 109": "NH1" <-> "NH2" Residue "F ARG 111": "NH1" <-> "NH2" Residue "F ARG 114": "NH1" <-> "NH2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F GLU 133": "OE1" <-> "OE2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G GLU 154": "OE1" <-> "OE2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G GLU 166": "OE1" <-> "OE2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "I GLU 49": "OE1" <-> "OE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K GLU 121": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L GLU 76": "OE1" <-> "OE2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L GLU 86": "OE1" <-> "OE2" Residue "L GLU 106": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M GLU 47": "OE1" <-> "OE2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 59": "NH1" <-> "NH2" Residue "M GLU 75": "OE1" <-> "OE2" Residue "M GLU 104": "OE1" <-> "OE2" Residue "M GLU 110": "OE1" <-> "OE2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "M PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 71": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 114": "OE1" <-> "OE2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O GLU 60": "OE1" <-> "OE2" Residue "O GLU 80": "OE1" <-> "OE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O GLU 112": "OE1" <-> "OE2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P GLU 33": "OE1" <-> "OE2" Residue "P ARG 38": "NH1" <-> "NH2" Residue "P GLU 43": "OE1" <-> "OE2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 61": "NH1" <-> "NH2" Residue "P ARG 88": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "Q ARG 2": "NH1" <-> "NH2" Residue "Q ARG 5": "NH1" <-> "NH2" Residue "Q ARG 12": "NH1" <-> "NH2" Residue "Q ARG 32": "NH1" <-> "NH2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q GLU 88": "OE1" <-> "OE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "OE1" <-> "OE2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 34": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R GLU 46": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R GLU 70": "OE1" <-> "OE2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 95": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 42": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ASP 8": "OD1" <-> "OD2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "V GLU 41": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "W GLU 16": "OE1" <-> "OE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "W PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 69": "OE1" <-> "OE2" Residue "W ARG 76": "NH1" <-> "NH2" Residue "W GLU 84": "OE1" <-> "OE2" Residue "X ARG 2": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 17": "NH1" <-> "NH2" Residue "X ARG 36": "NH1" <-> "NH2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y GLU 59": "OE1" <-> "OE2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z GLU 38": "OE1" <-> "OE2" Residue "Z ARG 44": "NH1" <-> "NH2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 90700 Number of models: 1 Model: "" Number of chains: 36 Chain: "0" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "1" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "2" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "3" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "4" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "5" Number of atoms: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1117 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 5, 'TRANS': 142} Chain: "6" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 227 Classifications: {'peptide': 30} Link IDs: {'TRANS': 29} Chain: "7" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Classifications: {'RNA': 3} Modifications used: {'5*END': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 61274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2854, 61274 Classifications: {'RNA': 2854} Modifications used: {'rna2p_pur': 270, 'rna2p_pyr': 144, 'rna3p_pur': 1378, 'rna3p_pyr': 1062} Link IDs: {'rna2p': 414, 'rna3p': 2439} Chain breaks: 3 Chain: "B" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 103} Chain: "C" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "F" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "G" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 166} Chain: "H" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 384 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "I" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1032 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "L" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1045 Classifications: {'peptide': 143} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "U" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 596 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'TRANS': 62} Chain: "Z" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 36 Classifications: {'peptide': 7} Incomplete info: {'c_alpha_only': 3} Link IDs: {'TRANS': 6} Unresolved chain links: 4 Unresolved chain link angles: 12 Unresolved chain link dihedrals: 12 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ERY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 34.63, per 1000 atoms: 0.38 Number of scatterers: 90700 At special positions: 0 Unit cell: (202.764, 208.304, 261.488, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 90 16.00 P 2974 15.00 O 25430 8.00 N 16874 7.00 C 45332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 14 " distance=2.06 Simple disulfide: pdb=" SG CYS 4 11 " - pdb=" SG CYS 4 27 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 14 " - pdb=" SG CYS 4 27 " distance=2.07 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 43.82 Conformation dependent library (CDL) restraints added in 3.9 seconds 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6302 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 106 helices and 41 sheets defined 24.5% alpha, 10.7% beta 965 base pairs and 1456 stacking pairs defined. Time for finding SS restraints: 44.11 Creating SS restraints... Processing helix chain '0' and resid 9 through 18 removed outlier: 4.721A pdb=" N HIS 0 18 " --> pdb=" O MET 0 14 " (cutoff:3.500A) Processing helix chain '2' and resid 9 through 16 Processing helix chain '2' and resid 18 through 23 Processing helix chain '2' and resid 25 through 36 Processing helix chain '3' and resid 7 through 10 No H-bonds generated for 'chain '3' and resid 7 through 10' Processing helix chain '3' and resid 37 through 43 Processing helix chain '3' and resid 54 through 60 Processing helix chain '4' and resid 31 through 33 No H-bonds generated for 'chain '4' and resid 31 through 33' Processing helix chain '5' and resid 4 through 7 No H-bonds generated for 'chain '5' and resid 4 through 7' Processing helix chain '5' and resid 9 through 18 removed outlier: 3.707A pdb=" N SER 5 16 " --> pdb=" O VAL 5 12 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU 5 17 " --> pdb=" O ALA 5 13 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL 5 18 " --> pdb=" O GLU 5 14 " (cutoff:3.500A) Processing helix chain '5' and resid 34 through 46 removed outlier: 3.584A pdb=" N GLU 5 40 " --> pdb=" O ASP 5 36 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ARG 5 42 " --> pdb=" O MET 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 60 through 63 No H-bonds generated for 'chain '5' and resid 60 through 63' Processing helix chain '5' and resid 95 through 103 removed outlier: 3.665A pdb=" N PHE 5 99 " --> pdb=" O LEU 5 95 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA 5 100 " --> pdb=" O PHE 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 137 Processing helix chain '5' and resid 140 through 147 removed outlier: 3.787A pdb=" N GLU 5 145 " --> pdb=" O ALA 5 141 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 6 No H-bonds generated for 'chain '6' and resid 4 through 6' Processing helix chain '6' and resid 16 through 19 No H-bonds generated for 'chain '6' and resid 16 through 19' Processing helix chain '6' and resid 25 through 28 No H-bonds generated for 'chain '6' and resid 25 through 28' Processing helix chain 'C' and resid 30 through 32 No H-bonds generated for 'chain 'C' and resid 30 through 32' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 198 through 201 Processing helix chain 'C' and resid 207 through 213 removed outlier: 3.502A pdb=" N ARG C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 223 No H-bonds generated for 'chain 'C' and resid 221 through 223' Processing helix chain 'C' and resid 263 through 265 No H-bonds generated for 'chain 'C' and resid 263 through 265' Processing helix chain 'D' and resid 57 through 59 No H-bonds generated for 'chain 'D' and resid 57 through 59' Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 98 through 101 Processing helix chain 'E' and resid 16 through 19 No H-bonds generated for 'chain 'E' and resid 16 through 19' Processing helix chain 'E' and resid 25 through 36 removed outlier: 3.591A pdb=" N VAL E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 98 through 112 Processing helix chain 'E' and resid 131 through 141 Processing helix chain 'E' and resid 155 through 159 Processing helix chain 'E' and resid 177 through 182 removed outlier: 3.547A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 199 removed outlier: 3.583A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 Processing helix chain 'F' and resid 12 through 19 removed outlier: 3.601A pdb=" N THR F 17 " --> pdb=" O LYS F 13 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 26 No H-bonds generated for 'chain 'F' and resid 24 through 26' Processing helix chain 'F' and resid 41 through 43 No H-bonds generated for 'chain 'F' and resid 41 through 43' Processing helix chain 'F' and resid 47 through 59 removed outlier: 3.673A pdb=" N ASN F 51 " --> pdb=" O LYS F 47 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ALA F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 104 Processing helix chain 'F' and resid 142 through 144 No H-bonds generated for 'chain 'F' and resid 142 through 144' Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 62 through 80 Processing helix chain 'G' and resid 137 through 151 removed outlier: 3.580A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 12 No H-bonds generated for 'chain 'H' and resid 10 through 12' Processing helix chain 'H' and resid 23 through 28 Processing helix chain 'H' and resid 43 through 46 No H-bonds generated for 'chain 'H' and resid 43 through 46' Processing helix chain 'I' and resid 24 through 27 removed outlier: 3.621A pdb=" N LEU I 27 " --> pdb=" O GLY I 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 24 through 27' Processing helix chain 'I' and resid 34 through 36 No H-bonds generated for 'chain 'I' and resid 34 through 36' Processing helix chain 'I' and resid 41 through 43 No H-bonds generated for 'chain 'I' and resid 41 through 43' Processing helix chain 'I' and resid 107 through 115 removed outlier: 4.481A pdb=" N LYS I 112 " --> pdb=" O ILE I 108 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ALA I 113 " --> pdb=" O ALA I 109 " (cutoff:3.500A) removed outlier: 5.263A pdb=" N ALA I 114 " --> pdb=" O GLN I 110 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ASP I 115 " --> pdb=" O THR I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 132 removed outlier: 3.929A pdb=" N ILE I 128 " --> pdb=" O MET I 124 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 8 through 10 No H-bonds generated for 'chain 'J' and resid 8 through 10' Processing helix chain 'J' and resid 27 through 37 removed outlier: 3.893A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 61 No H-bonds generated for 'chain 'J' and resid 59 through 61' Processing helix chain 'J' and resid 68 through 71 No H-bonds generated for 'chain 'J' and resid 68 through 71' Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 97 through 106 removed outlier: 3.940A pdb=" N ILE J 103 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 121 removed outlier: 3.573A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 133 through 135 No H-bonds generated for 'chain 'J' and resid 133 through 135' Processing helix chain 'K' and resid 72 through 74 No H-bonds generated for 'chain 'K' and resid 72 through 74' Processing helix chain 'K' and resid 105 through 107 No H-bonds generated for 'chain 'K' and resid 105 through 107' Processing helix chain 'K' and resid 113 through 117 Processing helix chain 'L' and resid 57 through 60 No H-bonds generated for 'chain 'L' and resid 57 through 60' Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 129 through 138 Processing helix chain 'M' and resid 43 through 57 removed outlier: 3.874A pdb=" N ALA M 56 " --> pdb=" O ALA M 52 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 123 removed outlier: 3.650A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 31 Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.526A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 60 through 68 Processing helix chain 'N' and resid 73 through 81 removed outlier: 4.465A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 87 Processing helix chain 'O' and resid 5 through 21 removed outlier: 4.275A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 56 through 59 No H-bonds generated for 'chain 'O' and resid 56 through 59' Processing helix chain 'O' and resid 68 through 85 removed outlier: 3.550A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) Processing helix chain 'O' and resid 104 through 112 removed outlier: 5.067A pdb=" N ALA O 109 " --> pdb=" O ALA O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 11 removed outlier: 3.688A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N GLU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 53 through 55 No H-bonds generated for 'chain 'P' and resid 53 through 55' Processing helix chain 'P' and resid 78 through 80 No H-bonds generated for 'chain 'P' and resid 78 through 80' Processing helix chain 'P' and resid 97 through 101 Processing helix chain 'P' and resid 104 through 106 No H-bonds generated for 'chain 'P' and resid 104 through 106' Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.968A pdb=" N GLN Q 19 " --> pdb=" O LYS Q 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 29 Processing helix chain 'Q' and resid 31 through 70 removed outlier: 4.149A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 84 Processing helix chain 'Q' and resid 94 through 100 removed outlier: 3.591A pdb=" N PHE Q 100 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 116 removed outlier: 3.602A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) Processing helix chain 'S' and resid 21 through 23 No H-bonds generated for 'chain 'S' and resid 21 through 23' Processing helix chain 'S' and resid 29 through 38 removed outlier: 3.646A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 61 Processing helix chain 'S' and resid 89 through 91 No H-bonds generated for 'chain 'S' and resid 89 through 91' Processing helix chain 'T' and resid 18 through 23 Processing helix chain 'T' and resid 41 through 52 removed outlier: 3.599A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N PHE T 51 " --> pdb=" O VAL T 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 68 No H-bonds generated for 'chain 'U' and resid 66 through 68' Processing helix chain 'V' and resid 14 through 23 Processing helix chain 'V' and resid 44 through 52 Processing helix chain 'V' and resid 54 through 58 Processing helix chain 'X' and resid 54 through 61 Processing helix chain 'X' and resid 63 through 71 removed outlier: 3.957A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 22 removed outlier: 3.617A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 33 Processing helix chain 'Y' and resid 40 through 58 removed outlier: 3.985A pdb=" N GLN Y 45 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 43 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG Y 47 " --> pdb=" O LYS Y 44 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ARG Y 48 " --> pdb=" O GLN Y 45 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU Y 56 " --> pdb=" O VAL Y 53 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N LEU Y 57 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ASN Y 58 " --> pdb=" O THR Y 55 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 26 Processing helix chain 'Z' and resid 41 through 49 Processing helix chain 'Z' and resid 51 through 53 No H-bonds generated for 'chain 'Z' and resid 51 through 53' Processing sheet with id= A, first strand: chain '0' and resid 27 through 29 Processing sheet with id= B, first strand: chain '1' and resid 6 through 11 Processing sheet with id= C, first strand: chain '1' and resid 35 through 39 Processing sheet with id= D, first strand: chain '4' and resid 17 through 19 Processing sheet with id= E, first strand: chain 'C' and resid 2 through 4 Processing sheet with id= F, first strand: chain 'C' and resid 79 through 81 removed outlier: 3.732A pdb=" N ARG C 79 " --> pdb=" O LEU C 92 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 180 through 183 removed outlier: 3.713A pdb=" N ALA C 165 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N ARG C 174 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ILE C 163 " --> pdb=" O ARG C 174 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 3 through 7 Processing sheet with id= I, first strand: chain 'D' and resid 12 through 15 Processing sheet with id= J, first strand: chain 'D' and resid 25 through 28 Processing sheet with id= K, first strand: chain 'D' and resid 80 through 83 removed outlier: 6.355A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 152 through 157 removed outlier: 6.828A pdb=" N THR F 67 " --> pdb=" O ILE F 84 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N CYS F 86 " --> pdb=" O LEU F 65 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU F 65 " --> pdb=" O CYS F 86 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 22 through 24 Processing sheet with id= N, first strand: chain 'G' and resid 40 through 43 Processing sheet with id= O, first strand: chain 'G' and resid 120 through 123 Processing sheet with id= P, first strand: chain 'J' and resid 17 through 19 removed outlier: 6.416A pdb=" N ILE J 55 " --> pdb=" O VAL J 18 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'J' and resid 75 through 77 Processing sheet with id= R, first strand: chain 'K' and resid 5 through 9 removed outlier: 3.509A pdb=" N CYS K 21 " --> pdb=" O GLN K 5 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N MET K 7 " --> pdb=" O VAL K 19 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N VAL K 19 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 74 through 76 removed outlier: 6.283A pdb=" N PHE L 107 " --> pdb=" O ALA L 75 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'L' and resid 89 through 91 removed outlier: 6.630A pdb=" N THR L 121 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS L 141 " --> pdb=" O VAL L 122 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'M' and resid 129 through 132 removed outlier: 3.693A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'M' and resid 39 through 42 Processing sheet with id= W, first strand: chain 'N' and resid 33 through 37 Processing sheet with id= X, first strand: chain 'O' and resid 91 through 93 removed outlier: 3.645A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'P' and resid 37 through 43 removed outlier: 3.778A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 70 through 74 removed outlier: 3.772A pdb=" N ALA P 48 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'R' and resid 11 through 14 removed outlier: 3.685A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N GLN R 6 " --> pdb=" O VAL R 38 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL R 38 " --> pdb=" O GLN R 6 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'R' and resid 20 through 23 Processing sheet with id= AC, first strand: chain 'R' and resid 32 through 35 Processing sheet with id= AD, first strand: chain 'R' and resid 72 through 78 removed outlier: 4.213A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'S' and resid 4 through 7 removed outlier: 6.577A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'T' and resid 61 through 63 removed outlier: 3.837A pdb=" N LEU T 61 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'T' and resid 11 through 14 removed outlier: 6.626A pdb=" N LYS T 33 " --> pdb=" O ARG T 12 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'U' and resid 21 through 23 Processing sheet with id= AI, first strand: chain 'U' and resid 40 through 45 Processing sheet with id= AJ, first strand: chain 'U' and resid 82 through 84 Processing sheet with id= AK, first strand: chain 'U' and resid 24 through 27 removed outlier: 6.884A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'V' and resid 62 through 65 removed outlier: 7.995A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL V 92 " --> pdb=" O ALA V 74 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N ALA V 74 " --> pdb=" O VAL V 92 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'X' and resid 12 through 14 Processing sheet with id= AN, first strand: chain 'X' and resid 35 through 38 Processing sheet with id= AO, first strand: chain 'Z' and resid 35 through 37 607 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2429 hydrogen bonds 3876 hydrogen bond angles 0 basepair planarities 965 basepair parallelities 1456 stacking parallelities Total time for adding SS restraints: 140.76 Time building geometry restraints manager: 46.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 9888 1.32 - 1.46: 47551 1.46 - 1.59: 37719 1.59 - 1.73: 3393 1.73 - 1.87: 163 Bond restraints: 98714 Sorted by residual: bond pdb=" C1 ERY A9000 " pdb=" O2 ERY A9000 " ideal model delta sigma weight residual 1.490 1.334 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" CA ILE W 35 " pdb=" CB ILE W 35 " ideal model delta sigma weight residual 1.544 1.621 -0.077 1.19e-02 7.06e+03 4.16e+01 bond pdb=" CA VAL 4 3 " pdb=" CB VAL 4 3 " ideal model delta sigma weight residual 1.545 1.491 0.054 9.10e-03 1.21e+04 3.54e+01 bond pdb=" CA VAL W 50 " pdb=" CB VAL W 50 " ideal model delta sigma weight residual 1.540 1.616 -0.076 1.36e-02 5.41e+03 3.11e+01 bond pdb=" CA GLU J 43 " pdb=" C GLU J 43 " ideal model delta sigma weight residual 1.524 1.453 0.071 1.32e-02 5.74e+03 2.86e+01 ... (remaining 98709 not shown) Histogram of bond angle deviations from ideal: 95.12 - 105.24: 15561 105.24 - 115.36: 68437 115.36 - 125.47: 53388 125.47 - 135.59: 10617 135.59 - 145.71: 22 Bond angle restraints: 148025 Sorted by residual: angle pdb=" C THR D 151 " pdb=" N PRO D 152 " pdb=" CA PRO D 152 " ideal model delta sigma weight residual 119.19 103.98 15.21 1.06e+00 8.90e-01 2.06e+02 angle pdb=" N THR 5 131 " pdb=" CA THR 5 131 " pdb=" C THR 5 131 " ideal model delta sigma weight residual 111.28 96.67 14.61 1.09e+00 8.42e-01 1.80e+02 angle pdb=" C ALA 5 92 " pdb=" N ALA 5 93 " pdb=" CA ALA 5 93 " ideal model delta sigma weight residual 121.54 145.71 -24.17 1.91e+00 2.74e-01 1.60e+02 angle pdb=" C ALA 5 93 " pdb=" N ARG 5 94 " pdb=" CA ARG 5 94 " ideal model delta sigma weight residual 121.54 144.35 -22.81 1.91e+00 2.74e-01 1.43e+02 angle pdb=" C LEU 5 72 " pdb=" N LYS 5 73 " pdb=" CA LYS 5 73 " ideal model delta sigma weight residual 121.18 140.14 -18.96 1.64e+00 3.72e-01 1.34e+02 ... (remaining 148020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.26: 55222 35.26 - 70.52: 7153 70.52 - 105.78: 835 105.78 - 141.04: 54 141.04 - 176.30: 33 Dihedral angle restraints: 63297 sinusoidal: 53516 harmonic: 9781 Sorted by residual: dihedral pdb=" C4' A 7 76 " pdb=" C3' A 7 76 " pdb=" C2' A 7 76 " pdb=" C1' A 7 76 " ideal model delta sinusoidal sigma weight residual 36.35 -35.91 72.26 1 3.10e+00 1.04e-01 6.95e+02 dihedral pdb=" O4' A 7 76 " pdb=" C4' A 7 76 " pdb=" C3' A 7 76 " pdb=" C2' A 7 76 " ideal model delta sinusoidal sigma weight residual -35.15 27.03 -62.18 1 4.00e+00 6.25e-02 3.20e+02 dihedral pdb=" O4' A 7 76 " pdb=" C2' A 7 76 " pdb=" C1' A 7 76 " pdb=" C3' A 7 76 " ideal model delta sinusoidal sigma weight residual 25.59 -33.41 59.00 3 3.80e+00 6.93e-02 1.48e+02 ... (remaining 63294 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.111: 18963 1.111 - 2.222: 7 2.222 - 3.333: 0 3.333 - 4.444: 0 4.444 - 5.556: 3 Chirality restraints: 18973 Sorted by residual: chirality pdb=" C6 ERY A9000 " pdb=" C32 ERY A9000 " pdb=" C5 ERY A9000 " pdb=" C7 ERY A9000 " both_signs ideal model delta sigma weight residual False -2.78 2.78 -5.56 2.00e-01 2.50e+01 7.72e+02 chirality pdb=" C12 ERY A9000 " pdb=" C11 ERY A9000 " pdb=" C13 ERY A9000 " pdb=" C35 ERY A9000 " both_signs ideal model delta sigma weight residual False -2.75 2.77 -5.52 2.00e-01 2.50e+01 7.62e+02 chirality pdb=" C16 ERY A9000 " pdb=" C15 ERY A9000 " pdb=" C17 ERY A9000 " pdb=" C19 ERY A9000 " both_signs ideal model delta sigma weight residual False 2.68 -2.61 5.29 2.00e-01 2.50e+01 6.99e+02 ... (remaining 18970 not shown) Planarity restraints: 7665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 ERY A9000 " 0.126 2.00e-02 2.50e+03 7.27e-02 5.29e+01 pdb=" C2 ERY A9000 " -0.037 2.00e-02 2.50e+03 pdb=" O1 ERY A9000 " -0.049 2.00e-02 2.50e+03 pdb=" O2 ERY A9000 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG K 71 " 0.070 5.00e-02 4.00e+02 1.06e-01 1.81e+01 pdb=" N PRO K 72 " -0.184 5.00e-02 4.00e+02 pdb=" CA PRO K 72 " 0.056 5.00e-02 4.00e+02 pdb=" CD PRO K 72 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' A A1509 " 0.055 2.00e-02 2.50e+03 2.43e-02 1.63e+01 pdb=" N9 A A1509 " -0.055 2.00e-02 2.50e+03 pdb=" C8 A A1509 " -0.003 2.00e-02 2.50e+03 pdb=" N7 A A1509 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A A1509 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A A1509 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A A1509 " 0.018 2.00e-02 2.50e+03 pdb=" N1 A A1509 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A A1509 " -0.001 2.00e-02 2.50e+03 pdb=" N3 A A1509 " -0.010 2.00e-02 2.50e+03 pdb=" C4 A A1509 " -0.010 2.00e-02 2.50e+03 ... (remaining 7662 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 23 2.12 - 2.82: 24399 2.82 - 3.51: 134016 3.51 - 4.21: 298887 4.21 - 4.90: 392909 Nonbonded interactions: 850234 Sorted by model distance: nonbonded pdb=" OP2 U A2506 " pdb=" N2 G A2576 " model vdw 1.426 2.520 nonbonded pdb=" C3' A 7 76 " pdb=" O ILE a 84 " model vdw 1.449 3.470 nonbonded pdb=" OP1 C A 912 " pdb=" NZ LYS M 8 " model vdw 1.791 2.520 nonbonded pdb=" O LEU 5 3 " pdb=" OD1 ASP 5 7 " model vdw 1.792 3.040 nonbonded pdb=" OP2 G A2061 " pdb=" NZ LYS E 63 " model vdw 1.881 2.520 ... (remaining 850229 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=0.89 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.420 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: 0.080 Extract box with map and model: 5.830 Check model and map are aligned: 1.260 Set scattering table: 0.780 Process input model: 319.870 Find NCS groups from input model: 1.790 Set up NCS constraints: 0.250 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 333.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 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 : 0.009 0.156 98714 Z= 0.568 Angle : 1.420 24.170 148025 Z= 0.747 Chirality : 0.095 5.556 18973 Planarity : 0.007 0.106 7665 Dihedral : 23.872 176.303 56986 Min Nonbonded Distance : 1.426 Molprobity Statistics. All-atom Clashscore : 11.65 Ramachandran Plot: Outliers : 6.47 % Allowed : 16.34 % Favored : 77.19 % Rotamer: Outliers : 10.91 % Allowed : 12.70 % Favored : 76.39 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.89 % Twisted General : 0.12 % 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: -5.00 (0.12), residues: 3385 helix: -3.74 (0.11), residues: 854 sheet: -2.82 (0.21), residues: 534 loop : -3.41 (0.12), residues: 1997 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP M 92 HIS 0.018 0.003 HIS S 7 PHE 0.038 0.004 PHE D 118 TYR 0.029 0.004 TYR J 75 ARG 0.026 0.002 ARG Q 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1266 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 304 poor density : 962 time to evaluate : 4.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 48 TYR cc_start: 0.8073 (t80) cc_final: 0.7861 (t80) REVERT: 2 9 VAL cc_start: 0.8276 (OUTLIER) cc_final: 0.7873 (t) REVERT: 2 13 ASN cc_start: 0.8530 (m-40) cc_final: 0.8032 (m-40) REVERT: 5 38 MET cc_start: 0.5084 (mtt) cc_final: 0.4492 (tpp) REVERT: 5 43 LYS cc_start: 0.3605 (OUTLIER) cc_final: 0.3180 (tmmm) REVERT: C 92 LEU cc_start: 0.7522 (tp) cc_final: 0.7189 (tp) REVERT: C 216 ARG cc_start: 0.8718 (mtp-110) cc_final: 0.8371 (ttp80) REVERT: D 188 LEU cc_start: 0.8117 (mt) cc_final: 0.7886 (mt) REVERT: D 193 VAL cc_start: 0.9263 (OUTLIER) cc_final: 0.9062 (m) REVERT: F 35 LEU cc_start: 0.0382 (OUTLIER) cc_final: 0.0138 (mt) REVERT: F 56 LEU cc_start: -0.3369 (OUTLIER) cc_final: -0.3642 (tt) REVERT: G 38 ASP cc_start: 0.4116 (OUTLIER) cc_final: 0.3632 (p0) REVERT: M 104 GLU cc_start: 0.7145 (mt-10) cc_final: 0.6801 (mt-10) REVERT: N 53 THR cc_start: 0.7002 (m) cc_final: 0.6597 (m) REVERT: O 10 ARG cc_start: 0.7243 (ttm110) cc_final: 0.6932 (mtp180) REVERT: P 16 VAL cc_start: 0.6799 (OUTLIER) cc_final: 0.6532 (t) REVERT: P 20 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6507 (ttt90) REVERT: Q 88 GLU cc_start: 0.6458 (OUTLIER) cc_final: 0.5274 (tt0) REVERT: R 1 MET cc_start: 0.4417 (tpp) cc_final: 0.3426 (ppp) REVERT: U 92 VAL cc_start: 0.7184 (OUTLIER) cc_final: 0.6786 (t) REVERT: X 39 VAL cc_start: 0.7256 (m) cc_final: 0.7030 (t) outliers start: 304 outliers final: 84 residues processed: 1139 average time/residue: 1.0216 time to fit residues: 1874.7761 Evaluate side-chains 797 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 703 time to evaluate : 3.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 8 ILE Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 2 residue 9 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 3 residue 31 ILE Chi-restraints excluded: chain 3 residue 56 LEU Chi-restraints excluded: chain 4 residue 27 CYS Chi-restraints excluded: chain 5 residue 26 VAL Chi-restraints excluded: chain 5 residue 42 ARG Chi-restraints excluded: chain 5 residue 43 LYS Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 70 GLU Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 125 ARG Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 12 LEU Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 151 ARG Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 82 LEU Chi-restraints excluded: chain L residue 100 ILE Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 72 PRO Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 70 THR Chi-restraints excluded: chain O residue 31 THR Chi-restraints excluded: chain O residue 36 TYR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 20 ARG Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 29 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 63 VAL Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 34 VAL Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 38 ILE Chi-restraints excluded: chain U residue 92 VAL Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 30 VAL Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 10 ARG Chi-restraints excluded: chain X residue 29 LEU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 9 THR Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 530 optimal weight: 9.9990 chunk 475 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 chunk 162 optimal weight: 20.0000 chunk 321 optimal weight: 20.0000 chunk 254 optimal weight: 30.0000 chunk 492 optimal weight: 0.0470 chunk 190 optimal weight: 30.0000 chunk 299 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 570 optimal weight: 10.0000 overall best weight: 7.8088 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 52 HIS C 69 ASN C 89 ASN ** C 141 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 130 GLN D 140 HIS E 163 ASN F 26 GLN F 62 GLN H 28 ASN J 40 HIS J 47 HIS J 58 ASN J 131 ASN L 99 ASN O 38 GLN O 43 ASN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN R 18 GLN R 66 HIS S 9 HIS T 15 HIS V 44 HIS V 80 HIS Y 15 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 98714 Z= 0.346 Angle : 0.914 27.108 148025 Z= 0.450 Chirality : 0.052 2.120 18973 Planarity : 0.007 0.102 7665 Dihedral : 23.874 178.982 50455 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.98 Ramachandran Plot: Outliers : 2.92 % Allowed : 12.26 % Favored : 84.82 % Rotamer: Outliers : 9.11 % Allowed : 19.95 % Favored : 70.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.33 % 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: -3.79 (0.13), residues: 3385 helix: -1.89 (0.16), residues: 854 sheet: -2.44 (0.20), residues: 568 loop : -2.93 (0.12), residues: 1963 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 125 HIS 0.016 0.002 HIS S 102 PHE 0.043 0.004 PHE U 86 TYR 0.027 0.003 TYR J 44 ARG 0.025 0.001 ARG S 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1032 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 778 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 28 ARG cc_start: 0.8460 (mtm-85) cc_final: 0.7988 (ttm-80) REVERT: 4 13 ASN cc_start: 0.7506 (m110) cc_final: 0.7210 (m-40) REVERT: 5 38 MET cc_start: 0.3647 (mtt) cc_final: 0.3122 (tpp) REVERT: 6 17 MET cc_start: 0.2809 (tpp) cc_final: 0.2565 (tpp) REVERT: C 81 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6414 (mt-10) REVERT: C 216 ARG cc_start: 0.8886 (mtp-110) cc_final: 0.8485 (ttp80) REVERT: D 13 ARG cc_start: 0.8363 (ptp90) cc_final: 0.7923 (ptm160) REVERT: D 159 LYS cc_start: 0.7989 (tptp) cc_final: 0.7738 (tppt) REVERT: D 160 LYS cc_start: 0.8418 (mttt) cc_final: 0.8048 (mttt) REVERT: D 201 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7809 (mp) REVERT: D 202 ILE cc_start: 0.9000 (mt) cc_final: 0.8423 (tt) REVERT: E 27 LEU cc_start: 0.8083 (OUTLIER) cc_final: 0.7681 (tp) REVERT: F 129 MET cc_start: 0.0504 (ptt) cc_final: -0.0237 (mmp) REVERT: I 48 ILE cc_start: 0.0488 (OUTLIER) cc_final: -0.0028 (mt) REVERT: J 128 ASN cc_start: 0.7587 (t0) cc_final: 0.7159 (m-40) REVERT: L 4 ASN cc_start: 0.7505 (p0) cc_final: 0.7051 (p0) REVERT: M 12 MET cc_start: 0.7731 (OUTLIER) cc_final: 0.7531 (mmt) REVERT: M 78 LEU cc_start: 0.7420 (tp) cc_final: 0.7203 (mm) REVERT: N 20 MET cc_start: 0.8092 (ttp) cc_final: 0.7669 (tmm) REVERT: N 71 ARG cc_start: 0.8584 (ttm-80) cc_final: 0.8274 (tpp80) REVERT: Q 18 LYS cc_start: 0.8197 (tppt) cc_final: 0.7964 (tptt) REVERT: Q 21 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7464 (ttpt) REVERT: Q 88 GLU cc_start: 0.6211 (OUTLIER) cc_final: 0.5303 (tt0) REVERT: R 83 TYR cc_start: 0.8607 (t80) cc_final: 0.8367 (t80) REVERT: S 6 LYS cc_start: 0.7373 (pttt) cc_final: 0.6841 (ptmt) REVERT: S 104 THR cc_start: 0.8781 (m) cc_final: 0.7977 (p) REVERT: T 37 ASP cc_start: 0.7372 (OUTLIER) cc_final: 0.6430 (t70) REVERT: T 54 GLU cc_start: 0.7729 (pm20) cc_final: 0.7067 (tm-30) REVERT: U 42 LYS cc_start: 0.6767 (OUTLIER) cc_final: 0.5981 (mtmt) REVERT: U 72 PHE cc_start: 0.5938 (t80) cc_final: 0.5517 (t80) REVERT: V 1 MET cc_start: 0.6557 (tmm) cc_final: 0.4975 (ptp) REVERT: V 83 LYS cc_start: 0.7929 (OUTLIER) cc_final: 0.7225 (mppt) REVERT: W 38 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7554 (mmt-90) REVERT: W 67 LYS cc_start: 0.8377 (tppt) cc_final: 0.7795 (ttmt) REVERT: Y 6 LEU cc_start: 0.6614 (tp) cc_final: 0.6349 (mm) outliers start: 254 outliers final: 152 residues processed: 937 average time/residue: 0.9457 time to fit residues: 1463.1766 Evaluate side-chains 841 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 679 time to evaluate : 3.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 42 ARG Chi-restraints excluded: chain 5 residue 43 LYS Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 96 PHE Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 125 ARG Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 194 VAL Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain D residue 201 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 27 LEU Chi-restraints excluded: chain E residue 28 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 118 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 180 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain G residue 3 VAL Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 110 HIS Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 3 VAL Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 84 ILE Chi-restraints excluded: chain J residue 105 VAL Chi-restraints excluded: chain J residue 129 GLU Chi-restraints excluded: chain J residue 140 LEU Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 63 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 67 THR Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 21 LYS Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 29 THR Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 42 LYS Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 92 VAL Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 38 ARG Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 46 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 35 VAL Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 43 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 316 optimal weight: 20.0000 chunk 176 optimal weight: 20.0000 chunk 474 optimal weight: 8.9990 chunk 388 optimal weight: 8.9990 chunk 157 optimal weight: 30.0000 chunk 571 optimal weight: 6.9990 chunk 617 optimal weight: 20.0000 chunk 508 optimal weight: 5.9990 chunk 566 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 458 optimal weight: 7.9990 overall best weight: 7.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 4 GLN 4 35 GLN ** 5 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN C 133 ASN C 152 GLN C 250 GLN D 150 GLN ** D 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 156 ASN E 163 ASN ** G 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN ** L 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 31 HIS O 104 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 71 ASN R 91 GLN ** S 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 19 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.5565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.108 98714 Z= 0.307 Angle : 0.800 27.048 148025 Z= 0.398 Chirality : 0.048 1.999 18973 Planarity : 0.006 0.107 7665 Dihedral : 23.737 179.649 50387 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 2.72 % Allowed : 12.58 % Favored : 84.70 % Rotamer: Outliers : 9.22 % Allowed : 22.57 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.36 (0.13), residues: 3385 helix: -1.22 (0.17), residues: 863 sheet: -2.37 (0.20), residues: 580 loop : -2.75 (0.13), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 78 HIS 0.008 0.002 HIS G 44 PHE 0.028 0.003 PHE N 67 TYR 0.018 0.002 TYR N 112 ARG 0.010 0.001 ARG L 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 752 time to evaluate : 3.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 4 LYS cc_start: 0.8489 (mttm) cc_final: 0.8062 (ttmm) REVERT: 4 13 ASN cc_start: 0.7405 (m110) cc_final: 0.6874 (m-40) REVERT: 5 38 MET cc_start: 0.4374 (mtt) cc_final: 0.2868 (tpp) REVERT: 5 52 MET cc_start: 0.3012 (mtp) cc_final: 0.2593 (mtp) REVERT: C 57 HIS cc_start: 0.7686 (OUTLIER) cc_final: 0.7294 (t-90) REVERT: C 110 LYS cc_start: 0.7753 (ptpt) cc_final: 0.7341 (ptpp) REVERT: C 127 ASN cc_start: 0.7246 (m-40) cc_final: 0.7010 (m-40) REVERT: C 191 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8039 (tt) REVERT: C 212 TRP cc_start: 0.8942 (p90) cc_final: 0.7625 (p90) REVERT: C 260 LYS cc_start: 0.8206 (mmmm) cc_final: 0.7880 (mmmm) REVERT: D 68 PHE cc_start: 0.6919 (m-80) cc_final: 0.6508 (m-80) REVERT: D 150 GLN cc_start: 0.8327 (tt0) cc_final: 0.8064 (tt0) REVERT: D 202 ILE cc_start: 0.9168 (mt) cc_final: 0.8755 (tt) REVERT: D 208 LYS cc_start: 0.5961 (mmtt) cc_final: 0.5331 (mmtp) REVERT: E 30 GLN cc_start: 0.8585 (tm-30) cc_final: 0.7813 (tm-30) REVERT: E 96 VAL cc_start: 0.8172 (t) cc_final: 0.7958 (t) REVERT: F 129 MET cc_start: 0.1277 (ptt) cc_final: 0.0225 (mmp) REVERT: H 1 MET cc_start: 0.6148 (tpp) cc_final: 0.5473 (tpp) REVERT: I 48 ILE cc_start: 0.0619 (OUTLIER) cc_final: 0.0095 (mt) REVERT: I 124 MET cc_start: -0.0219 (mmt) cc_final: -0.1345 (tmm) REVERT: I 135 MET cc_start: -0.0566 (mpp) cc_final: -0.0849 (mmm) REVERT: K 116 ILE cc_start: 0.7841 (tp) cc_final: 0.7603 (pt) REVERT: L 4 ASN cc_start: 0.7447 (p0) cc_final: 0.7002 (p0) REVERT: L 96 LYS cc_start: 0.7152 (ttmm) cc_final: 0.6645 (ttmm) REVERT: M 42 THR cc_start: 0.9345 (m) cc_final: 0.8703 (m) REVERT: N 20 MET cc_start: 0.8000 (ttp) cc_final: 0.7718 (tmm) REVERT: N 33 ILE cc_start: 0.8889 (tp) cc_final: 0.8452 (tt) REVERT: N 65 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7544 (mp) REVERT: O 38 GLN cc_start: 0.7872 (mp10) cc_final: 0.6762 (mt0) REVERT: O 103 VAL cc_start: 0.8443 (OUTLIER) cc_final: 0.8086 (t) REVERT: P 62 LYS cc_start: 0.8859 (tptm) cc_final: 0.8598 (tptm) REVERT: Q 18 LYS cc_start: 0.8547 (tppt) cc_final: 0.7907 (tptt) REVERT: Q 44 TYR cc_start: 0.8527 (m-80) cc_final: 0.8306 (m-80) REVERT: Q 55 GLN cc_start: 0.7949 (OUTLIER) cc_final: 0.7597 (mt0) REVERT: Q 88 GLU cc_start: 0.6017 (OUTLIER) cc_final: 0.5306 (tt0) REVERT: S 75 PHE cc_start: 0.8639 (p90) cc_final: 0.8419 (p90) REVERT: S 104 THR cc_start: 0.8683 (m) cc_final: 0.7862 (p) REVERT: T 79 ASP cc_start: 0.7660 (m-30) cc_final: 0.7408 (m-30) REVERT: V 1 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5424 (ptp) REVERT: V 18 ARG cc_start: 0.8386 (mmm-85) cc_final: 0.8177 (mmm-85) REVERT: V 78 GLN cc_start: 0.7852 (mm-40) cc_final: 0.7301 (mt0) REVERT: V 83 LYS cc_start: 0.7917 (OUTLIER) cc_final: 0.6943 (mppt) REVERT: W 37 VAL cc_start: 0.8314 (OUTLIER) cc_final: 0.7976 (t) REVERT: W 67 LYS cc_start: 0.8701 (tppt) cc_final: 0.8106 (ttmm) REVERT: X 33 HIS cc_start: 0.7078 (m90) cc_final: 0.6625 (m90) REVERT: Z 43 ILE cc_start: 0.8749 (pp) cc_final: 0.8170 (mt) outliers start: 257 outliers final: 155 residues processed: 911 average time/residue: 0.9160 time to fit residues: 1386.0270 Evaluate side-chains 828 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 663 time to evaluate : 3.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 180 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 35 LEU Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain F residue 114 ARG Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 102 GLU Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 46 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 65 LEU Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 104 GLN Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 69 VAL Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 58 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 66 ILE Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 18 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain W residue 37 VAL Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 50 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 564 optimal weight: 2.9990 chunk 429 optimal weight: 30.0000 chunk 296 optimal weight: 20.0000 chunk 63 optimal weight: 30.0000 chunk 272 optimal weight: 20.0000 chunk 383 optimal weight: 40.0000 chunk 573 optimal weight: 30.0000 chunk 607 optimal weight: 7.9990 chunk 299 optimal weight: 20.0000 chunk 543 optimal weight: 20.0000 chunk 163 optimal weight: 20.0000 overall best weight: 14.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 57 ASN C 36 ASN C 59 GLN C 238 ASN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN M 22 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 71 ASN R 6 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 60 HIS ** S 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS V 44 HIS X 16 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.7400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.118 98714 Z= 0.493 Angle : 1.042 27.404 148025 Z= 0.507 Chirality : 0.055 2.000 18973 Planarity : 0.008 0.105 7665 Dihedral : 24.156 179.854 50355 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 2.54 % Allowed : 13.80 % Favored : 83.66 % Rotamer: Outliers : 11.30 % Allowed : 23.90 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.71 (0.13), residues: 3385 helix: -1.70 (0.16), residues: 845 sheet: -2.49 (0.20), residues: 554 loop : -2.91 (0.12), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP Q 60 HIS 0.010 0.002 HIS N 16 PHE 0.039 0.004 PHE U 86 TYR 0.025 0.003 TYR F 127 ARG 0.017 0.001 ARG W 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1074 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 315 poor density : 759 time to evaluate : 3.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8186 (mtp180) cc_final: 0.7617 (ttm170) REVERT: 1 35 LEU cc_start: 0.7559 (OUTLIER) cc_final: 0.7346 (mp) REVERT: 3 4 LYS cc_start: 0.8991 (mttm) cc_final: 0.8409 (ttmm) REVERT: 4 13 ASN cc_start: 0.7122 (m110) cc_final: 0.6450 (m-40) REVERT: 5 38 MET cc_start: 0.4672 (mtt) cc_final: 0.2485 (tpp) REVERT: 5 52 MET cc_start: 0.3113 (mtp) cc_final: 0.2769 (mtp) REVERT: C 65 ASP cc_start: 0.8704 (t0) cc_final: 0.8357 (t0) REVERT: C 100 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7740 (mtm110) REVERT: C 166 ARG cc_start: 0.6250 (ptm160) cc_final: 0.5963 (ptp90) REVERT: C 191 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8428 (tt) REVERT: C 229 HIS cc_start: 0.8435 (t-90) cc_final: 0.8107 (t70) REVERT: D 13 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7823 (ptp90) REVERT: D 150 GLN cc_start: 0.8342 (tt0) cc_final: 0.8099 (tt0) REVERT: D 202 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8417 (tt) REVERT: D 208 LYS cc_start: 0.6706 (mmtt) cc_final: 0.6202 (mmtp) REVERT: E 30 GLN cc_start: 0.8856 (tm-30) cc_final: 0.8011 (tm-30) REVERT: E 73 ILE cc_start: 0.8928 (tp) cc_final: 0.8632 (tp) REVERT: E 199 MET cc_start: 0.7565 (ppp) cc_final: 0.6086 (mtp) REVERT: G 31 GLU cc_start: 0.4828 (OUTLIER) cc_final: 0.4195 (mp0) REVERT: G 148 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.7913 (ttt90) REVERT: I 16 MET cc_start: 0.5368 (mtp) cc_final: 0.5036 (mtp) REVERT: I 48 ILE cc_start: 0.0966 (OUTLIER) cc_final: 0.0003 (mm) REVERT: I 124 MET cc_start: 0.1047 (mmt) cc_final: -0.1480 (tmm) REVERT: K 106 GLU cc_start: 0.8496 (mm-30) cc_final: 0.8181 (mp0) REVERT: M 17 ASN cc_start: 0.8572 (t0) cc_final: 0.8235 (t0) REVERT: M 47 GLU cc_start: 0.7210 (OUTLIER) cc_final: 0.6945 (tm-30) REVERT: M 90 GLU cc_start: 0.6999 (OUTLIER) cc_final: 0.6723 (tt0) REVERT: N 20 MET cc_start: 0.8022 (ttp) cc_final: 0.7563 (tmm) REVERT: N 107 ASN cc_start: 0.7811 (t0) cc_final: 0.7091 (t0) REVERT: O 15 ARG cc_start: 0.8043 (mmt90) cc_final: 0.7822 (mmt90) REVERT: O 38 GLN cc_start: 0.7933 (mp10) cc_final: 0.7449 (mt0) REVERT: O 99 TYR cc_start: 0.7966 (t80) cc_final: 0.7628 (t80) REVERT: Q 44 TYR cc_start: 0.8672 (m-80) cc_final: 0.8350 (m-80) REVERT: Q 88 GLU cc_start: 0.6031 (OUTLIER) cc_final: 0.5512 (tt0) REVERT: R 84 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7625 (ptp-170) REVERT: S 68 ASP cc_start: 0.5697 (OUTLIER) cc_final: 0.5494 (p0) REVERT: S 69 LEU cc_start: 0.7028 (mt) cc_final: 0.6794 (mt) REVERT: S 75 PHE cc_start: 0.8692 (p90) cc_final: 0.8047 (p90) REVERT: T 18 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5573 (tt0) REVERT: T 37 ASP cc_start: 0.7346 (OUTLIER) cc_final: 0.6912 (t70) REVERT: U 72 PHE cc_start: 0.6766 (t80) cc_final: 0.6287 (t80) REVERT: V 78 GLN cc_start: 0.7906 (mm-40) cc_final: 0.7485 (mt0) REVERT: V 83 LYS cc_start: 0.8041 (OUTLIER) cc_final: 0.7192 (mppt) REVERT: W 67 LYS cc_start: 0.8779 (tppt) cc_final: 0.8227 (ttmm) REVERT: X 33 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6920 (m90) REVERT: Y 18 LEU cc_start: 0.8066 (tp) cc_final: 0.7861 (tp) REVERT: Y 42 LEU cc_start: 0.7532 (OUTLIER) cc_final: 0.7261 (mt) outliers start: 315 outliers final: 195 residues processed: 954 average time/residue: 0.9104 time to fit residues: 1445.4734 Evaluate side-chains 924 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 712 time to evaluate : 3.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 0 residue 27 LEU Chi-restraints excluded: chain 0 residue 42 ILE Chi-restraints excluded: chain 0 residue 43 THR Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 24 LYS Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 24 SER Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 6 residue 18 ASP Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 94 LEU Chi-restraints excluded: chain C residue 100 ARG Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 191 LEU Chi-restraints excluded: chain C residue 225 ASN Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 97 SER Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 15 SER Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 53 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 18 ILE Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 99 LYS Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 31 GLU Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 2 ILE Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 135 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 47 GLU Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 25 ARG Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 84 ARG Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 18 ARG Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 34 ASP Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 8 SER Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 40 GLU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 1 MET Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 41 HIS Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 505 optimal weight: 9.9990 chunk 344 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 451 optimal weight: 7.9990 chunk 250 optimal weight: 50.0000 chunk 518 optimal weight: 10.0000 chunk 419 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 309 optimal weight: 20.0000 chunk 544 optimal weight: 6.9990 chunk 153 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 152 GLN D 49 GLN ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 163 ASN E 195 GLN F 62 GLN G 37 ASN ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN H 28 ASN L 99 ASN ** N 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 104 GLN P 76 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 66 HIS ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN S 57 ASN W 49 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 98714 Z= 0.231 Angle : 0.744 27.723 148025 Z= 0.370 Chirality : 0.045 1.915 18973 Planarity : 0.005 0.108 7665 Dihedral : 23.814 179.340 50339 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 15.51 Ramachandran Plot: Outliers : 2.27 % Allowed : 12.82 % Favored : 84.90 % Rotamer: Outliers : 9.54 % Allowed : 26.26 % Favored : 64.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.28 (0.13), residues: 3385 helix: -1.14 (0.17), residues: 836 sheet: -2.21 (0.20), residues: 585 loop : -2.75 (0.12), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP Q 60 HIS 0.009 0.001 HIS G 114 PHE 0.035 0.002 PHE D 118 TYR 0.023 0.002 TYR H 25 ARG 0.014 0.001 ARG Q 50 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 994 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 728 time to evaluate : 3.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8074 (mtp180) cc_final: 0.7784 (ttp-110) REVERT: 3 4 LYS cc_start: 0.9006 (mttm) cc_final: 0.8428 (ttmm) REVERT: 4 13 ASN cc_start: 0.7037 (m110) cc_final: 0.6347 (m-40) REVERT: 5 38 MET cc_start: 0.4809 (mtt) cc_final: 0.2705 (tpp) REVERT: 5 52 MET cc_start: 0.3080 (OUTLIER) cc_final: 0.2675 (mtp) REVERT: 5 143 MET cc_start: 0.3950 (OUTLIER) cc_final: 0.3455 (tmt) REVERT: D 13 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.7532 (ptp90) REVERT: D 150 GLN cc_start: 0.8243 (tt0) cc_final: 0.8028 (tt0) REVERT: D 202 ILE cc_start: 0.9023 (mt) cc_final: 0.8570 (tt) REVERT: E 1 MET cc_start: 0.3234 (OUTLIER) cc_final: 0.2972 (ttt) REVERT: E 30 GLN cc_start: 0.8703 (tm-30) cc_final: 0.7810 (tm-30) REVERT: E 69 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7020 (mpt-90) REVERT: E 73 ILE cc_start: 0.8872 (tp) cc_final: 0.8582 (tp) REVERT: E 176 ASP cc_start: 0.6663 (p0) cc_final: 0.6457 (p0) REVERT: F 111 ARG cc_start: 0.4750 (OUTLIER) cc_final: 0.3635 (tpm170) REVERT: G 33 THR cc_start: 0.5952 (p) cc_final: 0.5587 (p) REVERT: G 112 VAL cc_start: 0.6043 (OUTLIER) cc_final: 0.5596 (t) REVERT: G 113 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6560 (m-30) REVERT: G 148 ARG cc_start: 0.8024 (ttm-80) cc_final: 0.7488 (ttt90) REVERT: I 16 MET cc_start: 0.5182 (mtp) cc_final: 0.4955 (mtp) REVERT: I 48 ILE cc_start: 0.1329 (OUTLIER) cc_final: 0.0314 (mm) REVERT: I 124 MET cc_start: 0.0825 (mmt) cc_final: -0.1388 (tmm) REVERT: L 100 ILE cc_start: 0.8542 (pp) cc_final: 0.8324 (pp) REVERT: N 20 MET cc_start: 0.7881 (ttp) cc_final: 0.7548 (tmm) REVERT: N 107 ASN cc_start: 0.7493 (t0) cc_final: 0.7138 (t0) REVERT: O 38 GLN cc_start: 0.7832 (mp10) cc_final: 0.7275 (mt0) REVERT: Q 44 TYR cc_start: 0.8512 (m-80) cc_final: 0.8199 (m-80) REVERT: Q 51 GLN cc_start: 0.6942 (tm-30) cc_final: 0.6149 (tm-30) REVERT: Q 88 GLU cc_start: 0.5853 (OUTLIER) cc_final: 0.5436 (tt0) REVERT: T 18 GLU cc_start: 0.5924 (OUTLIER) cc_final: 0.5233 (tp30) REVERT: T 37 ASP cc_start: 0.7065 (OUTLIER) cc_final: 0.6812 (t70) REVERT: T 48 GLN cc_start: 0.8375 (mm-40) cc_final: 0.8075 (mm110) REVERT: T 89 GLU cc_start: 0.7441 (tp30) cc_final: 0.7056 (tp30) REVERT: U 21 ARG cc_start: 0.6402 (ptp-110) cc_final: 0.5725 (ptp-110) REVERT: U 40 LEU cc_start: 0.8565 (mp) cc_final: 0.8239 (tt) REVERT: U 72 PHE cc_start: 0.6714 (t80) cc_final: 0.6309 (t80) REVERT: V 78 GLN cc_start: 0.7642 (mm-40) cc_final: 0.7290 (mt0) REVERT: V 83 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.7185 (mppt) REVERT: W 8 SER cc_start: 0.8390 (m) cc_final: 0.7788 (p) REVERT: X 33 HIS cc_start: 0.7003 (OUTLIER) cc_final: 0.6628 (m90) REVERT: Y 18 LEU cc_start: 0.7932 (tp) cc_final: 0.7548 (tt) REVERT: Z 43 ILE cc_start: 0.8951 (pp) cc_final: 0.8346 (mt) outliers start: 266 outliers final: 186 residues processed: 881 average time/residue: 0.9272 time to fit residues: 1366.1131 Evaluate side-chains 886 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 686 time to evaluate : 3.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 35 LEU Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 33 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 GLN Chi-restraints excluded: chain C residue 238 ASN Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 110 GLU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 88 ARG Chi-restraints excluded: chain P residue 91 VAL Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 22 VAL Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 204 optimal weight: 10.0000 chunk 546 optimal weight: 10.0000 chunk 119 optimal weight: 20.0000 chunk 356 optimal weight: 0.9980 chunk 149 optimal weight: 50.0000 chunk 607 optimal weight: 7.9990 chunk 504 optimal weight: 30.0000 chunk 281 optimal weight: 20.0000 chunk 50 optimal weight: 30.0000 chunk 200 optimal weight: 20.0000 chunk 318 optimal weight: 20.0000 overall best weight: 9.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 GLN E 163 ASN E 165 HIS ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 76 HIS Q 55 GLN ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN S 57 ASN S 61 ASN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.7902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.108 98714 Z= 0.344 Angle : 0.842 27.338 148025 Z= 0.413 Chirality : 0.049 1.957 18973 Planarity : 0.006 0.118 7665 Dihedral : 23.879 179.403 50339 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 18.19 Ramachandran Plot: Outliers : 2.16 % Allowed : 14.65 % Favored : 83.19 % Rotamer: Outliers : 10.33 % Allowed : 27.16 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.32 (0.13), residues: 3385 helix: -1.23 (0.17), residues: 834 sheet: -2.07 (0.21), residues: 556 loop : -2.79 (0.12), residues: 1995 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 61 HIS 0.012 0.002 HIS T 70 PHE 0.027 0.003 PHE Y 26 TYR 0.019 0.002 TYR 5 51 ARG 0.013 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1000 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 712 time to evaluate : 5.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8198 (mtp180) cc_final: 0.7876 (ttp-110) REVERT: 3 4 LYS cc_start: 0.9062 (mttm) cc_final: 0.8521 (ttmm) REVERT: 5 38 MET cc_start: 0.4994 (mtt) cc_final: 0.2719 (tpp) REVERT: 5 52 MET cc_start: 0.2937 (OUTLIER) cc_final: 0.1949 (mtm) REVERT: 5 143 MET cc_start: 0.4349 (OUTLIER) cc_final: 0.3681 (tmt) REVERT: C 57 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7228 (t-90) REVERT: C 184 GLU cc_start: 0.6536 (OUTLIER) cc_final: 0.6323 (tt0) REVERT: D 13 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7618 (ptp90) REVERT: D 150 GLN cc_start: 0.8258 (tt0) cc_final: 0.8053 (tt0) REVERT: D 202 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8645 (tt) REVERT: E 30 GLN cc_start: 0.8821 (tm-30) cc_final: 0.7913 (tm-30) REVERT: E 69 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7136 (mpt-90) REVERT: F 111 ARG cc_start: 0.5099 (OUTLIER) cc_final: 0.4666 (mpt180) REVERT: G 113 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6738 (m-30) REVERT: G 148 ARG cc_start: 0.8144 (ttm-80) cc_final: 0.7590 (ttt90) REVERT: I 16 MET cc_start: 0.5230 (mtp) cc_final: 0.4937 (mtp) REVERT: I 48 ILE cc_start: 0.1549 (OUTLIER) cc_final: 0.0732 (mm) REVERT: I 124 MET cc_start: 0.1026 (mmt) cc_final: -0.1322 (tmm) REVERT: K 106 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7484 (mm-30) REVERT: M 90 GLU cc_start: 0.7036 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: N 20 MET cc_start: 0.7861 (ttp) cc_final: 0.7554 (tmm) REVERT: O 38 GLN cc_start: 0.7901 (mp10) cc_final: 0.7421 (mt0) REVERT: O 61 GLN cc_start: 0.6109 (OUTLIER) cc_final: 0.5863 (pt0) REVERT: O 99 TYR cc_start: 0.7979 (t80) cc_final: 0.7629 (t80) REVERT: Q 44 TYR cc_start: 0.8556 (m-80) cc_final: 0.8242 (m-80) REVERT: Q 88 GLU cc_start: 0.5955 (OUTLIER) cc_final: 0.5472 (tt0) REVERT: T 18 GLU cc_start: 0.6279 (OUTLIER) cc_final: 0.5441 (tp30) REVERT: T 37 ASP cc_start: 0.7003 (OUTLIER) cc_final: 0.6696 (t70) REVERT: T 48 GLN cc_start: 0.8289 (mm-40) cc_final: 0.8083 (mm110) REVERT: T 89 GLU cc_start: 0.7455 (tp30) cc_final: 0.7070 (tp30) REVERT: U 21 ARG cc_start: 0.6666 (ptp-110) cc_final: 0.5882 (ptp-110) REVERT: U 40 LEU cc_start: 0.8530 (mp) cc_final: 0.8251 (tt) REVERT: U 72 PHE cc_start: 0.6763 (t80) cc_final: 0.6246 (t80) REVERT: V 78 GLN cc_start: 0.7721 (mm-40) cc_final: 0.7260 (mt0) REVERT: V 83 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7207 (mppt) REVERT: X 17 ARG cc_start: 0.7985 (mmt-90) cc_final: 0.7635 (mmt-90) REVERT: X 33 HIS cc_start: 0.7285 (OUTLIER) cc_final: 0.6883 (m90) REVERT: Y 18 LEU cc_start: 0.8016 (tp) cc_final: 0.7601 (tt) REVERT: Y 48 ARG cc_start: 0.8065 (mmt-90) cc_final: 0.7727 (mmt-90) REVERT: Z 43 ILE cc_start: 0.8982 (pp) cc_final: 0.8293 (mt) REVERT: a 84 ILE cc_start: 0.6837 (pt) cc_final: 0.6547 (pt) outliers start: 288 outliers final: 216 residues processed: 885 average time/residue: 0.8946 time to fit residues: 1332.0018 Evaluate side-chains 922 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 689 time to evaluate : 3.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 4 residue 10 LEU Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 4 residue 26 ILE Chi-restraints excluded: chain 5 residue 24 SER Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 102 TYR Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 97 ASN Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 ASN Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 48 ILE Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 69 VAL Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 90 GLU Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 119 LEU Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 52 SER Chi-restraints excluded: chain O residue 61 GLN Chi-restraints excluded: chain O residue 89 ASP Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 59 THR Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 89 ILE Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 15 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 28 LYS Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 58 VAL Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 10 VAL Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 42 LEU Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 585 optimal weight: 20.0000 chunk 68 optimal weight: 40.0000 chunk 346 optimal weight: 5.9990 chunk 443 optimal weight: 30.0000 chunk 343 optimal weight: 7.9990 chunk 511 optimal weight: 0.8980 chunk 339 optimal weight: 3.9990 chunk 605 optimal weight: 7.9990 chunk 378 optimal weight: 3.9990 chunk 369 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN P 76 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 56 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.8048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 98714 Z= 0.200 Angle : 0.701 27.658 148025 Z= 0.347 Chirality : 0.044 1.914 18973 Planarity : 0.005 0.107 7665 Dihedral : 23.733 179.617 50335 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 2.13 % Allowed : 12.61 % Favored : 85.26 % Rotamer: Outliers : 8.32 % Allowed : 29.71 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -3.04 (0.14), residues: 3385 helix: -0.99 (0.18), residues: 843 sheet: -1.91 (0.22), residues: 520 loop : -2.62 (0.13), residues: 2022 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP Q 60 HIS 0.011 0.001 HIS J 40 PHE 0.039 0.002 PHE N 67 TYR 0.019 0.002 TYR 5 51 ARG 0.011 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 951 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 719 time to evaluate : 3.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8131 (mtp180) cc_final: 0.7698 (ttp-110) REVERT: 3 4 LYS cc_start: 0.8979 (mttm) cc_final: 0.8483 (ttmm) REVERT: 5 38 MET cc_start: 0.4945 (mtt) cc_final: 0.2473 (tpp) REVERT: 5 52 MET cc_start: 0.3728 (OUTLIER) cc_final: 0.2469 (mtm) REVERT: 5 143 MET cc_start: 0.4193 (OUTLIER) cc_final: 0.3515 (tmt) REVERT: C 57 HIS cc_start: 0.8157 (OUTLIER) cc_final: 0.7189 (t-90) REVERT: C 184 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.6334 (tt0) REVERT: C 264 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.8003 (tttt) REVERT: D 13 ARG cc_start: 0.8250 (OUTLIER) cc_final: 0.7739 (ptm160) REVERT: D 202 ILE cc_start: 0.9100 (mt) cc_final: 0.8646 (tt) REVERT: E 1 MET cc_start: 0.4750 (OUTLIER) cc_final: 0.3216 (tmm) REVERT: E 30 GLN cc_start: 0.8756 (tm-30) cc_final: 0.7711 (tm-30) REVERT: E 47 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8246 (mtpp) REVERT: E 69 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6891 (mpt-90) REVERT: E 92 HIS cc_start: 0.8310 (m90) cc_final: 0.8083 (m170) REVERT: F 16 MET cc_start: 0.2092 (mmt) cc_final: 0.1668 (mmt) REVERT: F 111 ARG cc_start: 0.5208 (OUTLIER) cc_final: 0.3909 (tpm170) REVERT: G 74 MET cc_start: 0.6697 (tpp) cc_final: 0.6406 (tpt) REVERT: G 116 LEU cc_start: 0.6877 (OUTLIER) cc_final: 0.6669 (mm) REVERT: G 148 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7488 (ttt90) REVERT: I 16 MET cc_start: 0.5117 (mtp) cc_final: 0.4843 (mtp) REVERT: I 124 MET cc_start: 0.0521 (mmt) cc_final: -0.1693 (ttp) REVERT: N 20 MET cc_start: 0.7698 (ttp) cc_final: 0.7182 (ttt) REVERT: O 38 GLN cc_start: 0.7852 (mp10) cc_final: 0.7434 (mt0) REVERT: O 99 TYR cc_start: 0.7884 (t80) cc_final: 0.7595 (t80) REVERT: P 8 GLU cc_start: 0.7117 (mm-30) cc_final: 0.6706 (mm-30) REVERT: Q 44 TYR cc_start: 0.8471 (m-80) cc_final: 0.8177 (m-80) REVERT: Q 88 GLU cc_start: 0.5585 (OUTLIER) cc_final: 0.5249 (tt0) REVERT: T 18 GLU cc_start: 0.6173 (OUTLIER) cc_final: 0.5335 (tp30) REVERT: T 48 GLN cc_start: 0.8247 (mm-40) cc_final: 0.8013 (mm110) REVERT: U 40 LEU cc_start: 0.8500 (mp) cc_final: 0.8229 (tt) REVERT: V 83 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7214 (mppt) REVERT: W 8 SER cc_start: 0.8178 (m) cc_final: 0.7689 (p) REVERT: W 67 LYS cc_start: 0.8644 (tppt) cc_final: 0.8274 (ttmt) REVERT: X 17 ARG cc_start: 0.7808 (mmt-90) cc_final: 0.7515 (mmt-90) REVERT: X 33 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6595 (m90) REVERT: Y 8 GLU cc_start: 0.6655 (tp30) cc_final: 0.6358 (tt0) REVERT: Y 18 LEU cc_start: 0.7941 (tp) cc_final: 0.7599 (tt) REVERT: Z 43 ILE cc_start: 0.8901 (pp) cc_final: 0.8413 (mt) REVERT: a 84 ILE cc_start: 0.6673 (pt) cc_final: 0.6359 (pt) outliers start: 232 outliers final: 168 residues processed: 854 average time/residue: 0.9040 time to fit residues: 1290.9200 Evaluate side-chains 873 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 690 time to evaluate : 3.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 50 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 55 VAL Chi-restraints excluded: chain 5 residue 86 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 184 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain F residue 112 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain Q residue 106 THR Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 374 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 361 optimal weight: 0.0060 chunk 182 optimal weight: 20.0000 chunk 118 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 384 optimal weight: 30.0000 chunk 412 optimal weight: 10.0000 chunk 299 optimal weight: 20.0000 chunk 56 optimal weight: 30.0000 chunk 475 optimal weight: 7.9990 overall best weight: 7.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 238 ASN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 37 ASN ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN P 76 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.8159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 98714 Z= 0.266 Angle : 0.749 27.400 148025 Z= 0.368 Chirality : 0.045 1.926 18973 Planarity : 0.006 0.104 7665 Dihedral : 23.731 179.563 50331 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 2.10 % Allowed : 13.50 % Favored : 84.40 % Rotamer: Outliers : 8.86 % Allowed : 29.17 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -3.02 (0.14), residues: 3385 helix: -0.96 (0.18), residues: 837 sheet: -1.96 (0.22), residues: 538 loop : -2.59 (0.13), residues: 2010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Q 60 HIS 0.012 0.002 HIS G 114 PHE 0.032 0.002 PHE Y 26 TYR 0.018 0.002 TYR 5 51 ARG 0.014 0.001 ARG V 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 946 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 699 time to evaluate : 3.732 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8239 (mtp180) cc_final: 0.7784 (ttp-110) REVERT: 3 4 LYS cc_start: 0.9007 (mttm) cc_final: 0.8525 (ttmm) REVERT: 5 38 MET cc_start: 0.4704 (mtt) cc_final: 0.2252 (tpp) REVERT: 5 52 MET cc_start: 0.3825 (OUTLIER) cc_final: 0.2569 (mtm) REVERT: 5 143 MET cc_start: 0.4366 (OUTLIER) cc_final: 0.3598 (tmt) REVERT: C 57 HIS cc_start: 0.8192 (OUTLIER) cc_final: 0.7226 (t-90) REVERT: C 264 LYS cc_start: 0.8248 (OUTLIER) cc_final: 0.8034 (tttt) REVERT: D 13 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7509 (ptp90) REVERT: D 202 ILE cc_start: 0.9146 (mt) cc_final: 0.8678 (tt) REVERT: E 1 MET cc_start: 0.4984 (OUTLIER) cc_final: 0.3191 (tmm) REVERT: E 30 GLN cc_start: 0.8803 (tm-30) cc_final: 0.7798 (tm-30) REVERT: E 47 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8251 (mtpp) REVERT: E 69 ARG cc_start: 0.7976 (OUTLIER) cc_final: 0.6984 (mpt-90) REVERT: E 92 HIS cc_start: 0.8424 (m90) cc_final: 0.8186 (m170) REVERT: F 16 MET cc_start: 0.2391 (OUTLIER) cc_final: 0.1980 (mmt) REVERT: F 111 ARG cc_start: 0.5391 (OUTLIER) cc_final: 0.3997 (tpm170) REVERT: G 31 GLU cc_start: 0.4952 (OUTLIER) cc_final: 0.4008 (mp0) REVERT: G 74 MET cc_start: 0.6604 (tpp) cc_final: 0.6284 (tpt) REVERT: G 116 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6841 (mm) REVERT: G 148 ARG cc_start: 0.8008 (ttm-80) cc_final: 0.7475 (ttt90) REVERT: I 16 MET cc_start: 0.5126 (mtp) cc_final: 0.4838 (mtp) REVERT: I 124 MET cc_start: 0.0518 (mmt) cc_final: -0.1925 (ttm) REVERT: L 17 LYS cc_start: 0.6814 (mtpt) cc_final: 0.6601 (mtmt) REVERT: N 20 MET cc_start: 0.7747 (ttp) cc_final: 0.7215 (ttt) REVERT: N 33 ILE cc_start: 0.8945 (OUTLIER) cc_final: 0.8524 (tt) REVERT: O 38 GLN cc_start: 0.7879 (mp10) cc_final: 0.7355 (mt0) REVERT: O 99 TYR cc_start: 0.7876 (t80) cc_final: 0.7536 (t80) REVERT: Q 44 TYR cc_start: 0.8510 (m-80) cc_final: 0.8202 (m-80) REVERT: Q 88 GLU cc_start: 0.5387 (OUTLIER) cc_final: 0.4987 (tt0) REVERT: T 18 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.5384 (tp30) REVERT: T 48 GLN cc_start: 0.8269 (mm-40) cc_final: 0.8027 (mm110) REVERT: T 89 GLU cc_start: 0.7483 (tp30) cc_final: 0.7233 (tp30) REVERT: U 21 ARG cc_start: 0.7048 (ptp-110) cc_final: 0.6409 (ptp-110) REVERT: U 40 LEU cc_start: 0.8441 (mp) cc_final: 0.8183 (tt) REVERT: U 72 PHE cc_start: 0.6734 (t80) cc_final: 0.6278 (t80) REVERT: V 83 LYS cc_start: 0.8008 (OUTLIER) cc_final: 0.7269 (mppt) REVERT: W 8 SER cc_start: 0.8218 (m) cc_final: 0.7801 (p) REVERT: W 67 LYS cc_start: 0.8531 (tppt) cc_final: 0.8120 (ttmt) REVERT: X 17 ARG cc_start: 0.7862 (mmt-90) cc_final: 0.7529 (mmt-90) REVERT: X 33 HIS cc_start: 0.7061 (OUTLIER) cc_final: 0.6587 (m90) REVERT: Y 8 GLU cc_start: 0.6698 (tp30) cc_final: 0.6034 (tt0) REVERT: Y 18 LEU cc_start: 0.7925 (tp) cc_final: 0.7548 (tt) REVERT: Y 30 MET cc_start: 0.5270 (mmm) cc_final: 0.4967 (mmm) REVERT: Z 43 ILE cc_start: 0.8893 (pp) cc_final: 0.8189 (mt) outliers start: 247 outliers final: 197 residues processed: 850 average time/residue: 0.8983 time to fit residues: 1279.1126 Evaluate side-chains 896 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 682 time to evaluate : 3.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 24 SER Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 108 VAL Chi-restraints excluded: chain 5 residue 116 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain 6 residue 21 GLU Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 74 LYS Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 111 ARG Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 58 ASN Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 70 THR Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 81 SER Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain W residue 42 THR Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 49 ASN Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 39 VAL Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 550 optimal weight: 10.0000 chunk 579 optimal weight: 7.9990 chunk 529 optimal weight: 4.9990 chunk 564 optimal weight: 10.0000 chunk 339 optimal weight: 7.9990 chunk 245 optimal weight: 10.0000 chunk 442 optimal weight: 3.9990 chunk 173 optimal weight: 20.0000 chunk 509 optimal weight: 20.0000 chunk 533 optimal weight: 0.0570 chunk 562 optimal weight: 10.0000 overall best weight: 5.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN P 76 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN T 72 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 22 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.8371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 98714 Z= 0.204 Angle : 0.698 27.804 148025 Z= 0.344 Chirality : 0.043 1.908 18973 Planarity : 0.005 0.111 7665 Dihedral : 23.676 179.919 50331 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 14.80 Ramachandran Plot: Outliers : 2.04 % Allowed : 12.73 % Favored : 85.23 % Rotamer: Outliers : 8.07 % Allowed : 30.21 % Favored : 61.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.89 (0.14), residues: 3385 helix: -0.89 (0.18), residues: 844 sheet: -1.80 (0.24), residues: 483 loop : -2.51 (0.13), residues: 2058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 60 HIS 0.014 0.001 HIS G 114 PHE 0.028 0.002 PHE U 86 TYR 0.018 0.002 TYR O 99 ARG 0.015 0.001 ARG V 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 929 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 704 time to evaluate : 3.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8252 (mtp180) cc_final: 0.7776 (ttp-110) REVERT: 3 4 LYS cc_start: 0.8936 (mttm) cc_final: 0.8527 (ttmm) REVERT: 3 63 TYR cc_start: 0.7620 (m-80) cc_final: 0.7201 (m-80) REVERT: 5 36 ASP cc_start: 0.3865 (OUTLIER) cc_final: 0.3609 (m-30) REVERT: 5 37 LYS cc_start: 0.5249 (ttmt) cc_final: 0.5032 (tmtt) REVERT: 5 38 MET cc_start: 0.5194 (mtt) cc_final: 0.2632 (tpp) REVERT: 5 52 MET cc_start: 0.3892 (OUTLIER) cc_final: 0.2652 (mtm) REVERT: 5 143 MET cc_start: 0.4424 (OUTLIER) cc_final: 0.3555 (tmt) REVERT: C 57 HIS cc_start: 0.8118 (OUTLIER) cc_final: 0.7147 (t-90) REVERT: C 71 ASP cc_start: 0.7080 (OUTLIER) cc_final: 0.6798 (m-30) REVERT: C 264 LYS cc_start: 0.8142 (OUTLIER) cc_final: 0.7903 (tttt) REVERT: D 13 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7776 (ptm160) REVERT: D 202 ILE cc_start: 0.9123 (mt) cc_final: 0.8640 (tt) REVERT: E 1 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.3698 (tmm) REVERT: E 7 ASP cc_start: 0.3507 (OUTLIER) cc_final: 0.2271 (p0) REVERT: E 30 GLN cc_start: 0.8783 (tm-30) cc_final: 0.7735 (tm-30) REVERT: E 47 LYS cc_start: 0.8495 (OUTLIER) cc_final: 0.8253 (mtpp) REVERT: E 69 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.6873 (mpt-90) REVERT: E 92 HIS cc_start: 0.8412 (m90) cc_final: 0.8143 (m170) REVERT: F 16 MET cc_start: 0.2595 (OUTLIER) cc_final: 0.2253 (mmt) REVERT: G 31 GLU cc_start: 0.4918 (OUTLIER) cc_final: 0.4341 (mp0) REVERT: G 74 MET cc_start: 0.6599 (tpp) cc_final: 0.6270 (tpt) REVERT: G 116 LEU cc_start: 0.7111 (OUTLIER) cc_final: 0.6896 (mm) REVERT: G 148 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7373 (ttt90) REVERT: I 16 MET cc_start: 0.5240 (mtp) cc_final: 0.4976 (mtp) REVERT: I 124 MET cc_start: 0.0713 (mmt) cc_final: -0.1420 (ptp) REVERT: M 134 THR cc_start: 0.8166 (OUTLIER) cc_final: 0.7939 (p) REVERT: N 20 MET cc_start: 0.7676 (ttp) cc_final: 0.7427 (tmm) REVERT: N 33 ILE cc_start: 0.8899 (OUTLIER) cc_final: 0.8464 (tt) REVERT: O 38 GLN cc_start: 0.7938 (mp10) cc_final: 0.7416 (mt0) REVERT: O 43 ASN cc_start: 0.7316 (OUTLIER) cc_final: 0.6655 (p0) REVERT: O 81 ARG cc_start: 0.7641 (mtp85) cc_final: 0.7431 (mtp85) REVERT: O 99 TYR cc_start: 0.7864 (t80) cc_final: 0.7543 (t80) REVERT: Q 44 TYR cc_start: 0.8528 (m-80) cc_final: 0.8211 (m-80) REVERT: Q 88 GLU cc_start: 0.5353 (OUTLIER) cc_final: 0.5040 (tt0) REVERT: T 18 GLU cc_start: 0.6327 (OUTLIER) cc_final: 0.5370 (tp30) REVERT: T 48 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7933 (mm110) REVERT: T 79 ASP cc_start: 0.7599 (m-30) cc_final: 0.7227 (m-30) REVERT: U 40 LEU cc_start: 0.8475 (mp) cc_final: 0.8092 (tt) REVERT: V 83 LYS cc_start: 0.7970 (OUTLIER) cc_final: 0.7118 (mppt) REVERT: W 8 SER cc_start: 0.8173 (m) cc_final: 0.7796 (p) REVERT: W 67 LYS cc_start: 0.8384 (tppt) cc_final: 0.7984 (ttmt) REVERT: X 17 ARG cc_start: 0.7761 (mmt-90) cc_final: 0.7457 (mmt-90) REVERT: X 33 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6522 (m90) REVERT: Y 18 LEU cc_start: 0.7902 (tp) cc_final: 0.7553 (tt) REVERT: Z 43 ILE cc_start: 0.8888 (pp) cc_final: 0.8362 (mt) REVERT: a 84 ILE cc_start: 0.6929 (pt) cc_final: 0.6621 (pt) outliers start: 225 outliers final: 176 residues processed: 844 average time/residue: 0.9271 time to fit residues: 1303.8384 Evaluate side-chains 882 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 685 time to evaluate : 3.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 36 ASP Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 71 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 75 ILE Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 14 THR Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 1 MET Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 370 optimal weight: 3.9990 chunk 596 optimal weight: 8.9990 chunk 364 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 414 optimal weight: 8.9990 chunk 625 optimal weight: 9.9990 chunk 575 optimal weight: 7.9990 chunk 498 optimal weight: 30.0000 chunk 51 optimal weight: 20.0000 chunk 384 optimal weight: 0.9990 chunk 305 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN P 76 HIS ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.8442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 98714 Z= 0.236 Angle : 0.723 27.666 148025 Z= 0.355 Chirality : 0.044 1.915 18973 Planarity : 0.006 0.112 7665 Dihedral : 23.677 179.572 50328 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 2.04 % Allowed : 13.15 % Favored : 84.82 % Rotamer: Outliers : 7.50 % Allowed : 30.53 % Favored : 61.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.14), residues: 3385 helix: -0.94 (0.18), residues: 845 sheet: -1.76 (0.24), residues: 492 loop : -2.54 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP C 247 HIS 0.015 0.001 HIS J 40 PHE 0.040 0.002 PHE Y 26 TYR 0.017 0.002 TYR O 99 ARG 0.020 0.001 ARG U 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6770 Ramachandran restraints generated. 3385 Oldfield, 0 Emsley, 3385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 689 time to evaluate : 3.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 49 ARG cc_start: 0.8282 (mtp180) cc_final: 0.7793 (ttp-110) REVERT: 3 4 LYS cc_start: 0.8949 (mttm) cc_final: 0.8540 (ttmm) REVERT: 3 63 TYR cc_start: 0.7637 (m-80) cc_final: 0.7236 (m-80) REVERT: 5 37 LYS cc_start: 0.5429 (ttmt) cc_final: 0.5131 (tmtt) REVERT: 5 52 MET cc_start: 0.3962 (OUTLIER) cc_final: 0.2692 (mtm) REVERT: 5 143 MET cc_start: 0.4479 (OUTLIER) cc_final: 0.2662 (tmm) REVERT: C 57 HIS cc_start: 0.8147 (OUTLIER) cc_final: 0.7123 (t-90) REVERT: C 177 SER cc_start: 0.9151 (p) cc_final: 0.8881 (m) REVERT: C 264 LYS cc_start: 0.8110 (OUTLIER) cc_final: 0.7881 (tttt) REVERT: D 13 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7749 (ptm160) REVERT: D 202 ILE cc_start: 0.9118 (mt) cc_final: 0.8652 (tt) REVERT: E 1 MET cc_start: 0.5256 (OUTLIER) cc_final: 0.3842 (tmm) REVERT: E 5 LEU cc_start: 0.6157 (tt) cc_final: 0.5756 (tp) REVERT: E 7 ASP cc_start: 0.3354 (OUTLIER) cc_final: 0.2352 (p0) REVERT: E 30 GLN cc_start: 0.8812 (tm-30) cc_final: 0.7771 (tm-30) REVERT: E 47 LYS cc_start: 0.8504 (OUTLIER) cc_final: 0.8253 (mtpp) REVERT: E 69 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6936 (mpt-90) REVERT: E 92 HIS cc_start: 0.8448 (m90) cc_final: 0.8183 (m170) REVERT: F 16 MET cc_start: 0.2591 (OUTLIER) cc_final: 0.2249 (mmt) REVERT: G 31 GLU cc_start: 0.5015 (OUTLIER) cc_final: 0.4048 (mp0) REVERT: G 74 MET cc_start: 0.6625 (tpp) cc_final: 0.6288 (tpt) REVERT: G 116 LEU cc_start: 0.7224 (OUTLIER) cc_final: 0.6959 (mm) REVERT: G 148 ARG cc_start: 0.7988 (ttm-80) cc_final: 0.7461 (ttt90) REVERT: I 16 MET cc_start: 0.5257 (mtp) cc_final: 0.4991 (mtp) REVERT: I 124 MET cc_start: 0.0485 (mmt) cc_final: -0.1538 (ptp) REVERT: J 13 ARG cc_start: 0.8250 (mmt-90) cc_final: 0.8005 (mpt180) REVERT: M 104 GLU cc_start: 0.6422 (mt-10) cc_final: 0.6169 (mt-10) REVERT: M 134 THR cc_start: 0.8254 (OUTLIER) cc_final: 0.8052 (p) REVERT: N 20 MET cc_start: 0.7663 (ttp) cc_final: 0.7415 (tmm) REVERT: N 33 ILE cc_start: 0.8920 (OUTLIER) cc_final: 0.8500 (tt) REVERT: O 38 GLN cc_start: 0.7943 (mp10) cc_final: 0.7410 (mt0) REVERT: O 43 ASN cc_start: 0.7315 (OUTLIER) cc_final: 0.6670 (p0) REVERT: O 81 ARG cc_start: 0.7677 (mtp85) cc_final: 0.7473 (mtp85) REVERT: O 99 TYR cc_start: 0.7880 (t80) cc_final: 0.7549 (t80) REVERT: Q 44 TYR cc_start: 0.8541 (m-80) cc_final: 0.8230 (m-80) REVERT: Q 88 GLU cc_start: 0.5384 (OUTLIER) cc_final: 0.5041 (tt0) REVERT: S 75 PHE cc_start: 0.8729 (p90) cc_final: 0.7980 (p90) REVERT: T 18 GLU cc_start: 0.6402 (OUTLIER) cc_final: 0.5403 (tp30) REVERT: T 48 GLN cc_start: 0.8176 (mm-40) cc_final: 0.7955 (mm110) REVERT: T 79 ASP cc_start: 0.7680 (m-30) cc_final: 0.7298 (m-30) REVERT: U 40 LEU cc_start: 0.8486 (mp) cc_final: 0.8097 (tt) REVERT: V 68 LYS cc_start: 0.8264 (mmtp) cc_final: 0.7844 (mptt) REVERT: V 83 LYS cc_start: 0.8000 (OUTLIER) cc_final: 0.7157 (mppt) REVERT: W 8 SER cc_start: 0.8179 (m) cc_final: 0.7789 (p) REVERT: W 67 LYS cc_start: 0.8397 (tppt) cc_final: 0.8014 (ttmt) REVERT: X 17 ARG cc_start: 0.7780 (mmt-90) cc_final: 0.7475 (mmt-90) REVERT: X 33 HIS cc_start: 0.7040 (OUTLIER) cc_final: 0.6545 (m90) REVERT: Y 18 LEU cc_start: 0.7866 (tp) cc_final: 0.7549 (tt) REVERT: Z 43 ILE cc_start: 0.8890 (pp) cc_final: 0.8224 (mt) REVERT: a 84 ILE cc_start: 0.6954 (pt) cc_final: 0.6668 (pt) outliers start: 209 outliers final: 185 residues processed: 811 average time/residue: 0.9256 time to fit residues: 1254.2183 Evaluate side-chains 885 residues out of total 2790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 204 poor density : 681 time to evaluate : 5.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 4 GLN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 10 SER Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 1 residue 46 VAL Chi-restraints excluded: chain 1 residue 47 ILE Chi-restraints excluded: chain 2 residue 4 THR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 26 ASN Chi-restraints excluded: chain 3 residue 5 THR Chi-restraints excluded: chain 3 residue 6 VAL Chi-restraints excluded: chain 3 residue 25 HIS Chi-restraints excluded: chain 3 residue 37 THR Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 17 VAL Chi-restraints excluded: chain 5 residue 51 TYR Chi-restraints excluded: chain 5 residue 52 MET Chi-restraints excluded: chain 5 residue 107 GLU Chi-restraints excluded: chain 5 residue 123 ILE Chi-restraints excluded: chain 5 residue 130 PRO Chi-restraints excluded: chain 5 residue 143 MET Chi-restraints excluded: chain 6 residue 20 VAL Chi-restraints excluded: chain C residue 43 ASN Chi-restraints excluded: chain C residue 57 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 110 LYS Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 143 VAL Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 264 LYS Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 24 VAL Chi-restraints excluded: chain D residue 50 VAL Chi-restraints excluded: chain D residue 58 ASN Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 171 THR Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 178 VAL Chi-restraints excluded: chain D residue 200 ASP Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 32 VAL Chi-restraints excluded: chain E residue 47 LYS Chi-restraints excluded: chain E residue 48 THR Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 69 ARG Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 107 SER Chi-restraints excluded: chain E residue 132 LYS Chi-restraints excluded: chain E residue 154 ASP Chi-restraints excluded: chain E residue 157 LEU Chi-restraints excluded: chain E residue 167 VAL Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 193 VAL Chi-restraints excluded: chain E residue 200 LEU Chi-restraints excluded: chain F residue 5 ASP Chi-restraints excluded: chain F residue 9 ASP Chi-restraints excluded: chain F residue 16 MET Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 56 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 14 VAL Chi-restraints excluded: chain G residue 22 VAL Chi-restraints excluded: chain G residue 31 GLU Chi-restraints excluded: chain G residue 71 LEU Chi-restraints excluded: chain G residue 75 VAL Chi-restraints excluded: chain G residue 84 LYS Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 116 LEU Chi-restraints excluded: chain G residue 121 THR Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 176 LYS Chi-restraints excluded: chain H residue 9 VAL Chi-restraints excluded: chain I residue 60 VAL Chi-restraints excluded: chain I residue 61 TYR Chi-restraints excluded: chain I residue 70 THR Chi-restraints excluded: chain I residue 102 ARG Chi-restraints excluded: chain J residue 11 VAL Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 54 ILE Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 74 TYR Chi-restraints excluded: chain J residue 76 HIS Chi-restraints excluded: chain J residue 90 GLU Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 7 MET Chi-restraints excluded: chain K residue 41 ILE Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 100 PHE Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 54 GLN Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 89 VAL Chi-restraints excluded: chain L residue 99 ASN Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 122 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 20 LEU Chi-restraints excluded: chain M residue 44 ARG Chi-restraints excluded: chain M residue 80 VAL Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 97 GLN Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain M residue 134 THR Chi-restraints excluded: chain N residue 33 ILE Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 53 THR Chi-restraints excluded: chain N residue 57 THR Chi-restraints excluded: chain N residue 97 ILE Chi-restraints excluded: chain O residue 12 THR Chi-restraints excluded: chain O residue 18 LEU Chi-restraints excluded: chain O residue 43 ASN Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 45 VAL Chi-restraints excluded: chain P residue 47 ILE Chi-restraints excluded: chain P residue 49 ILE Chi-restraints excluded: chain P residue 50 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain Q residue 38 VAL Chi-restraints excluded: chain Q residue 55 GLN Chi-restraints excluded: chain Q residue 59 LEU Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 94 LEU Chi-restraints excluded: chain Q residue 97 ILE Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 27 ILE Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain R residue 38 VAL Chi-restraints excluded: chain R residue 40 MET Chi-restraints excluded: chain R residue 48 LYS Chi-restraints excluded: chain R residue 55 ASP Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 94 THR Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain S residue 33 LEU Chi-restraints excluded: chain S residue 40 ASN Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 48 LYS Chi-restraints excluded: chain S residue 67 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 18 GLU Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 28 ASN Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 62 VAL Chi-restraints excluded: chain T residue 67 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 11 ILE Chi-restraints excluded: chain U residue 12 VAL Chi-restraints excluded: chain U residue 32 LYS Chi-restraints excluded: chain U residue 33 VAL Chi-restraints excluded: chain U residue 58 VAL Chi-restraints excluded: chain U residue 64 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 29 ILE Chi-restraints excluded: chain V residue 31 TYR Chi-restraints excluded: chain V residue 77 VAL Chi-restraints excluded: chain V residue 83 LYS Chi-restraints excluded: chain V residue 86 LEU Chi-restraints excluded: chain W residue 9 THR Chi-restraints excluded: chain W residue 13 ARG Chi-restraints excluded: chain W residue 15 SER Chi-restraints excluded: chain W residue 23 LYS Chi-restraints excluded: chain W residue 24 ARG Chi-restraints excluded: chain W residue 39 GLN Chi-restraints excluded: chain W residue 44 PHE Chi-restraints excluded: chain W residue 80 SER Chi-restraints excluded: chain X residue 1 SER Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 19 HIS Chi-restraints excluded: chain X residue 33 HIS Chi-restraints excluded: chain X residue 66 VAL Chi-restraints excluded: chain X residue 77 TYR Chi-restraints excluded: chain Y residue 11 VAL Chi-restraints excluded: chain Y residue 57 LEU Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 40 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 628 random chunks: chunk 395 optimal weight: 0.4980 chunk 530 optimal weight: 10.0000 chunk 152 optimal weight: 20.0000 chunk 459 optimal weight: 4.9990 chunk 73 optimal weight: 30.0000 chunk 138 optimal weight: 20.0000 chunk 498 optimal weight: 4.9990 chunk 208 optimal weight: 20.0000 chunk 512 optimal weight: 7.9990 chunk 63 optimal weight: 30.0000 chunk 91 optimal weight: 20.0000 overall best weight: 5.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 31 GLN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.157923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.130553 restraints weight = 156673.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.131655 restraints weight = 93324.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.132705 restraints weight = 52961.389| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3444 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.89 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3444 r_free = 0.3444 target_work(ls_wunit_k1) = 0.126 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3444 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.8445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.170 98714 Z= 0.246 Angle : 0.750 59.194 148025 Z= 0.378 Chirality : 0.043 1.914 18973 Planarity : 0.006 0.119 7665 Dihedral : 23.679 179.572 50328 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 2.01 % Allowed : 13.03 % Favored : 84.96 % Rotamer: Outliers : 8.04 % Allowed : 30.18 % Favored : 61.79 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.03 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.92 (0.14), residues: 3385 helix: -0.94 (0.18), residues: 845 sheet: -1.78 (0.23), residues: 492 loop : -2.54 (0.13), residues: 2048 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP Q 60 HIS 0.014 0.001 HIS J 40 PHE 0.036 0.002 PHE U 72 TYR 0.017 0.002 TYR 5 51 ARG 0.037 0.001 ARG U 21 =============================================================================== Job complete usr+sys time: 19457.32 seconds wall clock time: 345 minutes 41.87 seconds (20741.87 seconds total)