Starting phenix.real_space_refine on Tue Mar 19 07:22:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/03_2024/7bl3_12216.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/03_2024/7bl3_12216.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/03_2024/7bl3_12216.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/03_2024/7bl3_12216.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/03_2024/7bl3_12216.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bl3_12216/03_2024/7bl3_12216.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.034 sd= 0.805 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3020 5.49 5 Mg 1 5.21 5 S 92 5.16 5 C 46441 2.51 5 N 17217 2.21 5 O 26059 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "9P ASP 5": "OD1" <-> "OD2" Residue "9P TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9P ASP 50": "OD1" <-> "OD2" Residue "9P TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9P ARG 129": "NH1" <-> "NH2" Residue "9P ARG 136": "NH1" <-> "NH2" Residue "9P PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9P ARG 177": "NH1" <-> "NH2" Residue "9P ARG 230": "NH1" <-> "NH2" Residue "9P ARG 239": "NH1" <-> "NH2" Residue "9P ASP 272": "OD1" <-> "OD2" Residue "9P GLU 307": "OE1" <-> "OE2" Residue "9P TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 51": "NH1" <-> "NH2" Residue "C ARG 62": "NH1" <-> "NH2" Residue "C PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 78": "OE1" <-> "OE2" Residue "C ARG 79": "NH1" <-> "NH2" Residue "C TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 99": "OE1" <-> "OE2" Residue "C ASP 113": "OD1" <-> "OD2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 202": "NH1" <-> "NH2" Residue "C ARG 211": "NH1" <-> "NH2" Residue "C PHE 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ASP 39": "OD1" <-> "OD2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ASP 103": "OD1" <-> "OD2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ASP 181": "OD1" <-> "OD2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ASP 22": "OD1" <-> "OD2" Residue "E GLU 25": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 61": "NH1" <-> "NH2" Residue "E ARG 88": "NH1" <-> "NH2" Residue "E TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "E PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "E PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "G ARG 2": "NH1" <-> "NH2" Residue "G PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 162": "NH1" <-> "NH2" Residue "G ARG 169": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ASP 14": "OD1" <-> "OD2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 90": "OE1" <-> "OE2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" 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 TYR 58": "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 106": "OE1" <-> "OE2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" 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 32": "OE1" <-> "OE2" 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 ASP 72": "OD1" <-> "OD2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O GLU 84": "OE1" <-> "OE2" Residue "O ASP 93": "OD1" <-> "OD2" 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 "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 PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 47": "NH1" <-> "NH2" Residue "Q ARG 50": "NH1" <-> "NH2" Residue "Q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 69": "NH1" <-> "NH2" Residue "Q PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 110": "OE1" <-> "OE2" Residue "R TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 31": "OE1" <-> "OE2" Residue "R GLU 45": "OE1" <-> "OE2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 80": "NH1" <-> "NH2" Residue "R TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ASP 22": "OD1" <-> "OD2" Residue "S TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 59": "OE1" <-> "OE2" Residue "S ASP 62": "OD1" <-> "OD2" Residue "S ASP 68": "OD1" <-> "OD2" 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 5": "OE1" <-> "OE2" Residue "T GLU 18": "OE1" <-> "OE2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "T GLU 54": "OE1" <-> "OE2" Residue "T ARG 73": "NH1" <-> "NH2" Residue "U ARG 5": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 81": "NH1" <-> "NH2" Residue "U PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 85": "NH1" <-> "NH2" Residue "U PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 93": "NH1" <-> "NH2" Residue "U PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 100": "OE1" <-> "OE2" Residue "V PHE 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 43": "OD1" <-> "OD2" Residue "V ASP 45": "OD1" <-> "OD2" Residue "V GLU 55": "OE1" <-> "OE2" Residue "V GLU 69": "OE1" <-> "OE2" Residue "V PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "W GLU 66": "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 PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 42": "OE1" <-> "OE2" Residue "X ARG 49": "NH1" <-> "NH2" Residue "X ARG 56": "NH1" <-> "NH2" Residue "X ARG 73": "NH1" <-> "NH2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 29": "NH1" <-> "NH2" Residue "Z ASP 39": "OD1" <-> "OD2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 9": "NH1" <-> "NH2" Residue "0 ARG 15": "NH1" <-> "NH2" Residue "0 ASP 30": "OD1" <-> "OD2" Residue "0 GLU 35": "OE1" <-> "OE2" Residue "0 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 51": "NH1" <-> "NH2" Residue "1 TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "I PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 4": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "P ARG 20": "NH1" <-> "NH2" Residue "P ARG 38": "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 "6 PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ASP 15": "OD1" <-> "OD2" Residue "6 ASP 21": "OD1" <-> "OD2" Residue "6 ARG 96": "NH1" <-> "NH2" Residue "H ARG 27": "NH1" <-> "NH2" Residue "H PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 48": "OE1" <-> "OE2" Residue "H GLU 70": "OE1" <-> "OE2" Residue "H GLU 114": "OE1" <-> "OE2" Residue "H PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 7": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 41": "OE1" <-> "OE2" Residue "F ASP 50": "OD1" <-> "OD2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 79": "NH1" <-> "NH2" Residue "F TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 91": "NH1" <-> "NH2" 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 PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 162": "OD1" <-> "OD2" Residue "F PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 92831 Number of models: 1 Model: "" Number of chains: 39 Chain: "A" Number of atoms: 62301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2902, 62301 Classifications: {'RNA': 2902} Modifications used: {'rna2p_pur': 272, 'rna2p_pyr': 149, 'rna3p_pur': 1403, 'rna3p_pyr': 1078} Link IDs: {'rna2p': 421, 'rna3p': 2480} Chain breaks: 2 Chain: "B" Number of atoms: 2548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2548 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "9P" Number of atoms: 2582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2582 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 14, 'TRANS': 323} Chain: "b" Number of atoms: 364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 364 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} 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: "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: {'PTRANS': 8, 'TRANS': 167} 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: "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: "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: "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: {'CIS': 1, 'PTRANS': 1, 'TRANS': 90} 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: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 575 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 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: "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: "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: "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: "P" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 911 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "6" Number of atoms: 780 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 780 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 1, 'TRANS': 100} Chain: "H" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 144} 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: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 35.84, per 1000 atoms: 0.39 Number of scatterers: 92831 At special positions: 0 Unit cell: (207.08, 226.92, 272.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 92 16.00 P 3020 15.00 Mg 1 11.99 O 26059 8.00 N 17217 7.00 C 46441 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS b 18 " - pdb=" SG CYS b 40 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 40.40 Conformation dependent library (CDL) restraints added in 4.2 seconds 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6570 Finding SS restraints... Secondary structure from input PDB file: 101 helices and 48 sheets defined 28.3% alpha, 18.5% beta 989 base pairs and 1529 stacking pairs defined. Time for finding SS restraints: 35.60 Creating SS restraints... Processing helix chain '9P' and resid 56 through 60 removed outlier: 3.851A pdb=" N ARG9P 60 " --> pdb=" O ILE9P 57 " (cutoff:3.500A) Processing helix chain '9P' and resid 126 through 131 Processing helix chain '9P' and resid 171 through 177 removed outlier: 3.685A pdb=" N ILE9P 176 " --> pdb=" O LYS9P 172 " (cutoff:3.500A) Processing helix chain '9P' and resid 228 through 235 removed outlier: 4.305A pdb=" N PHE9P 231 " --> pdb=" O GLY9P 228 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LYS9P 233 " --> pdb=" O ARG9P 230 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS9P 234 " --> pdb=" O PHE9P 231 " (cutoff:3.500A) Processing helix chain '9P' and resid 255 through 257 No H-bonds generated for 'chain '9P' and resid 255 through 257' Processing helix chain '9P' and resid 258 through 268 removed outlier: 4.078A pdb=" N ILE9P 262 " --> pdb=" O ASN9P 258 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER9P 264 " --> pdb=" O ARG9P 260 " (cutoff:3.500A) Processing helix chain '9P' and resid 271 through 276 removed outlier: 4.074A pdb=" N THR9P 275 " --> pdb=" O GLN9P 271 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS9P 276 " --> pdb=" O ASP9P 272 " (cutoff:3.500A) No H-bonds generated for 'chain '9P' and resid 271 through 276' Processing helix chain '9P' and resid 289 through 305 removed outlier: 4.273A pdb=" N GLU9P 295 " --> pdb=" O VAL9P 291 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU9P 304 " --> pdb=" O ILE9P 300 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY9P 305 " --> pdb=" O ALA9P 301 " (cutoff:3.500A) Processing helix chain '9P' and resid 321 through 334 removed outlier: 3.504A pdb=" N ASP9P 327 " --> pdb=" O ASP9P 323 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N VAL9P 328 " --> pdb=" O LEU9P 324 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N MET9P 329 " --> pdb=" O CYS9P 325 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N GLU9P 334 " --> pdb=" O THR9P 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 14 removed outlier: 4.244A pdb=" N HIS C 14 " --> pdb=" O GLY C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 31 No H-bonds generated for 'chain 'C' and resid 29 through 31' Processing helix chain 'C' and resid 197 through 202 removed outlier: 4.364A pdb=" N MET C 200 " --> pdb=" O ALA C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 212 removed outlier: 4.224A pdb=" N ALA C 210 " --> pdb=" O LYS C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 224 Processing helix chain 'C' and resid 262 through 266 Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.508A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 102 removed outlier: 3.619A pdb=" N LEU D 100 " --> pdb=" O SER D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 removed outlier: 3.572A pdb=" N PHE E 19 " --> pdb=" O SER E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 39 Processing helix chain 'E' and resid 97 through 115 removed outlier: 3.539A pdb=" N SER E 110 " --> pdb=" O LYS E 106 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 111 " --> pdb=" O SER E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 141 Processing helix chain 'E' and resid 154 through 162 removed outlier: 3.646A pdb=" N ALA E 160 " --> pdb=" O ASN E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 183 removed outlier: 3.734A pdb=" N LEU E 180 " --> pdb=" O ASP E 176 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE E 181 " --> pdb=" O PRO E 177 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N PHE E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) Processing helix chain 'E' and resid 190 through 201 removed outlier: 4.199A pdb=" N LYS E 194 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLN E 195 " --> pdb=" O ASP E 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 6 removed outlier: 3.726A pdb=" N ALA G 6 " --> pdb=" O ARG G 2 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 2 through 6' Processing helix chain 'G' and resid 60 through 80 removed outlier: 3.696A pdb=" N THR G 66 " --> pdb=" O ALA G 62 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE G 76 " --> pdb=" O ASN G 72 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 77 " --> pdb=" O SER G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 136 through 151 removed outlier: 3.774A pdb=" N TYR G 150 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG G 151 " --> pdb=" O LEU G 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 3.651A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY J 38 " --> pdb=" O ARG J 34 " (cutoff:3.500A) Processing helix chain 'J' and resid 58 through 62 Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 89 through 96 Processing helix chain 'J' and resid 98 through 109 removed outlier: 3.570A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 121 removed outlier: 4.004A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'L' and resid 56 through 61 removed outlier: 3.525A pdb=" N ARG L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 56 through 61' Processing helix chain 'L' and resid 95 through 99 Processing helix chain 'L' and resid 128 through 138 Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.838A pdb=" N GLY N 26 " --> pdb=" O ARG N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 55 removed outlier: 3.876A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 69 removed outlier: 3.555A pdb=" N ARG N 69 " --> pdb=" O LEU N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 79 Processing helix chain 'N' and resid 82 through 88 removed outlier: 3.503A pdb=" N PHE N 87 " --> pdb=" O LEU N 83 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 22 removed outlier: 4.390A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.148A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU O 84 " --> pdb=" O GLU O 80 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 114 removed outlier: 3.628A pdb=" N LEU O 106 " --> pdb=" O ARG O 102 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.849A pdb=" N ALA Q 11 " --> pdb=" O VAL Q 7 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG Q 12 " --> pdb=" O ILE Q 8 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LYS Q 15 " --> pdb=" O ALA Q 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 24 through 29 removed outlier: 3.564A pdb=" N SER Q 28 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 30 through 71 removed outlier: 4.111A pdb=" N GLN Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ARG Q 50 " --> pdb=" O TYR Q 46 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LYS Q 53 " --> pdb=" O ARG Q 49 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ARG Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE Q 56 " --> pdb=" O ARG Q 52 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLN Q 70 " --> pdb=" O ALA Q 66 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ASN Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 74 through 85 Processing helix chain 'Q' and resid 90 through 101 removed outlier: 3.713A pdb=" N VAL Q 99 " --> pdb=" O ALA Q 95 " (cutoff:3.500A) Processing helix chain 'Q' and resid 101 through 117 removed outlier: 3.654A pdb=" N PHE Q 105 " --> pdb=" O ASP Q 101 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA Q 107 " --> pdb=" O VAL Q 103 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU Q 108 " --> pdb=" O ALA Q 104 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ALA Q 115 " --> pdb=" O LYS Q 111 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA Q 117 " --> pdb=" O LYS Q 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.715A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 38 Processing helix chain 'S' and resid 41 through 60 removed outlier: 3.543A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) 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 3 through 10 removed outlier: 4.085A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.402A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER T 27 " --> pdb=" O ALA T 23 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 removed outlier: 3.529A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 19 Processing helix chain 'V' and resid 20 through 23 Processing helix chain 'V' and resid 44 through 52 removed outlier: 3.706A pdb=" N MET V 48 " --> pdb=" O HIS V 44 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN V 49 " --> pdb=" O ASP V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 57 Processing helix chain 'X' and resid 52 through 62 Processing helix chain 'X' and resid 62 through 73 removed outlier: 3.541A pdb=" N GLU X 69 " --> pdb=" O THR X 65 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU X 70 " --> pdb=" O VAL X 66 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) Processing helix chain 'Y' and resid 9 through 24 removed outlier: 3.660A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 24 through 34 removed outlier: 3.528A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 41 through 55 removed outlier: 4.103A pdb=" N GLN Y 45 " --> pdb=" O HIS Y 41 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL Y 46 " --> pdb=" O LEU Y 42 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA Y 51 " --> pdb=" O ARG Y 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 Processing helix chain 'Z' and resid 40 through 50 removed outlier: 3.576A pdb=" N ALA Z 49 " --> pdb=" O GLY Z 45 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N VAL Z 50 " --> pdb=" O MET Z 46 " (cutoff:3.500A) Processing helix chain '0' and resid 8 through 14 removed outlier: 3.549A pdb=" N ARG 0 12 " --> pdb=" O THR 0 8 " (cutoff:3.500A) Processing helix chain '0' and resid 15 through 19 removed outlier: 4.055A pdb=" N HIS 0 18 " --> pdb=" O ARG 0 15 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 24 removed outlier: 4.261A pdb=" N THR 2 24 " --> pdb=" O ALA 2 20 " (cutoff:3.500A) Processing helix chain '2' and resid 24 through 38 removed outlier: 3.695A pdb=" N ALA 2 36 " --> pdb=" O ALA 2 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 removed outlier: 4.019A pdb=" N CYS I 38 " --> pdb=" O MET I 35 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 82 removed outlier: 3.644A pdb=" N LYS I 81 " --> pdb=" O VAL I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 120 through 126 removed outlier: 3.545A pdb=" N MET I 124 " --> pdb=" O ASP I 120 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ARG I 126 " --> pdb=" O GLU I 122 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 removed outlier: 4.336A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 111 removed outlier: 3.723A pdb=" N LEU K 107 " --> pdb=" O THR K 104 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 118 removed outlier: 3.854A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Processing helix chain 'P' and resid 3 through 12 removed outlier: 3.995A pdb=" N LEU P 7 " --> pdb=" O ILE P 3 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N GLN P 9 " --> pdb=" O LYS P 5 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU P 10 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN P 11 " --> pdb=" O LEU P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 52 through 55 Processing helix chain 'P' and resid 96 through 100 Processing helix chain 'P' and resid 104 through 108 removed outlier: 4.072A pdb=" N ARG P 108 " --> pdb=" O LYS P 105 " (cutoff:3.500A) Processing helix chain '6' and resid 4 through 17 removed outlier: 3.591A pdb=" N ASP 6 8 " --> pdb=" O LYS 6 4 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS 6 13 " --> pdb=" O PHE 6 9 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU 6 17 " --> pdb=" O LYS 6 13 " (cutoff:3.500A) Processing helix chain '6' and resid 44 through 61 removed outlier: 3.505A pdb=" N ASP 6 53 " --> pdb=" O MET 6 49 " (cutoff:3.500A) Processing helix chain '6' and resid 92 through 96 removed outlier: 3.608A pdb=" N ARG 6 96 " --> pdb=" O GLU 6 92 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 92 through 96' Processing helix chain 'H' and resid 22 through 27 Processing helix chain 'H' and resid 42 through 71 removed outlier: 3.701A pdb=" N GLU H 48 " --> pdb=" O ILE H 44 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU H 55 " --> pdb=" O ARG H 51 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLU H 60 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N VAL H 61 " --> pdb=" O LYS H 57 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA H 65 " --> pdb=" O VAL H 61 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 71 " --> pdb=" O ALA H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 74 No H-bonds generated for 'chain 'H' and resid 72 through 74' Processing helix chain 'H' and resid 85 through 87 No H-bonds generated for 'chain 'H' and resid 85 through 87' Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'F' and resid 3 through 10 Processing helix chain 'F' and resid 10 through 20 removed outlier: 3.742A pdb=" N GLU F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 27 Processing helix chain 'F' and resid 46 through 60 Processing helix chain 'F' and resid 73 through 77 removed outlier: 3.538A pdb=" N PHE F 76 " --> pdb=" O VAL F 73 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 161 through 172 removed outlier: 3.894A pdb=" N ALA F 170 " --> pdb=" O ARG F 166 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '9P' and resid 64 through 66 removed outlier: 9.028A pdb=" N PHE9P 65 " --> pdb=" O SER9P 8 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N LEU9P 10 " --> pdb=" O PHE9P 65 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N THR9P 94 " --> pdb=" O ASP9P 107 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP9P 107 " --> pdb=" O THR9P 94 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N VAL9P 96 " --> pdb=" O MET9P 105 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '9P' and resid 22 through 23 Processing sheet with id=AA3, first strand: chain '9P' and resid 87 through 91 removed outlier: 6.516A pdb=" N TRP9P 46 " --> pdb=" O ILE9P 88 " (cutoff:3.500A) removed outlier: 7.368A pdb=" N VAL9P 90 " --> pdb=" O TRP9P 46 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N GLU9P 48 " --> pdb=" O VAL9P 90 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL9P 45 " --> pdb=" O VAL9P 117 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '9P' and resid 165 through 166 removed outlier: 3.936A pdb=" N LEU9P 165 " --> pdb=" O LEU9P 242 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU9P 244 " --> pdb=" O LEU9P 165 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '9P' and resid 197 through 199 Processing sheet with id=AA6, first strand: chain 'b' and resid 21 through 25 removed outlier: 3.959A pdb=" N LEU b 32 " --> pdb=" O THR b 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AA8, first strand: chain 'C' and resid 33 through 34 removed outlier: 3.575A pdb=" N TYR C 61 " --> pdb=" O GLU C 34 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 99 through 104 removed outlier: 3.530A pdb=" N GLU C 99 " --> pdb=" O TYR C 95 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ILE C 90 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N LEU C 80 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU C 92 " --> pdb=" O GLU C 78 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ILE C 73 " --> pdb=" O SER C 117 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N SER C 117 " --> pdb=" O ILE C 73 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 128 through 130 removed outlier: 4.061A pdb=" N VAL C 164 " --> pdb=" O THR C 172 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR C 172 " --> pdb=" O VAL C 164 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 175 removed outlier: 5.040A pdb=" N THR D 171 " --> pdb=" O GLY D 111 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N GLY D 111 " --> pdb=" O THR D 171 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N GLN D 173 " --> pdb=" O VAL D 109 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N VAL D 109 " --> pdb=" O GLN D 173 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N LYS D 8 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N GLU D 28 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N LEU D 186 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N VAL D 180 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU D 188 " --> pdb=" O VAL D 178 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 78 through 83 removed outlier: 4.016A pdb=" N GLY D 78 " --> pdb=" O THR D 52 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N THR D 52 " --> pdb=" O GLY D 78 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE D 48 " --> pdb=" O PHE D 82 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR D 51 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL D 34 " --> pdb=" O THR D 51 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 118 through 119 Processing sheet with id=AB5, first strand: chain 'E' and resid 2 through 3 removed outlier: 3.629A pdb=" N LEU E 12 " --> pdb=" O LEU E 3 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 118 through 121 removed outlier: 6.796A pdb=" N VAL E 146 " --> pdb=" O ASP E 168 " (cutoff:3.500A) removed outlier: 8.099A pdb=" N ARG E 170 " --> pdb=" O VAL E 146 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE E 148 " --> pdb=" O ARG E 170 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 17 through 18 Processing sheet with id=AB8, first strand: chain 'G' and resid 40 through 43 removed outlier: 3.749A pdb=" N LYS G 43 " --> pdb=" O THR G 50 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N THR G 50 " --> pdb=" O LYS G 43 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 120 through 123 Processing sheet with id=AC1, first strand: chain 'G' and resid 94 through 98 removed outlier: 3.554A pdb=" N ARG G 94 " --> pdb=" O SER G 105 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ILE G 102 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 122 through 124 removed outlier: 6.353A pdb=" N TYR J 16 " --> pdb=" O ILE J 55 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU J 57 " --> pdb=" O TYR J 16 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL J 18 " --> pdb=" O LEU J 57 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N TRP J 15 " --> pdb=" O GLN J 138 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'L' and resid 89 through 90 Processing sheet with id=AC5, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.483A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 47 through 51 removed outlier: 4.162A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR O 36 " --> pdb=" O HIS O 29 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLN O 38 " --> pdb=" O VAL O 27 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.642A pdb=" N TYR R 2 " --> pdb=" O ALA R 42 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA R 42 " --> pdb=" O TYR R 2 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE R 41 " --> pdb=" O VAL R 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'R' and resid 19 through 23 removed outlier: 3.657A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N PHE R 93 " --> pdb=" O HIS R 66 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N HIS R 66 " --> pdb=" O PHE R 93 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'R' and resid 72 through 75 Processing sheet with id=AD1, first strand: chain 'S' and resid 2 through 10 removed outlier: 3.622A pdb=" N HIS S 9 " --> pdb=" O SER S 101 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N SER S 101 " --> pdb=" O HIS S 9 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS S 98 " --> pdb=" O SER S 81 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N SER S 81 " --> pdb=" O LYS S 98 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N SER S 108 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N VAL S 71 " --> pdb=" O SER S 108 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 86 through 87 Processing sheet with id=AD3, first strand: chain 'T' and resid 11 through 14 removed outlier: 3.931A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 64 through 65 removed outlier: 6.470A pdb=" N LYS U 32 " --> pdb=" O VAL U 27 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N VAL U 27 " --> pdb=" O LYS U 32 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE U 34 " --> pdb=" O LYS U 25 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N GLU U 9 " --> pdb=" O PHE U 72 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN U 73 " --> pdb=" O LYS U 78 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS U 78 " --> pdb=" O ASN U 73 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AD6, first strand: chain 'U' and resid 82 through 85 removed outlier: 3.518A pdb=" N ARG U 85 " --> pdb=" O VAL U 92 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N VAL U 92 " --> pdb=" O ARG U 85 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 2 through 8 removed outlier: 7.985A pdb=" N ASN V 5 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N ASP V 43 " --> pdb=" O ASN V 5 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLU V 7 " --> pdb=" O GLU V 41 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N LYS V 25 " --> pdb=" O GLN V 87 " (cutoff:3.500A) removed outlier: 10.428A pdb=" N ILE V 89 " --> pdb=" O LYS V 25 " (cutoff:3.500A) removed outlier: 8.686A pdb=" N PHE V 91 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE V 29 " --> pdb=" O PHE V 91 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ARG V 93 " --> pdb=" O ILE V 29 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR V 31 " --> pdb=" O ARG V 93 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N LEU V 86 " --> pdb=" O ARG V 79 " (cutoff:3.500A) removed outlier: 8.383A pdb=" N ARG V 79 " --> pdb=" O LEU V 86 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N HIS V 88 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N VAL V 77 " --> pdb=" O HIS V 88 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP V 90 " --> pdb=" O GLN V 75 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN V 75 " --> pdb=" O ASP V 90 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N PHE V 2 " --> pdb=" O THR V 62 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL V 64 " --> pdb=" O PHE V 2 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE V 4 " --> pdb=" O VAL V 64 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'W' and resid 18 through 19 removed outlier: 6.961A pdb=" N LEU W 55 " --> pdb=" O ILE W 33 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N GLY W 48 " --> pdb=" O PHE W 56 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'W' and resid 26 through 27 removed outlier: 3.590A pdb=" N GLY W 61 " --> pdb=" O VAL W 27 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'X' and resid 12 through 15 removed outlier: 3.658A pdb=" N VAL X 12 " --> pdb=" O PHE X 28 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'X' and resid 32 through 39 removed outlier: 3.641A pdb=" N ARG X 44 " --> pdb=" O VAL X 39 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Z' and resid 35 through 38 removed outlier: 3.676A pdb=" N LYS Z 5 " --> pdb=" O GLU Z 57 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N GLU Z 57 " --> pdb=" O LYS Z 5 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '0' and resid 28 through 29 Processing sheet with id=AE5, first strand: chain '1' and resid 19 through 24 removed outlier: 3.647A pdb=" N VAL 1 11 " --> pdb=" O LYS 1 49 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLN 1 44 " --> pdb=" O ASP 1 39 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'K' and resid 6 through 10 removed outlier: 3.933A pdb=" N VAL K 10 " --> pdb=" O ARG K 17 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ARG K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N VAL K 24 " --> pdb=" O ILE K 38 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N ILE K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N CYS K 84 " --> pdb=" O MET K 7 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ASN K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N LEU K 86 " --> pdb=" O ASN K 9 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'K' and resid 70 through 71 removed outlier: 3.828A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N VAL K 76 " --> pdb=" O VAL P 72 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N VAL P 72 " --> pdb=" O VAL K 76 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE P 58 " --> pdb=" O PHE P 73 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG P 61 " --> pdb=" O VAL P 46 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N VAL P 46 " --> pdb=" O ARG P 61 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ILE P 63 " --> pdb=" O GLY P 44 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLY P 44 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG P 38 " --> pdb=" O VAL P 31 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR P 24 " --> pdb=" O LYS P 86 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER P 82 " --> pdb=" O LYS P 28 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N TRP P 30 " --> pdb=" O VAL P 80 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N VAL P 80 " --> pdb=" O TRP P 30 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '6' and resid 20 through 24 removed outlier: 3.845A pdb=" N GLN 6 20 " --> pdb=" O THR 6 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR 6 41 " --> pdb=" O GLN 6 20 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N ILE 6 22 " --> pdb=" O ILE 6 39 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ILE 6 39 " --> pdb=" O ILE 6 22 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ALA 6 24 " --> pdb=" O MET 6 37 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N MET 6 37 " --> pdb=" O ALA 6 24 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N CYS 6 36 " --> pdb=" O ILE 6 86 " (cutoff:3.500A) removed outlier: 8.321A pdb=" N HIS 6 88 " --> pdb=" O CYS 6 36 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE 6 38 " --> pdb=" O HIS 6 88 " (cutoff:3.500A) removed outlier: 7.789A pdb=" N MET 6 90 " --> pdb=" O ILE 6 38 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N CYS 6 40 " --> pdb=" O MET 6 90 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL 6 87 " --> pdb=" O VAL 6 80 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N VAL 6 80 " --> pdb=" O VAL 6 87 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AF1, first strand: chain 'H' and resid 77 through 82 removed outlier: 6.532A pdb=" N VAL H 78 " --> pdb=" O ASN H 145 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N VAL H 147 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N ILE H 80 " --> pdb=" O VAL H 147 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA H 140 " --> pdb=" O PHE H 132 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 89 through 94 removed outlier: 7.243A pdb=" N ARG H 123 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.689A pdb=" N ILE F 33 " --> pdb=" O LEU F 90 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS F 32 " --> pdb=" O THR F 156 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N THR F 154 " --> pdb=" O THR F 34 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ASN F 36 " --> pdb=" O ASP F 152 " (cutoff:3.500A) 839 hydrogen bonds defined for protein. 2298 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2507 hydrogen bonds 3952 hydrogen bond angles 0 basepair planarities 989 basepair parallelities 1529 stacking parallelities Total time for adding SS restraints: 152.93 Time building geometry restraints manager: 43.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 7487 1.29 - 1.42: 44665 1.42 - 1.56: 42602 1.56 - 1.69: 6039 1.69 - 1.82: 164 Bond restraints: 100957 Sorted by residual: bond pdb=" CG PRO G 111 " pdb=" CD PRO G 111 " ideal model delta sigma weight residual 1.503 1.161 0.342 3.40e-02 8.65e+02 1.01e+02 bond pdb=" N PRO G 111 " pdb=" CD PRO G 111 " ideal model delta sigma weight residual 1.473 1.526 -0.053 1.40e-02 5.10e+03 1.42e+01 bond pdb=" CB PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 1.492 1.602 -0.110 5.00e-02 4.00e+02 4.88e+00 bond pdb=" C THR D 151 " pdb=" N PRO D 152 " ideal model delta sigma weight residual 1.336 1.360 -0.024 1.20e-02 6.94e+03 3.92e+00 bond pdb=" N PHE9P 191 " pdb=" CA PHE9P 191 " ideal model delta sigma weight residual 1.457 1.479 -0.021 1.29e-02 6.01e+03 2.77e+00 ... (remaining 100952 not shown) Histogram of bond angle deviations from ideal: 83.65 - 93.74: 2 93.74 - 103.83: 7962 103.83 - 113.92: 73508 113.92 - 124.01: 56413 124.01 - 134.10: 13437 Bond angle restraints: 151322 Sorted by residual: angle pdb=" N PRO G 111 " pdb=" CD PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 103.20 83.65 19.55 1.50e+00 4.44e-01 1.70e+02 angle pdb=" CA PRO G 111 " pdb=" N PRO G 111 " pdb=" CD PRO G 111 " ideal model delta sigma weight residual 112.00 98.37 13.63 1.40e+00 5.10e-01 9.48e+01 angle pdb=" CA PRO G 111 " pdb=" CB PRO G 111 " pdb=" CG PRO G 111 " ideal model delta sigma weight residual 104.50 90.12 14.38 1.90e+00 2.77e-01 5.73e+01 angle pdb=" C ILE T 2 " pdb=" N ARG T 3 " pdb=" CA ARG T 3 " ideal model delta sigma weight residual 121.70 132.48 -10.78 1.80e+00 3.09e-01 3.58e+01 angle pdb=" N GLY D 147 " pdb=" CA GLY D 147 " pdb=" C GLY D 147 " ideal model delta sigma weight residual 110.29 117.33 -7.04 1.28e+00 6.10e-01 3.03e+01 ... (remaining 151317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 56656 35.88 - 71.76: 7062 71.76 - 107.64: 816 107.64 - 143.52: 6 143.52 - 179.41: 13 Dihedral angle restraints: 64553 sinusoidal: 54336 harmonic: 10217 Sorted by residual: dihedral pdb=" O4' U A 545 " pdb=" C1' U A 545 " pdb=" N1 U A 545 " pdb=" C2 U A 545 " ideal model delta sinusoidal sigma weight residual 200.00 60.41 139.59 1 1.50e+01 4.44e-03 7.52e+01 dihedral pdb=" O4' U A1340 " pdb=" C1' U A1340 " pdb=" N1 U A1340 " pdb=" C2 U A1340 " ideal model delta sinusoidal sigma weight residual -128.00 51.41 -179.41 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' C A 323 " pdb=" C1' C A 323 " pdb=" N1 C A 323 " pdb=" C2 C A 323 " ideal model delta sinusoidal sigma weight residual -128.00 50.05 -178.05 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 64550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 18202 0.054 - 0.108: 1031 0.108 - 0.162: 142 0.162 - 0.215: 14 0.215 - 0.269: 5 Chirality restraints: 19394 Sorted by residual: chirality pdb=" CA THR D 151 " pdb=" N THR D 151 " pdb=" C THR D 151 " pdb=" CB THR D 151 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.27 2.00e-01 2.50e+01 1.81e+00 chirality pdb=" CA ARG T 3 " pdb=" N ARG T 3 " pdb=" C ARG T 3 " pdb=" CB ARG T 3 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CB ILE N 113 " pdb=" CA ILE N 113 " pdb=" CG1 ILE N 113 " pdb=" CG2 ILE N 113 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 19391 not shown) Planarity restraints: 7943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE9P 29 " 0.071 5.00e-02 4.00e+02 1.08e-01 1.86e+01 pdb=" N PRO9P 30 " -0.187 5.00e-02 4.00e+02 pdb=" CA PRO9P 30 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO9P 30 " 0.058 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Z 16 " -0.067 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO Z 17 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO Z 17 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO Z 17 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G 110 " -0.071 5.00e-02 4.00e+02 9.74e-02 1.52e+01 pdb=" N PRO G 111 " 0.168 5.00e-02 4.00e+02 pdb=" CA PRO G 111 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO G 111 " -0.053 5.00e-02 4.00e+02 ... (remaining 7940 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 3480 2.65 - 3.21: 80059 3.21 - 3.78: 187333 3.78 - 4.34: 243004 4.34 - 4.90: 323768 Nonbonded interactions: 837644 Sorted by model distance: nonbonded pdb=" OG1 THR O 31 " pdb=" O HIS O 34 " model vdw 2.089 2.440 nonbonded pdb=" O PRO9P 190 " pdb=" OG1 THR9P 192 " model vdw 2.103 2.440 nonbonded pdb=" N6 A A1287 " pdb=" O2' G A1649 " model vdw 2.105 2.520 nonbonded pdb=" OP2 A A2530 " pdb=" NZ LYS G 174 " model vdw 2.110 2.520 nonbonded pdb=" O2 C A1800 " pdb=" O6 G A1817 " model vdw 2.130 2.432 ... (remaining 837639 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=0.00 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: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 9.700 Check model and map are aligned: 1.090 Set scattering table: 0.640 Process input model: 332.970 Find NCS groups from input model: 1.540 Set up NCS constraints: 0.210 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 351.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.002 0.342 100957 Z= 0.144 Angle : 0.481 19.552 151322 Z= 0.262 Chirality : 0.027 0.269 19394 Planarity : 0.004 0.108 7943 Dihedral : 23.017 179.406 57980 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.03 % Allowed : 0.34 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % 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: -1.33 (0.14), residues: 3554 helix: -0.40 (0.19), residues: 795 sheet: -0.01 (0.21), residues: 670 loop : -1.40 (0.13), residues: 2089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP C 212 HIS 0.006 0.001 HIS J 80 PHE 0.021 0.001 PHE 6 9 TYR 0.023 0.001 TYR S 38 ARG 0.026 0.001 ARG V 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 860 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 859 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9P 1 MET cc_start: -0.0876 (mmt) cc_final: -0.2758 (mtm) REVERT: 9P 209 PHE cc_start: 0.7443 (t80) cc_final: 0.7089 (t80) REVERT: 9P 282 PHE cc_start: 0.5608 (m-10) cc_final: 0.5015 (m-80) REVERT: C 239 PHE cc_start: 0.7043 (t80) cc_final: 0.6394 (t80) REVERT: D 174 SER cc_start: 0.8513 (t) cc_final: 0.8198 (t) REVERT: E 46 GLN cc_start: 0.8268 (mp10) cc_final: 0.7816 (mp10) REVERT: E 141 MET cc_start: 0.7597 (ppp) cc_final: 0.7349 (ppp) REVERT: E 181 ILE cc_start: 0.8218 (pt) cc_final: 0.8007 (pt) REVERT: G 57 TYR cc_start: 0.5681 (m-10) cc_final: 0.5431 (m-80) REVERT: J 95 ARG cc_start: 0.7230 (tmm-80) cc_final: 0.6659 (ttp80) REVERT: L 55 MET cc_start: 0.5662 (tpt) cc_final: 0.5124 (tpt) REVERT: O 88 LYS cc_start: 0.7917 (mtpt) cc_final: 0.7096 (tmtt) REVERT: R 6 GLN cc_start: 0.8164 (pp30) cc_final: 0.7534 (pp30) REVERT: R 13 ARG cc_start: 0.7646 (ttp-170) cc_final: 0.7178 (ttp-170) REVERT: R 27 ILE cc_start: 0.8586 (tt) cc_final: 0.8386 (tt) REVERT: W 66 GLU cc_start: 0.7332 (tt0) cc_final: 0.6966 (tt0) REVERT: I 135 MET cc_start: 0.5502 (tpt) cc_final: 0.4782 (mpp) REVERT: K 97 THR cc_start: 0.7475 (m) cc_final: 0.7262 (m) REVERT: 6 21 ASP cc_start: 0.8011 (t70) cc_final: 0.7652 (t0) REVERT: H 1 MET cc_start: 0.8229 (pmm) cc_final: 0.8008 (pmm) REVERT: H 15 LEU cc_start: 0.6757 (mp) cc_final: 0.6397 (tt) REVERT: H 48 GLU cc_start: 0.7337 (mp0) cc_final: 0.7135 (mp0) outliers start: 1 outliers final: 0 residues processed: 860 average time/residue: 0.8683 time to fit residues: 1286.2235 Evaluate side-chains 703 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 703 time to evaluate : 3.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 548 optimal weight: 6.9990 chunk 492 optimal weight: 9.9990 chunk 273 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 332 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 chunk 509 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 309 optimal weight: 20.0000 chunk 379 optimal weight: 4.9990 chunk 590 optimal weight: 10.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 111 HIS 9P 123 HIS ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 205 ASN C 85 ASN ** C 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 GLN E 30 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 136 GLN N 62 ASN O 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN R 91 GLN T 28 ASN ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN 0 3 GLN 0 18 HIS 1 18 HIS 2 13 ASN 6 88 HIS 6 91 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 100957 Z= 0.396 Angle : 0.721 12.820 151322 Z= 0.363 Chirality : 0.038 0.265 19394 Planarity : 0.006 0.073 7943 Dihedral : 23.374 178.214 51044 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 3.69 % Allowed : 14.70 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3554 helix: -0.41 (0.18), residues: 847 sheet: -0.49 (0.19), residues: 720 loop : -1.42 (0.14), residues: 1987 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP C 212 HIS 0.010 0.002 HIS N 3 PHE 0.042 0.003 PHE D 127 TYR 0.026 0.002 TYR 1 48 ARG 0.013 0.001 ARG9P 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 810 time to evaluate : 3.876 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: 9P 1 MET cc_start: 0.0006 (mmt) cc_final: -0.2763 (mpp) REVERT: 9P 25 ARG cc_start: 0.6491 (ppt170) cc_final: 0.6083 (pmt170) REVERT: 9P 51 GLU cc_start: 0.7602 (tt0) cc_final: 0.6954 (pp20) REVERT: 9P 105 MET cc_start: 0.7193 (tmm) cc_final: 0.6727 (tmm) REVERT: 9P 280 LEU cc_start: 0.5298 (mp) cc_final: 0.4718 (tp) REVERT: 9P 282 PHE cc_start: 0.5410 (m-10) cc_final: 0.4911 (m-80) REVERT: 9P 295 GLU cc_start: 0.6459 (mp0) cc_final: 0.6254 (mp0) REVERT: C 256 THR cc_start: 0.8215 (p) cc_final: 0.7918 (p) REVERT: E 46 GLN cc_start: 0.8549 (mp10) cc_final: 0.8150 (mp10) REVERT: E 140 ASP cc_start: 0.7550 (m-30) cc_final: 0.7110 (m-30) REVERT: E 186 VAL cc_start: 0.9374 (t) cc_final: 0.9106 (p) REVERT: G 57 TYR cc_start: 0.6329 (m-10) cc_final: 0.6111 (m-10) REVERT: G 174 LYS cc_start: 0.4591 (mptt) cc_final: 0.4051 (tttm) REVERT: J 19 ASP cc_start: 0.8095 (t70) cc_final: 0.7836 (t0) REVERT: L 4 ASN cc_start: 0.7044 (t0) cc_final: 0.6824 (t0) REVERT: N 54 LEU cc_start: 0.8563 (tp) cc_final: 0.8280 (tp) REVERT: O 17 LYS cc_start: 0.6794 (mmtm) cc_final: 0.5550 (tptp) REVERT: R 6 GLN cc_start: 0.8432 (pp30) cc_final: 0.7890 (pp30) REVERT: S 66 ILE cc_start: 0.8986 (tp) cc_final: 0.8624 (mp) REVERT: T 4 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7998 (tm-30) REVERT: T 32 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8931 (mp) REVERT: T 40 LYS cc_start: 0.8819 (mppt) cc_final: 0.8590 (mttp) REVERT: U 64 ILE cc_start: 0.8835 (mm) cc_final: 0.8528 (mm) REVERT: U 68 ASN cc_start: 0.7762 (m110) cc_final: 0.7314 (m110) REVERT: X 75 GLU cc_start: 0.7868 (tp30) cc_final: 0.7430 (tp30) REVERT: Y 17 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8928 (tm-30) REVERT: Z 26 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8832 (mm) REVERT: 0 30 ASP cc_start: 0.7494 (t0) cc_final: 0.7247 (t0) REVERT: I 135 MET cc_start: 0.5994 (tpt) cc_final: 0.5084 (mpp) REVERT: K 86 LEU cc_start: 0.8327 (OUTLIER) cc_final: 0.8116 (mm) REVERT: P 54 LEU cc_start: 0.8680 (pt) cc_final: 0.8476 (pt) REVERT: 6 21 ASP cc_start: 0.8082 (t70) cc_final: 0.7452 (t0) REVERT: 6 41 THR cc_start: 0.5754 (m) cc_final: 0.5230 (m) REVERT: H 1 MET cc_start: 0.8334 (pmm) cc_final: 0.7972 (pmm) REVERT: H 15 LEU cc_start: 0.6597 (mp) cc_final: 0.6118 (tt) outliers start: 108 outliers final: 76 residues processed: 850 average time/residue: 0.8622 time to fit residues: 1261.0766 Evaluate side-chains 788 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 709 time to evaluate : 3.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain 9P residue 250 ILE Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 16 ILE Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 53 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain F residue 140 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 328 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 491 optimal weight: 6.9990 chunk 401 optimal weight: 7.9990 chunk 162 optimal weight: 10.0000 chunk 591 optimal weight: 3.9990 chunk 638 optimal weight: 5.9990 chunk 526 optimal weight: 7.9990 chunk 586 optimal weight: 4.9990 chunk 201 optimal weight: 7.9990 chunk 474 optimal weight: 0.8980 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 143 ASN C 116 GLN C 162 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN E 115 GLN G 127 GLN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN Q 43 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 HIS ** U 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN I 106 GLN P 2 ASN ** 6 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 88 HIS ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 100957 Z= 0.226 Angle : 0.562 11.344 151322 Z= 0.288 Chirality : 0.033 0.257 19394 Planarity : 0.005 0.061 7943 Dihedral : 23.368 179.565 51044 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 4.34 % Allowed : 19.15 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.14), residues: 3554 helix: -0.20 (0.18), residues: 867 sheet: -0.44 (0.20), residues: 706 loop : -1.35 (0.14), residues: 1981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP 6 77 HIS 0.012 0.001 HIS J 80 PHE 0.033 0.002 PHE D 127 TYR 0.015 0.001 TYR C 82 ARG 0.009 0.001 ARG X 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 767 time to evaluate : 3.789 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: 9P 1 MET cc_start: 0.0263 (mmt) cc_final: -0.2521 (mpp) REVERT: 9P 25 ARG cc_start: 0.6725 (ppt170) cc_final: 0.6502 (pmt170) REVERT: 9P 280 LEU cc_start: 0.5797 (mp) cc_final: 0.4960 (tp) REVERT: 9P 282 PHE cc_start: 0.5486 (m-10) cc_final: 0.4930 (m-80) REVERT: C 256 THR cc_start: 0.8222 (p) cc_final: 0.7939 (p) REVERT: E 46 GLN cc_start: 0.8412 (mp10) cc_final: 0.8073 (mp10) REVERT: E 186 VAL cc_start: 0.9405 (t) cc_final: 0.9126 (p) REVERT: G 57 TYR cc_start: 0.6446 (m-10) cc_final: 0.6200 (m-10) REVERT: G 174 LYS cc_start: 0.5347 (mptt) cc_final: 0.4755 (tttm) REVERT: J 19 ASP cc_start: 0.7983 (t70) cc_final: 0.7765 (t0) REVERT: L 4 ASN cc_start: 0.6680 (t0) cc_final: 0.6451 (t0) REVERT: R 6 GLN cc_start: 0.8386 (pp30) cc_final: 0.7763 (pp30) REVERT: T 4 GLU cc_start: 0.8233 (tm-30) cc_final: 0.7937 (tm-30) REVERT: T 32 LEU cc_start: 0.9043 (mp) cc_final: 0.8835 (mp) REVERT: T 40 LYS cc_start: 0.8838 (mppt) cc_final: 0.8635 (mttp) REVERT: U 34 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8347 (tp) REVERT: U 68 ASN cc_start: 0.7910 (m110) cc_final: 0.7375 (m110) REVERT: V 18 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7058 (tmt170) REVERT: X 75 GLU cc_start: 0.7677 (tp30) cc_final: 0.7155 (tp30) REVERT: Y 17 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8883 (tm-30) REVERT: 0 12 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7607 (ttm170) REVERT: 1 33 LEU cc_start: 0.6950 (mp) cc_final: 0.6077 (tt) REVERT: I 79 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6128 (mt) REVERT: I 135 MET cc_start: 0.6167 (tpt) cc_final: 0.5212 (mpp) REVERT: K 86 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7942 (mm) REVERT: P 8 GLU cc_start: 0.7513 (tp30) cc_final: 0.6826 (mm-30) REVERT: P 26 GLU cc_start: 0.7686 (tp30) cc_final: 0.7416 (tp30) REVERT: 6 16 ASP cc_start: 0.6969 (t70) cc_final: 0.6508 (m-30) REVERT: 6 21 ASP cc_start: 0.7971 (t70) cc_final: 0.7237 (t70) REVERT: 6 41 THR cc_start: 0.5487 (m) cc_final: 0.5018 (m) REVERT: H 15 LEU cc_start: 0.6986 (mp) cc_final: 0.6619 (tt) REVERT: F 176 PHE cc_start: 0.3164 (OUTLIER) cc_final: 0.2834 (m-80) outliers start: 127 outliers final: 90 residues processed: 821 average time/residue: 0.9353 time to fit residues: 1337.8389 Evaluate side-chains 811 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 716 time to evaluate : 3.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 101 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 76 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 140 ILE Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 176 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 584 optimal weight: 7.9990 chunk 444 optimal weight: 9.9990 chunk 306 optimal weight: 20.0000 chunk 65 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 397 optimal weight: 10.0000 chunk 593 optimal weight: 0.0670 chunk 628 optimal weight: 40.0000 chunk 310 optimal weight: 0.8980 chunk 562 optimal weight: 7.9990 chunk 169 optimal weight: 10.0000 overall best weight: 5.3924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN J 58 ASN ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Q 51 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 68 ASN ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 20 GLN 6 54 HIS H 43 ASN H 133 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 100957 Z= 0.267 Angle : 0.609 11.960 151322 Z= 0.311 Chirality : 0.035 0.305 19394 Planarity : 0.005 0.068 7943 Dihedral : 23.370 178.823 51044 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 16.58 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.36 % Favored : 91.62 % Rotamer: Outliers : 6.67 % Allowed : 20.07 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.14), residues: 3554 helix: -0.27 (0.18), residues: 856 sheet: -0.64 (0.19), residues: 720 loop : -1.40 (0.14), residues: 1978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP T 80 HIS 0.012 0.002 HIS J 80 PHE 0.037 0.002 PHE D 127 TYR 0.022 0.002 TYR 1 48 ARG 0.006 0.001 ARG O 13 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 956 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 195 poor density : 761 time to evaluate : 5.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 9P 1 MET cc_start: 0.0061 (mmt) cc_final: -0.2055 (mtm) REVERT: 9P 25 ARG cc_start: 0.6621 (ppt170) cc_final: 0.6334 (ptt-90) REVERT: 9P 167 MET cc_start: 0.5906 (mtt) cc_final: 0.5361 (tmm) REVERT: 9P 282 PHE cc_start: 0.5896 (m-10) cc_final: 0.5616 (m-80) REVERT: C 86 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6761 (mtt-85) REVERT: C 256 THR cc_start: 0.8402 (p) cc_final: 0.8152 (p) REVERT: E 186 VAL cc_start: 0.9411 (t) cc_final: 0.9121 (p) REVERT: G 171 LYS cc_start: 0.6476 (pttp) cc_final: 0.5305 (tmtt) REVERT: G 174 LYS cc_start: 0.5880 (mptt) cc_final: 0.5312 (tttm) REVERT: J 31 GLU cc_start: 0.7724 (tm-30) cc_final: 0.7401 (tm-30) REVERT: L 4 ASN cc_start: 0.6392 (t0) cc_final: 0.6059 (t0) REVERT: O 17 LYS cc_start: 0.6813 (mmtm) cc_final: 0.6096 (tptp) REVERT: R 6 GLN cc_start: 0.8665 (pp30) cc_final: 0.7989 (pp30) REVERT: T 32 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8881 (mp) REVERT: U 34 ILE cc_start: 0.8713 (OUTLIER) cc_final: 0.8306 (tt) REVERT: U 64 ILE cc_start: 0.8771 (mm) cc_final: 0.8543 (mm) REVERT: U 68 ASN cc_start: 0.7815 (m-40) cc_final: 0.7062 (m-40) REVERT: V 7 GLU cc_start: 0.7208 (pm20) cc_final: 0.5768 (mm-30) REVERT: V 40 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.7874 (mm) REVERT: V 41 GLU cc_start: 0.7665 (mp0) cc_final: 0.7162 (mm-30) REVERT: V 48 MET cc_start: 0.5740 (mtm) cc_final: 0.4932 (mtt) REVERT: X 71 ARG cc_start: 0.8256 (mpp-170) cc_final: 0.7968 (mtm-85) REVERT: X 75 GLU cc_start: 0.7784 (tp30) cc_final: 0.7097 (tp30) REVERT: Y 13 GLU cc_start: 0.8531 (tt0) cc_final: 0.7888 (tt0) REVERT: Y 17 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8911 (tm-30) REVERT: Y 24 GLU cc_start: 0.7333 (mm-30) cc_final: 0.7129 (mm-30) REVERT: Z 26 LEU cc_start: 0.9079 (mm) cc_final: 0.8863 (mm) REVERT: 0 5 ASN cc_start: 0.8135 (OUTLIER) cc_final: 0.7538 (m-40) REVERT: 0 12 ARG cc_start: 0.8316 (ttp80) cc_final: 0.7884 (ttm170) REVERT: 1 44 GLN cc_start: 0.6391 (mm-40) cc_final: 0.6154 (mm-40) REVERT: 2 33 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8507 (ptp90) REVERT: I 35 MET cc_start: 0.2606 (ppp) cc_final: 0.0775 (ttt) REVERT: I 79 LEU cc_start: 0.6618 (OUTLIER) cc_final: 0.6121 (mt) REVERT: I 135 MET cc_start: 0.6380 (tpt) cc_final: 0.5280 (mpp) REVERT: K 86 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7850 (mm) REVERT: P 26 GLU cc_start: 0.7681 (tp30) cc_final: 0.7346 (tp30) REVERT: 6 16 ASP cc_start: 0.7205 (t70) cc_final: 0.6765 (m-30) REVERT: 6 18 LYS cc_start: 0.8691 (tptt) cc_final: 0.8477 (tptt) REVERT: 6 21 ASP cc_start: 0.7700 (t70) cc_final: 0.6913 (t70) REVERT: 6 26 ASP cc_start: 0.7359 (t70) cc_final: 0.7156 (t0) REVERT: 6 41 THR cc_start: 0.5237 (m) cc_final: 0.4770 (m) REVERT: 6 49 MET cc_start: 0.5711 (tpt) cc_final: 0.4860 (ttt) REVERT: 6 90 MET cc_start: 0.6329 (ppp) cc_final: 0.6023 (ppp) REVERT: 6 98 TYR cc_start: 0.7428 (m-80) cc_final: 0.7221 (m-80) REVERT: H 15 LEU cc_start: 0.6989 (mp) cc_final: 0.6771 (tt) REVERT: H 22 LYS cc_start: 0.5439 (pttm) cc_final: 0.5026 (pttp) REVERT: F 94 ARG cc_start: 0.5173 (tpt90) cc_final: 0.4029 (mtt180) REVERT: F 176 PHE cc_start: 0.3547 (OUTLIER) cc_final: 0.3342 (m-10) outliers start: 195 outliers final: 135 residues processed: 859 average time/residue: 0.8661 time to fit residues: 1287.5015 Evaluate side-chains 845 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 701 time to evaluate : 3.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain 9P residue 94 THR Chi-restraints excluded: chain 9P residue 101 THR Chi-restraints excluded: chain 9P residue 250 ILE Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 35 ASP Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 49 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 96 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 108 ILE Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 121 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 23 ILE Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 65 ASP Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 48 VAL Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain X residue 63 ILE Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 33 ARG Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 61 VAL Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 64 SER Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain 6 residue 14 ILE Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 176 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 523 optimal weight: 9.9990 chunk 356 optimal weight: 8.9990 chunk 9 optimal weight: 10.0000 chunk 467 optimal weight: 8.9990 chunk 259 optimal weight: 10.0000 chunk 536 optimal weight: 8.9990 chunk 434 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 320 optimal weight: 7.9990 chunk 563 optimal weight: 9.9990 chunk 158 optimal weight: 20.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9P 123 HIS ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN J 58 ASN J 80 HIS ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN 1 45 HIS ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.166 100957 Z= 0.390 Angle : 0.735 13.118 151322 Z= 0.374 Chirality : 0.041 0.355 19394 Planarity : 0.006 0.070 7943 Dihedral : 23.566 177.984 51044 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 20.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 8.58 % Favored : 91.39 % Rotamer: Outliers : 7.15 % Allowed : 22.46 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.13), residues: 3554 helix: -0.65 (0.17), residues: 885 sheet: -1.18 (0.18), residues: 713 loop : -1.62 (0.13), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP T 80 HIS 0.014 0.002 HIS S 102 PHE 0.044 0.003 PHE9P 191 TYR 0.022 0.002 TYR C 82 ARG 0.014 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 731 time to evaluate : 3.969 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: 9P 1 MET cc_start: -0.0080 (mmt) cc_final: -0.1550 (mtm) REVERT: 9P 24 ARG cc_start: 0.8179 (tmt170) cc_final: 0.7786 (ttp80) REVERT: 9P 97 ILE cc_start: 0.6725 (OUTLIER) cc_final: 0.6415 (mt) REVERT: 9P 167 MET cc_start: 0.6053 (mtt) cc_final: 0.5438 (tmm) REVERT: 9P 280 LEU cc_start: 0.4811 (mp) cc_final: 0.4522 (tp) REVERT: C 86 ARG cc_start: 0.7913 (OUTLIER) cc_final: 0.6719 (mtt-85) REVERT: C 116 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7071 (tm-30) REVERT: C 212 TRP cc_start: 0.8244 (p90) cc_final: 0.6902 (p90) REVERT: C 256 THR cc_start: 0.8917 (p) cc_final: 0.8685 (p) REVERT: E 140 ASP cc_start: 0.7647 (m-30) cc_final: 0.7261 (m-30) REVERT: E 164 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7716 (mm) REVERT: Q 43 GLN cc_start: 0.8401 (mt0) cc_final: 0.8107 (mt0) REVERT: R 6 GLN cc_start: 0.8698 (pp30) cc_final: 0.8021 (pp30) REVERT: R 24 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8418 (ttmm) REVERT: R 31 GLU cc_start: 0.7712 (tm-30) cc_final: 0.7512 (tm-30) REVERT: S 77 ASP cc_start: 0.8445 (m-30) cc_final: 0.8206 (m-30) REVERT: T 4 GLU cc_start: 0.8388 (tm-30) cc_final: 0.8111 (tm-30) REVERT: T 32 LEU cc_start: 0.9164 (OUTLIER) cc_final: 0.8841 (mp) REVERT: T 50 LEU cc_start: 0.8912 (tt) cc_final: 0.8314 (mt) REVERT: U 17 ASP cc_start: 0.8121 (p0) cc_final: 0.7480 (p0) REVERT: U 34 ILE cc_start: 0.8760 (OUTLIER) cc_final: 0.8281 (tp) REVERT: V 18 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7577 (ttt-90) REVERT: V 40 ILE cc_start: 0.8652 (OUTLIER) cc_final: 0.8362 (mm) REVERT: V 79 ARG cc_start: 0.7048 (tpp80) cc_final: 0.6493 (tpp80) REVERT: V 85 LYS cc_start: 0.8694 (mmtm) cc_final: 0.8302 (mmtt) REVERT: W 15 LYS cc_start: 0.8338 (mmtm) cc_final: 0.7994 (mmtm) REVERT: X 24 THR cc_start: 0.8155 (p) cc_final: 0.7933 (p) REVERT: Y 13 GLU cc_start: 0.8591 (tt0) cc_final: 0.8244 (tt0) REVERT: Y 17 GLU cc_start: 0.9213 (tm-30) cc_final: 0.8969 (tm-30) REVERT: Y 45 GLN cc_start: 0.8252 (pm20) cc_final: 0.8029 (pm20) REVERT: Y 57 LEU cc_start: 0.7695 (mt) cc_final: 0.7327 (mt) REVERT: Z 26 LEU cc_start: 0.9146 (mm) cc_final: 0.8843 (mm) REVERT: 0 12 ARG cc_start: 0.8433 (ttp80) cc_final: 0.8042 (ttm170) REVERT: 1 33 LEU cc_start: 0.7044 (mp) cc_final: 0.6298 (tt) REVERT: 1 38 PHE cc_start: 0.8091 (t80) cc_final: 0.7692 (t80) REVERT: I 79 LEU cc_start: 0.6550 (OUTLIER) cc_final: 0.6011 (mt) REVERT: I 116 MET cc_start: 0.0870 (mmm) cc_final: 0.0525 (mmp) REVERT: I 135 MET cc_start: 0.6626 (tpt) cc_final: 0.5409 (mpp) REVERT: K 1 MET cc_start: 0.7906 (mmm) cc_final: 0.7532 (mmp) REVERT: K 78 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7045 (mtp85) REVERT: K 86 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7911 (mm) REVERT: 6 16 ASP cc_start: 0.7546 (t70) cc_final: 0.7110 (m-30) REVERT: 6 21 ASP cc_start: 0.7890 (t70) cc_final: 0.7155 (t70) REVERT: 6 35 ASP cc_start: 0.8578 (p0) cc_final: 0.7765 (p0) REVERT: 6 41 THR cc_start: 0.5809 (m) cc_final: 0.5423 (m) REVERT: 6 49 MET cc_start: 0.5603 (tpt) cc_final: 0.5229 (ttp) REVERT: 6 84 ASP cc_start: 0.6934 (t0) cc_final: 0.6152 (t0) REVERT: 6 90 MET cc_start: 0.6124 (ppp) cc_final: 0.5722 (ppp) REVERT: H 7 ASP cc_start: 0.8150 (t70) cc_final: 0.7669 (t0) REVERT: H 22 LYS cc_start: 0.6166 (pttm) cc_final: 0.5667 (pttp) REVERT: H 80 ILE cc_start: 0.4839 (OUTLIER) cc_final: 0.4624 (mp) REVERT: F 94 ARG cc_start: 0.5386 (tpt90) cc_final: 0.4277 (mtt180) outliers start: 209 outliers final: 143 residues processed: 841 average time/residue: 0.8498 time to fit residues: 1241.1643 Evaluate side-chains 845 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 689 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain 9P residue 97 ILE Chi-restraints excluded: chain 9P residue 101 THR Chi-restraints excluded: chain 9P residue 128 THR Chi-restraints excluded: chain 9P residue 142 THR Chi-restraints excluded: chain 9P residue 250 ILE Chi-restraints excluded: chain 9P residue 323 ASP Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 35 ASP Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 70 LYS Chi-restraints excluded: chain C residue 85 ASN Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 249 VAL Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 207 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 80 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain G residue 103 ASN Chi-restraints excluded: chain G residue 168 VAL Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 74 SER Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 20 VAL Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 82 LYS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain U residue 99 SER Chi-restraints excluded: chain V residue 18 ARG Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 66 ASP Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain I residue 91 LYS Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 112 PHE Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 71 ARG Chi-restraints excluded: chain P residue 75 THR Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain 6 residue 14 ILE Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 85 VAL Chi-restraints excluded: chain 6 residue 87 VAL Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 176 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 211 optimal weight: 50.0000 chunk 565 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 368 optimal weight: 1.9990 chunk 155 optimal weight: 10.0000 chunk 628 optimal weight: 20.0000 chunk 522 optimal weight: 2.9990 chunk 291 optimal weight: 40.0000 chunk 52 optimal weight: 10.0000 chunk 208 optimal weight: 10.0000 chunk 330 optimal weight: 8.9990 overall best weight: 6.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9P 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN G 127 GLN J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 3 GLN ** P 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.091 100957 Z= 0.296 Angle : 0.639 11.502 151322 Z= 0.327 Chirality : 0.037 0.341 19394 Planarity : 0.005 0.062 7943 Dihedral : 23.534 179.282 51044 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 6.84 % Allowed : 23.66 % Favored : 69.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3554 helix: -0.39 (0.18), residues: 875 sheet: -1.06 (0.19), residues: 689 loop : -1.56 (0.13), residues: 1990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP T 80 HIS 0.029 0.002 HIS J 80 PHE 0.027 0.002 PHE C 265 TYR 0.023 0.002 TYR9P 189 ARG 0.011 0.001 ARG R 80 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 926 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 726 time to evaluate : 3.958 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: 9P 1 MET cc_start: -0.0193 (mmt) cc_final: -0.1525 (mtm) REVERT: 9P 24 ARG cc_start: 0.8131 (tmt170) cc_final: 0.7823 (ttp80) REVERT: 9P 51 GLU cc_start: 0.7804 (tt0) cc_final: 0.7409 (pt0) REVERT: 9P 97 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6329 (mt) REVERT: 9P 167 MET cc_start: 0.6054 (mtt) cc_final: 0.5554 (tmm) REVERT: 9P 280 LEU cc_start: 0.5434 (mp) cc_final: 0.4552 (tt) REVERT: 9P 286 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: 9P 302 GLU cc_start: 0.7205 (mm-30) cc_final: 0.6623 (pt0) REVERT: C 86 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6685 (mtt-85) REVERT: C 116 GLN cc_start: 0.7371 (OUTLIER) cc_final: 0.7006 (tm-30) REVERT: D 13 ARG cc_start: 0.8876 (OUTLIER) cc_final: 0.8430 (ptt-90) REVERT: E 111 GLU cc_start: 0.7689 (tp30) cc_final: 0.7460 (tp30) REVERT: E 140 ASP cc_start: 0.7683 (m-30) cc_final: 0.7275 (m-30) REVERT: E 164 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7644 (mm) REVERT: G 42 VAL cc_start: 0.6390 (OUTLIER) cc_final: 0.6187 (t) REVERT: G 174 LYS cc_start: 0.5658 (tptt) cc_final: 0.5099 (tttp) REVERT: J 31 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7393 (tm-30) REVERT: J 49 ASP cc_start: 0.7691 (t70) cc_final: 0.7376 (t0) REVERT: R 6 GLN cc_start: 0.8642 (pp30) cc_final: 0.7907 (pp30) REVERT: S 77 ASP cc_start: 0.8410 (m-30) cc_final: 0.8207 (m-30) REVERT: T 4 GLU cc_start: 0.8375 (tm-30) cc_final: 0.8013 (tm-30) REVERT: T 32 LEU cc_start: 0.9098 (OUTLIER) cc_final: 0.8792 (mp) REVERT: T 50 LEU cc_start: 0.8754 (tt) cc_final: 0.8512 (mt) REVERT: T 54 GLU cc_start: 0.7036 (pp20) cc_final: 0.6711 (pp20) REVERT: U 17 ASP cc_start: 0.8065 (p0) cc_final: 0.7731 (p0) REVERT: U 34 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8320 (tt) REVERT: V 40 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8168 (mm) REVERT: V 48 MET cc_start: 0.5926 (mtm) cc_final: 0.5627 (mtm) REVERT: X 24 THR cc_start: 0.8091 (p) cc_final: 0.7886 (p) REVERT: Y 13 GLU cc_start: 0.8425 (tt0) cc_final: 0.8115 (tt0) REVERT: Y 17 GLU cc_start: 0.9199 (tm-30) cc_final: 0.8949 (tm-30) REVERT: Y 57 LEU cc_start: 0.7638 (mt) cc_final: 0.7370 (mt) REVERT: Z 2 LYS cc_start: 0.6895 (OUTLIER) cc_final: 0.5749 (tttt) REVERT: Z 26 LEU cc_start: 0.9166 (mm) cc_final: 0.8826 (mm) REVERT: 0 5 ASN cc_start: 0.8219 (OUTLIER) cc_final: 0.7686 (m-40) REVERT: 0 12 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7856 (ttm170) REVERT: 1 33 LEU cc_start: 0.7021 (mp) cc_final: 0.6244 (tt) REVERT: 1 38 PHE cc_start: 0.8071 (t80) cc_final: 0.7621 (t80) REVERT: I 79 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6146 (mt) REVERT: I 116 MET cc_start: 0.1453 (mmm) cc_final: 0.1240 (mmp) REVERT: I 135 MET cc_start: 0.6627 (tpt) cc_final: 0.5393 (mpp) REVERT: K 86 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7969 (mm) REVERT: 6 7 GLN cc_start: 0.7998 (mp10) cc_final: 0.7631 (pm20) REVERT: 6 8 ASP cc_start: 0.8321 (m-30) cc_final: 0.8048 (m-30) REVERT: 6 16 ASP cc_start: 0.7566 (t70) cc_final: 0.7142 (m-30) REVERT: 6 21 ASP cc_start: 0.7612 (t70) cc_final: 0.6817 (t70) REVERT: 6 35 ASP cc_start: 0.8421 (p0) cc_final: 0.7769 (p0) REVERT: 6 41 THR cc_start: 0.5030 (m) cc_final: 0.4638 (m) REVERT: 6 49 MET cc_start: 0.5642 (tpt) cc_final: 0.5194 (ttp) REVERT: 6 84 ASP cc_start: 0.6829 (t0) cc_final: 0.6110 (t0) REVERT: 6 98 TYR cc_start: 0.7919 (m-80) cc_final: 0.7567 (m-80) REVERT: H 1 MET cc_start: 0.8297 (pmm) cc_final: 0.7701 (pmm) REVERT: H 22 LYS cc_start: 0.6424 (pttm) cc_final: 0.5873 (pttp) REVERT: H 80 ILE cc_start: 0.4977 (OUTLIER) cc_final: 0.4767 (mp) REVERT: F 94 ARG cc_start: 0.5301 (tpt90) cc_final: 0.4183 (mtt180) outliers start: 200 outliers final: 149 residues processed: 835 average time/residue: 0.8568 time to fit residues: 1241.9449 Evaluate side-chains 871 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 707 time to evaluate : 3.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain 9P residue 75 SER Chi-restraints excluded: chain 9P residue 97 ILE Chi-restraints excluded: chain 9P residue 101 THR Chi-restraints excluded: chain 9P residue 130 PHE Chi-restraints excluded: chain 9P residue 159 LEU Chi-restraints excluded: chain 9P residue 191 PHE Chi-restraints excluded: chain 9P residue 200 VAL Chi-restraints excluded: chain 9P residue 250 ILE Chi-restraints excluded: chain 9P residue 286 ASP Chi-restraints excluded: chain 9P residue 323 ASP Chi-restraints excluded: chain 9P residue 324 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain b residue 35 ASP Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 86 ARG Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 116 GLN Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 172 THR Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 22 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 10 SER Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 150 THR Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 42 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain J residue 30 THR Chi-restraints excluded: chain J residue 32 LEU Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 7 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 27 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 82 LYS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 34 VAL Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 24 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 19 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 78 ARG Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 117 SER Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 71 ARG Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain 6 residue 59 SER Chi-restraints excluded: chain 6 residue 103 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain H residue 80 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 78 ILE Chi-restraints excluded: chain F residue 88 VAL Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 176 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 606 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 358 optimal weight: 0.9990 chunk 459 optimal weight: 10.0000 chunk 355 optimal weight: 0.5980 chunk 529 optimal weight: 20.0000 chunk 351 optimal weight: 0.7980 chunk 626 optimal weight: 20.0000 chunk 392 optimal weight: 0.9990 chunk 381 optimal weight: 10.0000 chunk 289 optimal weight: 40.0000 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 9P 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9P 123 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 152 GLN ** D 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 127 GLN J 58 ASN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 GLN Q 51 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS Y 25 GLN ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.070 100957 Z= 0.147 Angle : 0.550 11.472 151322 Z= 0.284 Chirality : 0.032 0.289 19394 Planarity : 0.004 0.052 7943 Dihedral : 23.468 178.016 51044 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 5.23 % Allowed : 25.57 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.14), residues: 3554 helix: -0.21 (0.18), residues: 880 sheet: -0.93 (0.19), residues: 683 loop : -1.42 (0.14), residues: 1991 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP T 80 HIS 0.010 0.001 HIS O 34 PHE 0.029 0.002 PHE9P 209 TYR 0.019 0.001 TYR C 82 ARG 0.010 0.001 ARG D 128 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 914 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 761 time to evaluate : 3.853 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: 9P 1 MET cc_start: -0.0384 (mmt) cc_final: -0.1690 (mtt) REVERT: 9P 24 ARG cc_start: 0.8113 (tmt170) cc_final: 0.7801 (ttp80) REVERT: 9P 97 ILE cc_start: 0.6829 (OUTLIER) cc_final: 0.6526 (mt) REVERT: 9P 167 MET cc_start: 0.6105 (mtt) cc_final: 0.5591 (tmm) REVERT: 9P 201 VAL cc_start: 0.7670 (t) cc_final: 0.7333 (t) REVERT: 9P 280 LEU cc_start: 0.5350 (mp) cc_final: 0.4636 (tt) REVERT: 9P 286 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7817 (m-30) REVERT: 9P 302 GLU cc_start: 0.7172 (mm-30) cc_final: 0.6759 (pt0) REVERT: C 61 TYR cc_start: 0.8586 (t80) cc_final: 0.7959 (t80) REVERT: C 212 TRP cc_start: 0.8144 (p90) cc_final: 0.7249 (p-90) REVERT: C 256 THR cc_start: 0.8800 (p) cc_final: 0.8582 (p) REVERT: E 43 THR cc_start: 0.8603 (p) cc_final: 0.8352 (p) REVERT: E 111 GLU cc_start: 0.7703 (tp30) cc_final: 0.7434 (tp30) REVERT: E 140 ASP cc_start: 0.7598 (m-30) cc_final: 0.7213 (m-30) REVERT: G 34 ARG cc_start: 0.7829 (tmm160) cc_final: 0.7612 (tmm160) REVERT: G 174 LYS cc_start: 0.5343 (tptt) cc_final: 0.4915 (tttp) REVERT: J 31 GLU cc_start: 0.7614 (tm-30) cc_final: 0.7324 (tm-30) REVERT: J 49 ASP cc_start: 0.7496 (t70) cc_final: 0.7199 (t0) REVERT: R 6 GLN cc_start: 0.8551 (pp30) cc_final: 0.7899 (pp30) REVERT: R 24 LYS cc_start: 0.8819 (OUTLIER) cc_final: 0.8569 (ttmm) REVERT: S 68 ASP cc_start: 0.7868 (t70) cc_final: 0.7654 (t70) REVERT: S 77 ASP cc_start: 0.8184 (m-30) cc_final: 0.7978 (m-30) REVERT: S 84 ARG cc_start: 0.7832 (mtt-85) cc_final: 0.7515 (mmt-90) REVERT: T 4 GLU cc_start: 0.8319 (tm-30) cc_final: 0.7997 (tm-30) REVERT: T 32 LEU cc_start: 0.9024 (mp) cc_final: 0.8778 (mp) REVERT: T 50 LEU cc_start: 0.8675 (tt) cc_final: 0.8468 (mt) REVERT: T 87 LEU cc_start: 0.8845 (mt) cc_final: 0.8607 (mp) REVERT: U 17 ASP cc_start: 0.7585 (p0) cc_final: 0.7247 (p0) REVERT: U 34 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8144 (tt) REVERT: U 68 ASN cc_start: 0.8033 (m-40) cc_final: 0.7278 (m-40) REVERT: V 40 ILE cc_start: 0.8553 (OUTLIER) cc_final: 0.8180 (mm) REVERT: Y 13 GLU cc_start: 0.8430 (tt0) cc_final: 0.8219 (tt0) REVERT: Y 17 GLU cc_start: 0.9162 (tm-30) cc_final: 0.8890 (tm-30) REVERT: Z 2 LYS cc_start: 0.6965 (OUTLIER) cc_final: 0.5874 (tttt) REVERT: Z 26 LEU cc_start: 0.9070 (OUTLIER) cc_final: 0.8687 (mm) REVERT: 0 5 ASN cc_start: 0.7968 (OUTLIER) cc_final: 0.7488 (m-40) REVERT: 0 16 ARG cc_start: 0.8457 (mtt180) cc_final: 0.8175 (mtt180) REVERT: 1 33 LEU cc_start: 0.6753 (mp) cc_final: 0.6110 (tt) REVERT: 1 38 PHE cc_start: 0.7954 (t80) cc_final: 0.7533 (t80) REVERT: I 79 LEU cc_start: 0.6649 (OUTLIER) cc_final: 0.6263 (mt) REVERT: I 135 MET cc_start: 0.6494 (tpt) cc_final: 0.5357 (mpp) REVERT: K 20 MET cc_start: 0.7666 (ttp) cc_final: 0.7359 (ttm) REVERT: K 86 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.8088 (mt) REVERT: 6 7 GLN cc_start: 0.7976 (mp10) cc_final: 0.7531 (pm20) REVERT: 6 8 ASP cc_start: 0.8295 (m-30) cc_final: 0.7990 (m-30) REVERT: 6 21 ASP cc_start: 0.7443 (t70) cc_final: 0.6616 (t70) REVERT: 6 35 ASP cc_start: 0.8451 (p0) cc_final: 0.8220 (p0) REVERT: 6 49 MET cc_start: 0.5630 (tpt) cc_final: 0.5286 (ttp) REVERT: 6 84 ASP cc_start: 0.6949 (t0) cc_final: 0.6611 (t0) REVERT: H 22 LYS cc_start: 0.6300 (OUTLIER) cc_final: 0.5987 (pttm) REVERT: F 94 ARG cc_start: 0.5237 (tpt90) cc_final: 0.4144 (mtt180) outliers start: 153 outliers final: 103 residues processed: 836 average time/residue: 0.8740 time to fit residues: 1259.0978 Evaluate side-chains 831 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 717 time to evaluate : 3.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain 9P residue 75 SER Chi-restraints excluded: chain 9P residue 97 ILE Chi-restraints excluded: chain 9P residue 133 SER Chi-restraints excluded: chain 9P residue 142 THR Chi-restraints excluded: chain 9P residue 159 LEU Chi-restraints excluded: chain 9P residue 286 ASP Chi-restraints excluded: chain 9P residue 323 ASP Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 115 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 24 LYS Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 60 LYS Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 61 ASN Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 82 LYS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain W residue 77 SER Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Z residue 2 LYS Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 51 LYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain 6 residue 31 SER Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 174 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 387 optimal weight: 8.9990 chunk 250 optimal weight: 10.0000 chunk 374 optimal weight: 5.9990 chunk 188 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 398 optimal weight: 2.9990 chunk 426 optimal weight: 0.0470 chunk 309 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 492 optimal weight: 10.0000 overall best weight: 5.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9P 113 GLN 9P 123 HIS ** 9P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 ASN E 115 GLN G 127 GLN J 58 ASN ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 19 GLN Q 36 GLN ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 55 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.4296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 100957 Z= 0.250 Angle : 0.601 11.961 151322 Z= 0.307 Chirality : 0.035 0.325 19394 Planarity : 0.005 0.067 7943 Dihedral : 23.433 177.554 51044 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.61 % Favored : 91.39 % Rotamer: Outliers : 5.50 % Allowed : 26.12 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.14), residues: 3554 helix: -0.24 (0.18), residues: 871 sheet: -1.02 (0.19), residues: 719 loop : -1.40 (0.14), residues: 1964 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Q 60 HIS 0.011 0.001 HIS O 34 PHE 0.024 0.002 PHE H 47 TYR 0.021 0.002 TYR C 82 ARG 0.014 0.001 ARG V 18 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 885 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 724 time to evaluate : 3.913 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: 9P 1 MET cc_start: -0.0325 (mmt) cc_final: -0.1634 (mtt) REVERT: 9P 24 ARG cc_start: 0.8061 (tmt170) cc_final: 0.7766 (ttp80) REVERT: 9P 51 GLU cc_start: 0.7734 (tt0) cc_final: 0.7420 (pt0) REVERT: 9P 97 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6672 (mt) REVERT: 9P 113 GLN cc_start: 0.8965 (OUTLIER) cc_final: 0.8415 (pp30) REVERT: 9P 167 MET cc_start: 0.6138 (mtt) cc_final: 0.5589 (ppp) REVERT: 9P 201 VAL cc_start: 0.7878 (t) cc_final: 0.7616 (t) REVERT: 9P 280 LEU cc_start: 0.5405 (mp) cc_final: 0.4490 (tt) REVERT: 9P 302 GLU cc_start: 0.7082 (mm-30) cc_final: 0.6678 (pt0) REVERT: C 144 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7446 (mt-10) REVERT: C 212 TRP cc_start: 0.8227 (p90) cc_final: 0.7247 (p90) REVERT: E 111 GLU cc_start: 0.7746 (tp30) cc_final: 0.7507 (tp30) REVERT: E 140 ASP cc_start: 0.7629 (m-30) cc_final: 0.7246 (m-30) REVERT: E 164 LEU cc_start: 0.7882 (OUTLIER) cc_final: 0.7623 (mm) REVERT: G 34 ARG cc_start: 0.7904 (tmm160) cc_final: 0.7317 (tmm160) REVERT: J 13 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7949 (mmt-90) REVERT: J 31 GLU cc_start: 0.7632 (tm-30) cc_final: 0.7307 (tm-30) REVERT: J 49 ASP cc_start: 0.7560 (t70) cc_final: 0.7175 (t0) REVERT: J 96 ARG cc_start: 0.6977 (ttp80) cc_final: 0.6712 (mtm110) REVERT: J 106 LYS cc_start: 0.8708 (tppt) cc_final: 0.8224 (tppt) REVERT: R 6 GLN cc_start: 0.8652 (pp30) cc_final: 0.7966 (pp30) REVERT: T 4 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8088 (tm-30) REVERT: T 32 LEU cc_start: 0.9083 (mp) cc_final: 0.8810 (mp) REVERT: T 50 LEU cc_start: 0.8708 (tt) cc_final: 0.8484 (mt) REVERT: U 17 ASP cc_start: 0.7740 (p0) cc_final: 0.7352 (p0) REVERT: U 34 ILE cc_start: 0.8678 (OUTLIER) cc_final: 0.8198 (tt) REVERT: U 68 ASN cc_start: 0.7891 (m-40) cc_final: 0.7105 (m-40) REVERT: V 40 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8182 (mm) REVERT: V 85 LYS cc_start: 0.8813 (mmtm) cc_final: 0.8587 (mmtm) REVERT: W 15 LYS cc_start: 0.8339 (mmtm) cc_final: 0.7916 (mmtm) REVERT: Y 1 MET cc_start: 0.6808 (ptp) cc_final: 0.6585 (ptt) REVERT: Y 17 GLU cc_start: 0.9181 (tm-30) cc_final: 0.8917 (tm-30) REVERT: Z 26 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8717 (mm) REVERT: 0 5 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7563 (m-40) REVERT: I 79 LEU cc_start: 0.6758 (OUTLIER) cc_final: 0.6282 (mt) REVERT: I 116 MET cc_start: 0.1098 (mmm) cc_final: 0.0790 (mmp) REVERT: I 135 MET cc_start: 0.6447 (tpt) cc_final: 0.5339 (mpp) REVERT: K 86 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.7890 (mm) REVERT: 6 7 GLN cc_start: 0.7999 (mp10) cc_final: 0.7708 (pm20) REVERT: 6 8 ASP cc_start: 0.8318 (m-30) cc_final: 0.8027 (m-30) REVERT: 6 21 ASP cc_start: 0.7508 (t70) cc_final: 0.6699 (t70) REVERT: 6 35 ASP cc_start: 0.8347 (p0) cc_final: 0.7877 (p0) REVERT: 6 49 MET cc_start: 0.5652 (tpt) cc_final: 0.5360 (ttp) REVERT: 6 84 ASP cc_start: 0.6926 (t0) cc_final: 0.6408 (t0) REVERT: 6 98 TYR cc_start: 0.8190 (m-80) cc_final: 0.7979 (m-80) REVERT: H 22 LYS cc_start: 0.6570 (OUTLIER) cc_final: 0.5931 (pttp) REVERT: F 94 ARG cc_start: 0.5469 (tpt90) cc_final: 0.4401 (ttt180) outliers start: 161 outliers final: 125 residues processed: 810 average time/residue: 0.8542 time to fit residues: 1200.6173 Evaluate side-chains 839 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 703 time to evaluate : 3.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 11 VAL Chi-restraints excluded: chain 9P residue 75 SER Chi-restraints excluded: chain 9P residue 97 ILE Chi-restraints excluded: chain 9P residue 113 GLN Chi-restraints excluded: chain 9P residue 142 THR Chi-restraints excluded: chain 9P residue 159 LEU Chi-restraints excluded: chain 9P residue 286 ASP Chi-restraints excluded: chain 9P residue 324 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 27 LYS Chi-restraints excluded: chain C residue 50 THR Chi-restraints excluded: chain C residue 63 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 144 GLU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 201 LEU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain C residue 258 SER Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 143 LEU Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 76 ILE Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain L residue 126 ARG Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 34 HIS Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain O residue 106 LEU Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 39 ILE Chi-restraints excluded: chain Q residue 76 SER Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 76 LYS Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 30 ILE Chi-restraints excluded: chain T residue 82 LYS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain X residue 7 THR Chi-restraints excluded: chain Y residue 20 ASN Chi-restraints excluded: chain Z residue 4 ILE Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 31 ILE Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 1 residue 22 THR Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain P residue 3 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 23 ASP Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 174 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 569 optimal weight: 6.9990 chunk 600 optimal weight: 2.9990 chunk 547 optimal weight: 0.0670 chunk 583 optimal weight: 0.6980 chunk 351 optimal weight: 0.6980 chunk 254 optimal weight: 10.0000 chunk 458 optimal weight: 4.9990 chunk 179 optimal weight: 10.0000 chunk 527 optimal weight: 5.9990 chunk 552 optimal weight: 10.0000 chunk 581 optimal weight: 8.9990 overall best weight: 1.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9P 123 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN G 127 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 100 HIS O 104 GLN Q 43 GLN Q 51 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS Y 20 ASN I 42 ASN ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 91 GLN ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 100957 Z= 0.145 Angle : 0.545 11.821 151322 Z= 0.279 Chirality : 0.032 0.309 19394 Planarity : 0.004 0.048 7943 Dihedral : 23.409 178.392 51044 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 3.97 % Allowed : 27.79 % Favored : 68.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.14), residues: 3554 helix: -0.19 (0.18), residues: 873 sheet: -0.78 (0.19), residues: 687 loop : -1.39 (0.14), residues: 1994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP Q 60 HIS 0.010 0.001 HIS O 34 PHE 0.025 0.002 PHE H 47 TYR 0.022 0.001 TYR C 82 ARG 0.010 0.001 ARG T 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 737 time to evaluate : 5.147 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: 9P 1 MET cc_start: -0.0254 (mmt) cc_final: -0.1764 (mtp) REVERT: 9P 24 ARG cc_start: 0.7988 (tmt170) cc_final: 0.7694 (ttp80) REVERT: 9P 51 GLU cc_start: 0.7701 (tt0) cc_final: 0.7349 (pt0) REVERT: 9P 97 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.6560 (mt) REVERT: 9P 167 MET cc_start: 0.5952 (mtt) cc_final: 0.5553 (tmm) REVERT: 9P 201 VAL cc_start: 0.7796 (t) cc_final: 0.7528 (t) REVERT: 9P 280 LEU cc_start: 0.5322 (mp) cc_final: 0.4478 (tt) REVERT: 9P 302 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6796 (pt0) REVERT: C 61 TYR cc_start: 0.8541 (t80) cc_final: 0.7858 (t80) REVERT: C 212 TRP cc_start: 0.8127 (p90) cc_final: 0.7350 (p90) REVERT: C 256 THR cc_start: 0.8776 (p) cc_final: 0.8548 (p) REVERT: E 46 GLN cc_start: 0.8504 (mp10) cc_final: 0.8115 (mp10) REVERT: E 111 GLU cc_start: 0.7733 (tp30) cc_final: 0.7484 (tp30) REVERT: E 140 ASP cc_start: 0.7573 (m-30) cc_final: 0.7254 (m-30) REVERT: G 163 TYR cc_start: 0.6973 (m-10) cc_final: 0.6563 (m-10) REVERT: G 174 LYS cc_start: 0.5299 (tptt) cc_final: 0.4815 (tttm) REVERT: J 13 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7691 (mmt-90) REVERT: J 49 ASP cc_start: 0.7297 (t70) cc_final: 0.6942 (t0) REVERT: R 6 GLN cc_start: 0.8490 (pp30) cc_final: 0.7793 (pp30) REVERT: T 4 GLU cc_start: 0.8464 (tm-30) cc_final: 0.8136 (tm-30) REVERT: T 32 LEU cc_start: 0.9098 (mp) cc_final: 0.8835 (mp) REVERT: U 17 ASP cc_start: 0.7292 (p0) cc_final: 0.7010 (p0) REVERT: U 68 ASN cc_start: 0.7892 (m-40) cc_final: 0.7199 (m-40) REVERT: V 8 VAL cc_start: 0.8080 (p) cc_final: 0.7753 (t) REVERT: V 40 ILE cc_start: 0.8493 (OUTLIER) cc_final: 0.8109 (mm) REVERT: X 40 GLU cc_start: 0.7414 (mp0) cc_final: 0.7140 (mp0) REVERT: Y 17 GLU cc_start: 0.9176 (tm-30) cc_final: 0.8933 (tm-30) REVERT: Z 26 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8656 (mm) REVERT: Z 31 ILE cc_start: 0.9244 (mt) cc_final: 0.9037 (mm) REVERT: Z 38 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7646 (mm-30) REVERT: 0 5 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7496 (m-40) REVERT: 1 38 PHE cc_start: 0.7570 (t80) cc_final: 0.7336 (t80) REVERT: I 135 MET cc_start: 0.6026 (tpt) cc_final: 0.5089 (mpp) REVERT: K 86 LEU cc_start: 0.8271 (OUTLIER) cc_final: 0.8062 (mt) REVERT: 6 7 GLN cc_start: 0.7988 (mp10) cc_final: 0.7686 (pm20) REVERT: 6 8 ASP cc_start: 0.8283 (m-30) cc_final: 0.8007 (m-30) REVERT: 6 21 ASP cc_start: 0.7437 (t70) cc_final: 0.6600 (t70) REVERT: 6 35 ASP cc_start: 0.8291 (p0) cc_final: 0.7884 (p0) REVERT: 6 84 ASP cc_start: 0.6793 (t0) cc_final: 0.6307 (t0) REVERT: 6 98 TYR cc_start: 0.8173 (m-80) cc_final: 0.7874 (m-80) REVERT: H 1 MET cc_start: 0.8290 (pmm) cc_final: 0.7892 (pmm) REVERT: H 22 LYS cc_start: 0.6513 (OUTLIER) cc_final: 0.6181 (pttm) REVERT: F 94 ARG cc_start: 0.5540 (tpt90) cc_final: 0.4353 (mtt180) outliers start: 116 outliers final: 96 residues processed: 793 average time/residue: 0.8654 time to fit residues: 1187.9159 Evaluate side-chains 807 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 705 time to evaluate : 3.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 75 SER Chi-restraints excluded: chain 9P residue 97 ILE Chi-restraints excluded: chain 9P residue 159 LEU Chi-restraints excluded: chain 9P residue 229 ILE Chi-restraints excluded: chain 9P residue 286 ASP Chi-restraints excluded: chain 9P residue 324 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 82 LYS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 80 ASP Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 174 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 383 optimal weight: 5.9990 chunk 617 optimal weight: 10.0000 chunk 376 optimal weight: 9.9990 chunk 292 optimal weight: 40.0000 chunk 429 optimal weight: 6.9990 chunk 647 optimal weight: 0.9990 chunk 596 optimal weight: 6.9990 chunk 515 optimal weight: 7.9990 chunk 53 optimal weight: 10.0000 chunk 398 optimal weight: 1.9990 chunk 316 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9P 123 HIS ** 9P 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN G 127 GLN ** O 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 51 GLN Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 100957 Z= 0.233 Angle : 0.590 18.591 151322 Z= 0.301 Chirality : 0.034 0.318 19394 Planarity : 0.005 0.060 7943 Dihedral : 23.387 177.520 51044 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 4.31 % Allowed : 27.83 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.14), residues: 3554 helix: -0.19 (0.18), residues: 873 sheet: -0.96 (0.19), residues: 739 loop : -1.33 (0.14), residues: 1942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Q 60 HIS 0.023 0.001 HIS O 100 PHE 0.026 0.002 PHE H 47 TYR 0.020 0.002 TYR9P 189 ARG 0.014 0.001 ARG R 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7108 Ramachandran restraints generated. 3554 Oldfield, 0 Emsley, 3554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 710 time to evaluate : 3.830 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: 9P 1 MET cc_start: -0.0317 (mmt) cc_final: -0.1745 (mtp) REVERT: 9P 24 ARG cc_start: 0.8017 (tmt170) cc_final: 0.7716 (ttp80) REVERT: 9P 51 GLU cc_start: 0.7829 (tt0) cc_final: 0.7413 (pp20) REVERT: 9P 97 ILE cc_start: 0.6850 (OUTLIER) cc_final: 0.6554 (mt) REVERT: 9P 167 MET cc_start: 0.5920 (mtt) cc_final: 0.5665 (tmm) REVERT: 9P 201 VAL cc_start: 0.7828 (t) cc_final: 0.7582 (t) REVERT: C 61 TYR cc_start: 0.8601 (t80) cc_final: 0.8011 (t80) REVERT: C 212 TRP cc_start: 0.8204 (p90) cc_final: 0.7260 (p90) REVERT: D 13 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8241 (ptt-90) REVERT: E 140 ASP cc_start: 0.7566 (m-30) cc_final: 0.7181 (m-30) REVERT: J 13 ARG cc_start: 0.8131 (mmt-90) cc_final: 0.7872 (mmt-90) REVERT: J 49 ASP cc_start: 0.7482 (t70) cc_final: 0.7117 (t0) REVERT: R 6 GLN cc_start: 0.8606 (pp30) cc_final: 0.7928 (pp30) REVERT: T 4 GLU cc_start: 0.8448 (tm-30) cc_final: 0.8136 (tm-30) REVERT: T 32 LEU cc_start: 0.9115 (mp) cc_final: 0.8856 (mp) REVERT: U 17 ASP cc_start: 0.7633 (p0) cc_final: 0.7286 (p0) REVERT: U 34 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8193 (tt) REVERT: V 40 ILE cc_start: 0.8521 (OUTLIER) cc_final: 0.8153 (mm) REVERT: Y 17 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8909 (tm-30) REVERT: Z 26 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8747 (mm) REVERT: Z 38 GLU cc_start: 0.7933 (mm-30) cc_final: 0.7696 (mm-30) REVERT: 0 5 ASN cc_start: 0.8067 (OUTLIER) cc_final: 0.7603 (m-40) REVERT: 1 33 LEU cc_start: 0.6452 (mp) cc_final: 0.5697 (tt) REVERT: 1 38 PHE cc_start: 0.7568 (t80) cc_final: 0.7280 (t80) REVERT: I 79 LEU cc_start: 0.6671 (OUTLIER) cc_final: 0.6291 (mt) REVERT: I 135 MET cc_start: 0.6275 (tpt) cc_final: 0.5131 (mpp) REVERT: K 82 ASN cc_start: 0.9060 (m-40) cc_final: 0.8740 (m110) REVERT: K 86 LEU cc_start: 0.8357 (OUTLIER) cc_final: 0.7884 (mm) REVERT: P 67 GLU cc_start: 0.7424 (tp30) cc_final: 0.7222 (tp30) REVERT: 6 7 GLN cc_start: 0.8017 (mp10) cc_final: 0.7723 (pm20) REVERT: 6 8 ASP cc_start: 0.8284 (m-30) cc_final: 0.7991 (m-30) REVERT: 6 21 ASP cc_start: 0.7543 (t70) cc_final: 0.6722 (t70) REVERT: 6 35 ASP cc_start: 0.8334 (p0) cc_final: 0.7839 (p0) REVERT: 6 84 ASP cc_start: 0.6905 (t0) cc_final: 0.6369 (t0) REVERT: 6 98 TYR cc_start: 0.8124 (m-80) cc_final: 0.7779 (m-80) REVERT: H 22 LYS cc_start: 0.6670 (OUTLIER) cc_final: 0.6023 (pttp) REVERT: F 94 ARG cc_start: 0.5595 (tpt90) cc_final: 0.4357 (mtt180) outliers start: 126 outliers final: 102 residues processed: 781 average time/residue: 0.8481 time to fit residues: 1145.2056 Evaluate side-chains 801 residues out of total 2927 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 690 time to evaluate : 3.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 9P residue 75 SER Chi-restraints excluded: chain 9P residue 97 ILE Chi-restraints excluded: chain 9P residue 142 THR Chi-restraints excluded: chain 9P residue 159 LEU Chi-restraints excluded: chain 9P residue 229 ILE Chi-restraints excluded: chain 9P residue 286 ASP Chi-restraints excluded: chain 9P residue 324 LEU Chi-restraints excluded: chain b residue 27 THR Chi-restraints excluded: chain C residue 53 ILE Chi-restraints excluded: chain C residue 120 ASP Chi-restraints excluded: chain C residue 198 GLU Chi-restraints excluded: chain C residue 254 LYS Chi-restraints excluded: chain D residue 2 ILE Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 186 LEU Chi-restraints excluded: chain E residue 84 THR Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 149 ILE Chi-restraints excluded: chain E residue 155 GLU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 49 LEU Chi-restraints excluded: chain G residue 61 TRP Chi-restraints excluded: chain G residue 89 VAL Chi-restraints excluded: chain G residue 91 VAL Chi-restraints excluded: chain J residue 52 ASP Chi-restraints excluded: chain J residue 60 ASP Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 80 HIS Chi-restraints excluded: chain J residue 101 ILE Chi-restraints excluded: chain J residue 118 MET Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain L residue 19 LEU Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain N residue 11 ASN Chi-restraints excluded: chain N residue 36 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 58 ASP Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 98 LEU Chi-restraints excluded: chain N residue 113 ILE Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 29 HIS Chi-restraints excluded: chain O residue 49 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 100 HIS Chi-restraints excluded: chain Q residue 3 VAL Chi-restraints excluded: chain Q residue 82 LEU Chi-restraints excluded: chain Q residue 116 LEU Chi-restraints excluded: chain R residue 25 LEU Chi-restraints excluded: chain R residue 39 LEU Chi-restraints excluded: chain R residue 70 GLU Chi-restraints excluded: chain R residue 75 VAL Chi-restraints excluded: chain R residue 85 LYS Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 21 SER Chi-restraints excluded: chain T residue 82 LYS Chi-restraints excluded: chain U residue 7 ASP Chi-restraints excluded: chain U residue 24 VAL Chi-restraints excluded: chain U residue 27 VAL Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 82 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 41 GLU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain W residue 12 SER Chi-restraints excluded: chain W residue 31 SER Chi-restraints excluded: chain W residue 32 ILE Chi-restraints excluded: chain Y residue 16 THR Chi-restraints excluded: chain Z residue 6 ILE Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 26 LEU Chi-restraints excluded: chain Z residue 40 THR Chi-restraints excluded: chain Z residue 56 VAL Chi-restraints excluded: chain 0 residue 2 VAL Chi-restraints excluded: chain 0 residue 5 ASN Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 47 TYR Chi-restraints excluded: chain 0 residue 53 VAL Chi-restraints excluded: chain 2 residue 43 THR Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 79 LEU Chi-restraints excluded: chain K residue 21 CYS Chi-restraints excluded: chain K residue 62 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 24 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 51 ASN Chi-restraints excluded: chain P residue 55 HIS Chi-restraints excluded: chain P residue 83 ILE Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 19 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 44 ILE Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 105 ILE Chi-restraints excluded: chain F residue 120 SER Chi-restraints excluded: chain F residue 154 THR Chi-restraints excluded: chain F residue 172 PHE Chi-restraints excluded: chain F residue 174 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 650 random chunks: chunk 409 optimal weight: 0.7980 chunk 549 optimal weight: 3.9990 chunk 157 optimal weight: 10.0000 chunk 475 optimal weight: 0.9990 chunk 76 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 chunk 516 optimal weight: 8.9990 chunk 216 optimal weight: 50.0000 chunk 530 optimal weight: 5.9990 chunk 65 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 9P 123 HIS ** C 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 115 GLN G 127 GLN O 19 GLN O 100 HIS ** Q 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 70 GLN ** Q 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 20 ASN P 2 ASN ** 6 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.114829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.088158 restraints weight = 266844.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.090203 restraints weight = 83201.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 71)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.091372 restraints weight = 43844.546| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 100957 Z= 0.213 Angle : 0.581 17.777 151322 Z= 0.297 Chirality : 0.033 0.319 19394 Planarity : 0.005 0.063 7943 Dihedral : 23.401 177.853 51044 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.31 % Allowed : 27.93 % Favored : 67.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.48 (0.14), residues: 3554 helix: -0.20 (0.18), residues: 874 sheet: -0.90 (0.19), residues: 728 loop : -1.37 (0.14), residues: 1952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP T 80 HIS 0.009 0.001 HIS O 34 PHE 0.027 0.002 PHE H 47 TYR 0.022 0.001 TYR C 82 ARG 0.013 0.001 ARG R 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18994.72 seconds wall clock time: 338 minutes 20.36 seconds (20300.36 seconds total)