Starting phenix.real_space_refine on Tue Mar 19 11:52:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwl_21420/03_2024/6vwl_21420.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwl_21420/03_2024/6vwl_21420.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwl_21420/03_2024/6vwl_21420.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwl_21420/03_2024/6vwl_21420.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwl_21420/03_2024/6vwl_21420.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vwl_21420/03_2024/6vwl_21420.pdb" } resolution = 3.1 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= 0.189 sd= 1.179 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: 6 Type Number sf(0) Gaussians P 4591 5.49 5 Mg 34 5.21 5 S 134 5.16 5 C 70294 2.51 5 N 26185 2.21 5 O 39365 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 62": "NH1" <-> "NH2" Residue "A ARG 68": "NH1" <-> "NH2" Residue "A TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 86": "NH1" <-> "NH2" Residue "A TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 166": "NH1" <-> "NH2" Residue "A ARG 257": "NH1" <-> "NH2" Residue "A ARG 268": "NH1" <-> "NH2" Residue "B ARG 13": "NH1" <-> "NH2" Residue "B ARG 59": "NH1" <-> "NH2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 83": "NH1" <-> "NH2" Residue "B ARG 169": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "C GLU 2": "OE1" <-> "OE2" Residue "C ARG 21": "NH1" <-> "NH2" Residue "C TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C ARG 61": "NH1" <-> "NH2" Residue "C ARG 88": "NH1" <-> "NH2" Residue "C ARG 102": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "C ARG 170": "NH1" <-> "NH2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 21": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 70": "NH1" <-> "NH2" Residue "D PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 79": "NH1" <-> "NH2" Residue "D ARG 91": "NH1" <-> "NH2" Residue "D ARG 101": "NH1" <-> "NH2" Residue "D ARG 109": "NH1" <-> "NH2" Residue "D ARG 111": "NH1" <-> "NH2" Residue "D ARG 114": "NH1" <-> "NH2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D PHE 176": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 46": "OD1" <-> "OD2" Residue "E PHE 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 59": "OD1" <-> "OD2" Residue "E ARG 152": "NH1" <-> "NH2" Residue "E TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 169": "NH1" <-> "NH2" Residue "F PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 37": "NH1" <-> "NH2" Residue "G TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 96": "NH1" <-> "NH2" Residue "G ARG 120": "NH1" <-> "NH2" Residue "I ARG 31": "NH1" <-> "NH2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 108": "NH1" <-> "NH2" Residue "J ARG 41": "NH1" <-> "NH2" Residue "J ARG 47": "NH1" <-> "NH2" Residue "J ARG 60": "NH1" <-> "NH2" Residue "J ARG 69": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J GLU 86": "OE1" <-> "OE2" Residue "J ARG 126": "NH1" <-> "NH2" Residue "K ARG 10": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 40": "NH1" <-> "NH2" Residue "K ARG 50": "NH1" <-> "NH2" Residue "K ARG 51": "NH1" <-> "NH2" Residue "K ARG 114": "NH1" <-> "NH2" Residue "K PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2": "NH1" <-> "NH2" Residue "L ARG 8": "NH1" <-> "NH2" Residue "L ARG 12": "NH1" <-> "NH2" Residue "L ARG 17": "NH1" <-> "NH2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "L ARG 30": "NH1" <-> "NH2" Residue "L ARG 45": "NH1" <-> "NH2" Residue "L ARG 46": "NH1" <-> "NH2" Residue "L ARG 63": "NH1" <-> "NH2" Residue "L ARG 64": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 71": "NH1" <-> "NH2" Residue "L ARG 96": "NH1" <-> "NH2" Residue "L PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 7": "NH1" <-> "NH2" Residue "M ARG 16": "NH1" <-> "NH2" Residue "M ARG 25": "NH1" <-> "NH2" Residue "M TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 60": "OE1" <-> "OE2" Residue "M GLU 80": "OE1" <-> "OE2" Residue "M ARG 81": "NH1" <-> "NH2" Residue "M ARG 102": "NH1" <-> "NH2" Residue "M ARG 111": "NH1" <-> "NH2" Residue "N ARG 20": "NH1" <-> "NH2" Residue "N PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 61": "NH1" <-> "NH2" Residue "N PHE 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 88": "NH1" <-> "NH2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "O ARG 2": "NH1" <-> "NH2" Residue "O ARG 5": "NH1" <-> "NH2" Residue "O ARG 12": "NH1" <-> "NH2" Residue "O ARG 32": "NH1" <-> "NH2" Residue "O ARG 47": "NH1" <-> "NH2" Residue "O ARG 52": "NH1" <-> "NH2" Residue "O ARG 69": "NH1" <-> "NH2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 68": "NH1" <-> "NH2" Residue "P ARG 78": "NH1" <-> "NH2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P ARG 84": "NH1" <-> "NH2" Residue "P ASP 95": "OD1" <-> "OD2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "Q ARG 88": "NH1" <-> "NH2" Residue "Q ARG 95": "NH1" <-> "NH2" Residue "Q ARG 110": "NH1" <-> "NH2" Residue "R ARG 69": "NH1" <-> "NH2" Residue "R ARG 73": "NH1" <-> "NH2" Residue "R GLU 89": "OE1" <-> "OE2" Residue "S ARG 5": "NH1" <-> "NH2" Residue "S ASP 8": "OD1" <-> "OD2" Residue "S ARG 81": "NH1" <-> "NH2" Residue "S ARG 85": "NH1" <-> "NH2" Residue "S ARG 93": "NH1" <-> "NH2" Residue "T TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 7": "NH1" <-> "NH2" Residue "U PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ASP 59": "OD1" <-> "OD2" Residue "W ARG 23": "NH1" <-> "NH2" Residue "W ARG 29": "NH1" <-> "NH2" Residue "W ARG 47": "NH1" <-> "NH2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "X ARG 10": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "Y ARG 9": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 39": "NH1" <-> "NH2" Residue "Y ARG 51": "NH1" <-> "NH2" Residue "Z PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 43": "NH1" <-> "NH2" Residue "AA ARG 3": "NH1" <-> "NH2" Residue "AA ARG 12": "NH1" <-> "NH2" Residue "AA ARG 14": "NH1" <-> "NH2" Residue "AA ARG 19": "NH1" <-> "NH2" Residue "AA ARG 21": "NH1" <-> "NH2" Residue "AA ARG 33": "NH1" <-> "NH2" Residue "AA ARG 41": "NH1" <-> "NH2" Residue "AB ARG 12": "NH1" <-> "NH2" Residue "AB ARG 29": "NH1" <-> "NH2" Residue "AB ARG 41": "NH1" <-> "NH2" Residue "AB TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "AC ARG 4": "NH1" <-> "NH2" Residue "AC ARG 12": "NH1" <-> "NH2" Residue "AC ARG 24": "NH1" <-> "NH2" Residue "a GLU 55": "OE1" <-> "OE2" Residue "a ARG 73": "NH1" <-> "NH2" Residue "a ARG 94": "NH1" <-> "NH2" Residue "a ASP 164": "OD1" <-> "OD2" Residue "a GLU 168": "OE1" <-> "OE2" Residue "a PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ASP 193": "OD1" <-> "OD2" Residue "b ASP 33": "OD1" <-> "OD2" Residue "b ARG 64": "NH1" <-> "NH2" Residue "b ARG 71": "NH1" <-> "NH2" Residue "b GLU 124": "OE1" <-> "OE2" Residue "c TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 55": "NH1" <-> "NH2" Residue "c ARG 61": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "c PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 87": "OE1" <-> "OE2" Residue "c ARG 96": "NH1" <-> "NH2" Residue "c ASP 98": "OD1" <-> "OD2" Residue "c ARG 110": "NH1" <-> "NH2" Residue "c TYR 134": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 153": "NH1" <-> "NH2" Residue "c GLU 159": "OE1" <-> "OE2" Residue "c GLU 178": "OE1" <-> "OE2" Residue "c ARG 187": "NH1" <-> "NH2" Residue "d PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 156": "NH1" <-> "NH2" Residue "e GLU 33": "OE1" <-> "OE2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 4": "NH1" <-> "NH2" Residue "f PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 91": "NH1" <-> "NH2" Residue "f ARG 94": "NH1" <-> "NH2" Residue "f ARG 118": "NH1" <-> "NH2" Residue "f ASP 125": "OD1" <-> "OD2" Residue "g TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h GLU 96": "OE1" <-> "OE2" Residue "h ARG 112": "NH1" <-> "NH2" Residue "i ARG 7": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i GLU 81": "OE1" <-> "OE2" Residue "i ASP 85": "OD1" <-> "OD2" Residue "j ASP 17": "OD1" <-> "OD2" Residue "j PHE 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 55": "NH1" <-> "NH2" Residue "k GLU 75": "OE1" <-> "OE2" Residue "l PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ARG 70": "NH1" <-> "NH2" Residue "m ASP 32": "OD1" <-> "OD2" Residue "m GLU 38": "OE1" <-> "OE2" Residue "n ASP 67": "OD1" <-> "OD2" Residue "o PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ARG 28": "NH1" <-> "NH2" Residue "o ASP 53": "OD1" <-> "OD2" Residue "p GLU 17": "OE1" <-> "OE2" Residue "r ARG 80": "NH1" <-> "NH2" Residue "s PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 39": "OE1" <-> "OE2" Residue "t ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 140603 Number of models: 1 Model: "" Number of chains: 58 Chain: "A" 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: "B" 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: "C" 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: "D" Number of atoms: 1396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1396 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 6, 'TRANS': 168} Chain: "E" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1298 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 8, 'TRANS': 164} Chain: "F" Number of atoms: 440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 440 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "G" 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: "I" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 947 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "J" Number of atoms: 1043 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1043 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "K" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "L" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "M" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 875 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "N" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "O" 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: "P" 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: "Q" 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: "R" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 714 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 1, 'TRANS': 88} Chain: "S" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 735 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain breaks: 1 Chain: "T" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 88} Chain: "U" Number of atoms: 575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 575 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "V" 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: "W" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 491 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "X" 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: "Y" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "Z" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 396 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "AA" 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: "AB" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2568 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 5, 'rna3p_pur': 61, 'rna3p_pyr': 50} Link IDs: {'rna2p': 9, 'rna3p': 110} Chain: "5" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1625 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 34, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "AC" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "2" Number of atoms: 60819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2833, 60819 Classifications: {'RNA': 2833} Modifications used: {'5*END': 1, 'rna2p_pur': 248, 'rna2p_pyr': 128, 'rna3p_pur': 1386, 'rna3p_pyr': 1071} Link IDs: {'rna2p': 375, 'rna3p': 2457} Chain breaks: 1 Chain: "a" Number of atoms: 1689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1689 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 214} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "b" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1502 Classifications: {'peptide': 197} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 10} Link IDs: {'PTRANS': 7, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 41 Chain: "c" Number of atoms: 1262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1262 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 154} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "d" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1137 Classifications: {'peptide': 156} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 150} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "e" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 5, 'TRANS': 96} Chain: "f" Number of atoms: 837 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 837 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "g" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "h" Number of atoms: 1006 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1006 Classifications: {'peptide': 127} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 123} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "i" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "j" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "k" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 940 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 7, 'TRANS': 113} Chain: "l" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 806 Classifications: {'peptide': 106} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 103} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "m" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "n" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "o" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "p" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "q" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 443 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "r" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 644 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 5, 'TRANS': 74} Chain: "s" Number of atoms: 660 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 660 Classifications: {'peptide': 85} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 83} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "t" Number of atoms: 566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 566 Classifications: {'peptide': 68} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 65} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "1" Number of atoms: 32632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1521, 32632 Classifications: {'RNA': 1521} Modifications used: {'rna2p_pur': 111, 'rna2p_pyr': 70, 'rna3p_pur': 754, 'rna3p_pyr': 586} Link IDs: {'rna2p': 180, 'rna3p': 1340} Chain breaks: 2 Chain: "4" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 926 Classifications: {'RNA': 43} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 1, 'rna3p_pur': 24, 'rna3p_pyr': 16} Link IDs: {'rna2p': 2, 'rna3p': 40} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "3" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "2" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Unusual residues: {' MG': 26} Classifications: {'undetermined': 26} Link IDs: {None: 25} Chain: "1" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 52.90, per 1000 atoms: 0.38 Number of scatterers: 140603 At special positions: 0 Unit cell: (263.61, 278.76, 223.21, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 134 16.00 P 4591 15.00 Mg 34 11.99 O 39365 8.00 N 26185 7.00 C 70294 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS k 33 " - pdb=" SG CYS k 52 " 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: 57.52 Conformation dependent library (CDL) restraints added in 7.1 seconds 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9890 Finding SS restraints... Secondary structure from input PDB file: 166 helices and 67 sheets defined 37.1% alpha, 20.3% beta 1578 base pairs and 2376 stacking pairs defined. Time for finding SS restraints: 50.31 Creating SS restraints... Processing helix chain 'A' and resid 11 through 14 removed outlier: 3.983A pdb=" N HIS A 14 " --> pdb=" O GLY A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 14' Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 196 through 200 removed outlier: 3.668A pdb=" N MET A 200 " --> pdb=" O ALA A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 214 removed outlier: 3.942A pdb=" N ALA A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 44 Processing helix chain 'B' and resid 61 through 72 Processing helix chain 'B' and resid 97 through 103 removed outlier: 4.152A pdb=" N LEU B 100 " --> pdb=" O SER B 97 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N ASP B 103 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 126 Processing helix chain 'C' and resid 15 through 20 Processing helix chain 'C' and resid 24 through 40 Processing helix chain 'C' and resid 97 through 115 Processing helix chain 'C' and resid 130 through 141 Processing helix chain 'C' and resid 154 through 164 Processing helix chain 'C' and resid 176 through 183 Processing helix chain 'C' and resid 190 through 201 Processing helix chain 'D' and resid 4 through 15 Processing helix chain 'D' and resid 48 through 60 Processing helix chain 'D' and resid 91 through 106 removed outlier: 4.435A pdb=" N GLU D 97 " --> pdb=" O GLU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 110 removed outlier: 3.708A pdb=" N ILE D 110 " --> pdb=" O VAL D 107 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 107 through 110' Processing helix chain 'D' and resid 133 through 137 removed outlier: 4.099A pdb=" N ILE D 136 " --> pdb=" O GLU D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 173 Processing helix chain 'E' and resid 59 through 80 Processing helix chain 'E' and resid 136 through 151 Processing helix chain 'F' and resid 22 through 29 Processing helix chain 'F' and resid 40 through 50 removed outlier: 3.692A pdb=" N ALA F 49 " --> pdb=" O GLU F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 55 Processing helix chain 'G' and resid 24 through 38 Processing helix chain 'G' and resid 58 through 62 removed outlier: 3.881A pdb=" N VAL G 62 " --> pdb=" O ALA G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 Processing helix chain 'G' and resid 89 through 96 Processing helix chain 'G' and resid 97 through 109 removed outlier: 4.696A pdb=" N ILE G 101 " --> pdb=" O PRO G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 121 Processing helix chain 'G' and resid 132 through 136 removed outlier: 3.505A pdb=" N GLN G 135 " --> pdb=" O HIS G 132 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN G 136 " --> pdb=" O ALA G 133 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 132 through 136' Processing helix chain 'I' and resid 104 through 108 removed outlier: 3.949A pdb=" N LEU I 107 " --> pdb=" O THR I 104 " (cutoff:3.500A) Processing helix chain 'I' and resid 112 through 119 Processing helix chain 'J' and resid 1 through 5 removed outlier: 4.292A pdb=" N ASN J 4 " --> pdb=" O MET J 1 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 78 through 84 Processing helix chain 'J' and resid 91 through 98 Processing helix chain 'J' and resid 128 through 139 Processing helix chain 'K' and resid 43 through 58 Processing helix chain 'K' and resid 109 through 124 Processing helix chain 'L' and resid 13 through 32 Processing helix chain 'L' and resid 38 through 57 removed outlier: 3.876A pdb=" N ARG L 46 " --> pdb=" O LYS L 42 " (cutoff:3.500A) Proline residue: L 50 - end of helix removed outlier: 3.925A pdb=" N THR L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 59 through 71 Processing helix chain 'L' and resid 72 through 82 Processing helix chain 'L' and resid 82 through 87 removed outlier: 3.680A pdb=" N PHE L 87 " --> pdb=" O LEU L 83 " (cutoff:3.500A) Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'M' and resid 5 through 22 removed outlier: 3.669A pdb=" N LEU M 21 " --> pdb=" O LYS M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 55 through 62 Processing helix chain 'M' and resid 67 through 86 Processing helix chain 'M' and resid 101 through 114 Processing helix chain 'N' and resid 2 through 12 Processing helix chain 'N' and resid 52 through 55 Processing helix chain 'N' and resid 98 through 103 removed outlier: 3.941A pdb=" N THR N 103 " --> pdb=" O LEU N 99 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 108 Processing helix chain 'O' and resid 5 through 20 removed outlier: 3.627A pdb=" N ALA O 9 " --> pdb=" O ARG O 5 " (cutoff:3.500A) Processing helix chain 'O' and resid 24 through 29 removed outlier: 3.571A pdb=" N SER O 28 " --> pdb=" O GLY O 25 " (cutoff:3.500A) Processing helix chain 'O' and resid 30 through 72 removed outlier: 4.003A pdb=" N GLN O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ARG O 50 " --> pdb=" O TYR O 46 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N LYS O 53 " --> pdb=" O ARG O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 74 through 85 Processing helix chain 'O' and resid 90 through 101 Processing helix chain 'O' and resid 101 through 117 Processing helix chain 'Q' and resid 13 through 22 Processing helix chain 'Q' and resid 28 through 39 Processing helix chain 'Q' and resid 42 through 61 Processing helix chain 'Q' and resid 89 through 91 No H-bonds generated for 'chain 'Q' and resid 89 through 91' Processing helix chain 'R' and resid 4 through 10 Processing helix chain 'R' and resid 17 through 27 Processing helix chain 'R' and resid 39 through 52 Processing helix chain 'T' and resid 13 through 23 Processing helix chain 'T' and resid 44 through 52 Processing helix chain 'T' and resid 54 through 58 removed outlier: 4.115A pdb=" N TYR T 57 " --> pdb=" O ALA T 54 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER T 58 " --> pdb=" O GLU T 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 54 through 58' Processing helix chain 'V' and resid 51 through 62 Processing helix chain 'V' and resid 62 through 74 Processing helix chain 'W' and resid 3 through 9 Processing helix chain 'W' and resid 10 through 35 Processing helix chain 'W' and resid 40 through 61 removed outlier: 4.188A pdb=" N LYS W 44 " --> pdb=" O SER W 40 " (cutoff:3.500A) Processing helix chain 'X' and resid 16 through 27 Processing helix chain 'X' and resid 40 through 50 Processing helix chain 'Y' and resid 8 through 18 Processing helix chain 'AA' and resid 8 through 17 Processing helix chain 'AA' and resid 17 through 24 removed outlier: 4.173A pdb=" N THRAA 24 " --> pdb=" O ALAAA 20 " (cutoff:3.500A) Processing helix chain 'AA' and resid 24 through 38 Processing helix chain 'AB' and resid 6 through 13 Processing helix chain 'AB' and resid 36 through 44 Processing helix chain 'AB' and resid 50 through 61 Processing helix chain 'AC' and resid 30 through 33 removed outlier: 3.961A pdb=" N HISAC 33 " --> pdb=" O GLUAC 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'AC' and resid 30 through 33' Processing helix chain 'a' and resid 23 through 27 removed outlier: 3.620A pdb=" N LYS a 27 " --> pdb=" O PRO a 24 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 62 Proline residue: a 47 - end of helix Processing helix chain 'a' and resid 76 through 87 Processing helix chain 'a' and resid 102 through 123 removed outlier: 5.043A pdb=" N GLN a 108 " --> pdb=" O LYS a 104 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N SER a 109 " --> pdb=" O THR a 105 " (cutoff:3.500A) Processing helix chain 'a' and resid 129 through 148 Processing helix chain 'a' and resid 169 through 179 Processing helix chain 'a' and resid 205 through 226 Processing helix chain 'b' and resid 5 through 11 Processing helix chain 'b' and resid 24 through 46 Processing helix chain 'b' and resid 47 through 49 No H-bonds generated for 'chain 'b' and resid 47 through 49' Processing helix chain 'b' and resid 71 through 75 removed outlier: 3.964A pdb=" N ILE b 74 " --> pdb=" O ARG b 71 " (cutoff:3.500A) Processing helix chain 'b' and resid 88 through 94 Processing helix chain 'b' and resid 107 through 110 Processing helix chain 'b' and resid 111 through 125 Processing helix chain 'b' and resid 128 through 143 Processing helix chain 'b' and resid 155 through 159 removed outlier: 3.668A pdb=" N GLY b 158 " --> pdb=" O ARG b 155 " (cutoff:3.500A) Processing helix chain 'c' and resid 48 through 65 removed outlier: 3.595A pdb=" N VAL c 52 " --> pdb=" O SER c 48 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 81 Processing helix chain 'c' and resid 84 through 95 Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 109 through 119 Processing helix chain 'c' and resid 145 through 150 removed outlier: 4.281A pdb=" N LYS c 150 " --> pdb=" O GLU c 146 " (cutoff:3.500A) Processing helix chain 'c' and resid 151 through 165 Processing helix chain 'c' and resid 196 through 204 Processing helix chain 'd' and resid 54 through 69 Processing helix chain 'd' and resid 108 through 118 Processing helix chain 'd' and resid 131 through 145 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 159 through 165 Processing helix chain 'e' and resid 12 through 15 Processing helix chain 'e' and resid 17 through 32 removed outlier: 4.362A pdb=" N ALA e 32 " --> pdb=" O ALA e 28 " (cutoff:3.500A) Processing helix chain 'e' and resid 67 through 81 Processing helix chain 'f' and resid 19 through 30 Processing helix chain 'f' and resid 34 through 54 Processing helix chain 'f' and resid 56 through 68 removed outlier: 3.628A pdb=" N ALA f 60 " --> pdb=" O SER f 56 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE f 61 " --> pdb=" O GLU f 57 " (cutoff:3.500A) Processing helix chain 'f' and resid 91 through 109 Processing helix chain 'f' and resid 114 through 127 Processing helix chain 'g' and resid 4 through 20 Processing helix chain 'g' and resid 29 through 43 Processing helix chain 'g' and resid 87 through 91 removed outlier: 3.761A pdb=" N LEU g 91 " --> pdb=" O LYS g 88 " (cutoff:3.500A) Processing helix chain 'g' and resid 111 through 119 Processing helix chain 'h' and resid 41 through 53 Proline residue: h 50 - end of helix Processing helix chain 'h' and resid 70 through 90 Processing helix chain 'h' and resid 93 through 101 Processing helix chain 'i' and resid 14 through 33 Processing helix chain 'i' and resid 80 through 89 Processing helix chain 'j' and resid 46 through 50 Processing helix chain 'j' and resid 53 through 57 removed outlier: 3.832A pdb=" N LYS j 56 " --> pdb=" O GLY j 53 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N SER j 57 " --> pdb=" O SER j 54 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 53 through 57' Processing helix chain 'j' and resid 58 through 74 Processing helix chain 'j' and resid 75 through 77 No H-bonds generated for 'chain 'j' and resid 75 through 77' Processing helix chain 'j' and resid 93 through 103 Processing helix chain 'k' and resid 2 through 9 Processing helix chain 'l' and resid 13 through 21 Processing helix chain 'l' and resid 25 through 37 removed outlier: 4.004A pdb=" N ALA l 35 " --> pdb=" O ALA l 31 " (cutoff:3.500A) Processing helix chain 'l' and resid 51 through 61 removed outlier: 3.746A pdb=" N LEU l 55 " --> pdb=" O GLN l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 66 through 83 Processing helix chain 'l' and resid 85 through 93 Processing helix chain 'm' and resid 2 through 19 Processing helix chain 'm' and resid 19 through 32 removed outlier: 3.672A pdb=" N ARG m 23 " --> pdb=" O TYR m 19 " (cutoff:3.500A) Processing helix chain 'm' and resid 36 through 50 Processing helix chain 'm' and resid 79 through 90 Processing helix chain 'n' and resid 3 through 15 Processing helix chain 'n' and resid 23 through 45 removed outlier: 3.779A pdb=" N GLY n 40 " --> pdb=" O ASN n 36 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N GLU n 44 " --> pdb=" O GLY n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 73 removed outlier: 4.216A pdb=" N GLY n 54 " --> pdb=" O HIS n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 85 Processing helix chain 'o' and resid 53 through 64 Processing helix chain 'o' and resid 68 through 82 Processing helix chain 'q' and resid 24 through 29 Processing helix chain 'q' and resid 30 through 32 No H-bonds generated for 'chain 'q' and resid 30 through 32' Processing helix chain 'q' and resid 40 through 45 Processing helix chain 'q' and resid 47 through 64 Processing helix chain 'r' and resid 11 through 24 removed outlier: 4.007A pdb=" N LYS r 17 " --> pdb=" O HIS r 13 " (cutoff:3.500A) Processing helix chain 'r' and resid 70 through 74 removed outlier: 4.390A pdb=" N PHE r 73 " --> pdb=" O LEU r 70 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 39 Processing helix chain 's' and resid 42 through 64 Proline residue: s 55 - end of helix Processing helix chain 's' and resid 68 through 85 Processing helix chain 't' and resid 10 through 26 Processing helix chain 't' and resid 26 through 35 Processing helix chain 't' and resid 39 through 67 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 4 Processing sheet with id=AA2, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 104 removed outlier: 6.636A pdb=" N ILE A 90 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU A 80 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU A 92 " --> pdb=" O GLU A 78 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 6.208A pdb=" N ILE A 163 " --> pdb=" O ARG A 174 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ARG A 174 " --> pdb=" O ILE A 163 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA A 165 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N MET A 180 " --> pdb=" O VAL A 267 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 143 through 144 removed outlier: 6.092A pdb=" N VAL A 143 " --> pdb=" O GLN A 152 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 15 removed outlier: 5.622A pdb=" N LYS B 8 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU B 28 " --> pdb=" O LYS B 8 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLY B 10 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N LYS B 190 " --> pdb=" O VAL B 177 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL B 177 " --> pdb=" O LYS B 190 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N THR B 171 " --> pdb=" O GLY B 111 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N GLY B 111 " --> pdb=" O THR B 171 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N GLN B 173 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N VAL B 109 " --> pdb=" O GLN B 173 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N THR B 112 " --> pdb=" O ASP B 200 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ASP B 200 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.536A pdb=" N ALA B 47 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N VAL B 37 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLN B 49 " --> pdb=" O THR B 35 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.552A pdb=" N GLY B 117 " --> pdb=" O MET B 165 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 2 through 4 Processing sheet with id=AB1, first strand: chain 'C' and resid 118 through 121 Processing sheet with id=AB2, first strand: chain 'D' and resid 65 through 68 removed outlier: 3.846A pdb=" N LEU D 65 " --> pdb=" O LYS D 87 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 15 through 19 removed outlier: 3.751A pdb=" N VAL E 22 " --> pdb=" O ASN E 19 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'E' and resid 120 through 123 removed outlier: 3.533A pdb=" N VAL E 89 " --> pdb=" O GLY E 160 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 94 through 98 removed outlier: 3.840A pdb=" N VAL E 101 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 18 through 20 Processing sheet with id=AB8, first strand: chain 'G' and resid 122 through 124 removed outlier: 6.842A pdb=" N TYR G 16 " --> pdb=" O ILE G 55 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N LEU G 57 " --> pdb=" O TYR G 16 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL G 18 " --> pdb=" O LEU G 57 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N TRP G 15 " --> pdb=" O GLN G 138 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 73 through 77 Processing sheet with id=AC1, first strand: chain 'I' and resid 6 through 10 removed outlier: 3.727A pdb=" N THR I 6 " --> pdb=" O CYS I 21 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N VAL I 10 " --> pdb=" O ARG I 17 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG I 17 " --> pdb=" O VAL I 10 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ARG I 17 " --> pdb=" O ALA I 46 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ALA I 46 " --> pdb=" O ARG I 17 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N VAL I 19 " --> pdb=" O LYS I 44 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N LYS I 44 " --> pdb=" O VAL I 19 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N CYS I 21 " --> pdb=" O THR I 42 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR I 42 " --> pdb=" O CYS I 21 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS I 59 " --> pdb=" O LEU I 87 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA I 83 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 8.353A pdb=" N CYS I 84 " --> pdb=" O MET I 7 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ASN I 9 " --> pdb=" O CYS I 84 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N LEU I 86 " --> pdb=" O ASN I 9 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'I' and resid 69 through 70 removed outlier: 3.518A pdb=" N VAL I 69 " --> pdb=" O ILE I 77 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE I 77 " --> pdb=" O VAL I 69 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL I 76 " --> pdb=" O VAL N 72 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N ALA N 57 " --> pdb=" O ILE N 49 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ILE N 49 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N THR N 59 " --> pdb=" O ILE N 47 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE N 63 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 9.089A pdb=" N GLU N 43 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N THR N 24 " --> pdb=" O VAL N 85 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N VAL N 85 " --> pdb=" O THR N 24 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU N 26 " --> pdb=" O ILE N 83 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ILE N 83 " --> pdb=" O GLU N 26 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LYS N 28 " --> pdb=" O ASP N 81 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AC4, first strand: chain 'J' and resid 89 through 90 Processing sheet with id=AC5, first strand: chain 'K' and resid 62 through 65 removed outlier: 5.801A pdb=" N VAL K 101 " --> pdb=" O ALA K 35 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA K 35 " --> pdb=" O VAL K 101 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 39 through 42 removed outlier: 3.821A pdb=" N ASN K 88 " --> pdb=" O GLU K 75 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N ILE K 73 " --> pdb=" O GLU K 90 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N TRP K 92 " --> pdb=" O LYS K 71 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LYS K 71 " --> pdb=" O TRP K 92 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 33 through 37 removed outlier: 6.767A pdb=" N MET L 110 " --> pdb=" O CYS L 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 47 through 52 removed outlier: 4.153A pdb=" N VAL M 49 " --> pdb=" O VAL M 39 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL M 28 " --> pdb=" O ASP M 93 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'P' and resid 10 through 15 removed outlier: 7.258A pdb=" N GLN P 6 " --> pdb=" O VAL P 38 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL P 38 " --> pdb=" O GLN P 6 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU P 46 " --> pdb=" O ASN P 43 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'P' and resid 19 through 23 removed outlier: 6.511A pdb=" N PHE P 93 " --> pdb=" O HIS P 66 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N HIS P 66 " --> pdb=" O PHE P 93 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ASP P 95 " --> pdb=" O VAL P 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS P 60 " --> pdb=" O THR P 99 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ILE P 101 " --> pdb=" O VAL P 58 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL P 58 " --> pdb=" O ILE P 101 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'P' and resid 72 through 78 removed outlier: 4.071A pdb=" N TYR P 83 " --> pdb=" O ARG P 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'Q' and resid 2 through 10 removed outlier: 5.487A pdb=" N ILE Q 4 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL Q 107 " --> pdb=" O ILE Q 4 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LYS Q 6 " --> pdb=" O VAL Q 105 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N VAL Q 105 " --> pdb=" O LYS Q 6 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N ARG Q 8 " --> pdb=" O ILE Q 103 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE Q 103 " --> pdb=" O ARG Q 8 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS Q 73 " --> pdb=" O VAL Q 106 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N SER Q 108 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL Q 71 " --> pdb=" O SER Q 108 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Q' and resid 82 through 87 Processing sheet with id=AD5, first strand: chain 'R' and resid 11 through 14 removed outlier: 4.012A pdb=" N LYS R 81 " --> pdb=" O VAL R 34 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN R 59 " --> pdb=" O TYR R 84 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL R 57 " --> pdb=" O THR R 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 67 through 69 Processing sheet with id=AD7, first strand: chain 'S' and resid 64 through 65 removed outlier: 6.795A pdb=" N LYS S 32 " --> pdb=" O VAL S 27 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N VAL S 27 " --> pdb=" O LYS S 32 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE S 34 " --> pdb=" O LYS S 25 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'S' and resid 40 through 45 Processing sheet with id=AD9, first strand: chain 'S' and resid 82 through 87 Processing sheet with id=AE1, first strand: chain 'T' and resid 3 through 8 removed outlier: 7.864A pdb=" N ASN T 5 " --> pdb=" O ASP T 43 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP T 43 " --> pdb=" O ASN T 5 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N GLN T 87 " --> pdb=" O LYS T 25 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN T 78 " --> pdb=" O GLN T 87 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ILE T 89 " --> pdb=" O ASP T 76 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N ASP T 76 " --> pdb=" O ILE T 89 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N PHE T 91 " --> pdb=" O ALA T 74 " (cutoff:3.500A) removed outlier: 7.235A pdb=" N ALA T 74 " --> pdb=" O PHE T 91 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG T 93 " --> pdb=" O VAL T 72 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N VAL T 72 " --> pdb=" O ARG T 93 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 18 through 19 removed outlier: 6.650A pdb=" N LEU U 55 " --> pdb=" O ILE U 33 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'U' and resid 26 through 27 Processing sheet with id=AE4, first strand: chain 'V' and resid 12 through 17 Processing sheet with id=AE5, first strand: chain 'V' and resid 33 through 39 Processing sheet with id=AE6, first strand: chain 'X' and resid 34 through 38 Processing sheet with id=AE7, first strand: chain 'Y' and resid 27 through 29 Processing sheet with id=AE8, first strand: chain 'Z' and resid 19 through 23 removed outlier: 3.711A pdb=" N LYS Z 9 " --> pdb=" O ALA Z 51 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'AB' and resid 14 through 15 Processing sheet with id=AF1, first strand: chain 'AC' and resid 2 through 3 removed outlier: 7.042A pdb=" N LYSAC 2 " --> pdb=" O ARGAC 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'AC' and resid 15 through 19 Processing sheet with id=AF3, first strand: chain 'a' and resid 15 through 18 removed outlier: 4.867A pdb=" N HIS a 17 " --> pdb=" O HIS a 38 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 89 through 91 removed outlier: 3.737A pdb=" N PHE a 89 " --> pdb=" O ILE a 66 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N LEU a 67 " --> pdb=" O PHE a 161 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU a 160 " --> pdb=" O PHE a 183 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ILE a 185 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N VAL a 162 " --> pdb=" O ILE a 185 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N VAL a 182 " --> pdb=" O PHE a 197 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N ILE a 199 " --> pdb=" O VAL a 182 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA a 184 " --> pdb=" O ILE a 199 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'b' and resid 19 through 20 Processing sheet with id=AF6, first strand: chain 'b' and resid 163 through 170 removed outlier: 5.728A pdb=" N GLY b 196 " --> pdb=" O ALA b 188 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N ALA b 188 " --> pdb=" O GLY b 196 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LYS b 198 " --> pdb=" O SER b 186 " (cutoff:3.500A) removed outlier: 7.231A pdb=" N SER b 186 " --> pdb=" O LYS b 198 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N TRP b 200 " --> pdb=" O ASN b 184 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ASN b 184 " --> pdb=" O TRP b 200 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N PHE b 202 " --> pdb=" O ASP b 182 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ASP b 182 " --> pdb=" O PHE b 202 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY b 204 " --> pdb=" O ASP b 180 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'c' and resid 127 through 128 removed outlier: 3.577A pdb=" N GLU c 171 " --> pdb=" O THR c 180 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'd' and resid 11 through 23 removed outlier: 6.992A pdb=" N LEU d 35 " --> pdb=" O ILE d 15 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N VAL d 17 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N THR d 33 " --> pdb=" O VAL d 17 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ARG d 19 " --> pdb=" O SER d 31 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N SER d 31 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N SER d 21 " --> pdb=" O ILE d 29 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE d 29 " --> pdb=" O SER d 21 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'd' and resid 84 through 87 removed outlier: 6.565A pdb=" N ILE d 105 " --> pdb=" O ALA d 124 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N ALA d 126 " --> pdb=" O ILE d 105 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'e' and resid 35 through 46 removed outlier: 6.555A pdb=" N ASN e 63 " --> pdb=" O HIS e 37 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N LEU e 39 " --> pdb=" O LEU e 61 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N LEU e 61 " --> pdb=" O LEU e 39 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ASP e 41 " --> pdb=" O TYR e 59 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR e 59 " --> pdb=" O ASP e 41 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N GLY e 43 " --> pdb=" O ALA e 57 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N ALA e 57 " --> pdb=" O GLY e 43 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N HIS e 3 " --> pdb=" O THR e 92 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 23 through 27 removed outlier: 3.590A pdb=" N ASP g 47 " --> pdb=" O THR g 61 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 64 through 65 Processing sheet with id=AG4, first strand: chain 'g' and resid 73 through 76 removed outlier: 6.690A pdb=" N VAL g 102 " --> pdb=" O ILE g 125 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N TYR g 127 " --> pdb=" O ILE g 100 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N ILE g 100 " --> pdb=" O TYR g 127 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'h' and resid 8 through 10 removed outlier: 6.856A pdb=" N VAL h 28 " --> pdb=" O ILE h 64 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N VAL h 66 " --> pdb=" O VAL h 28 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'i' and resid 39 through 52 removed outlier: 8.020A pdb=" N ASP i 75 " --> pdb=" O PRO i 39 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU i 73 " --> pdb=" O PRO i 41 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU i 71 " --> pdb=" O PRO i 43 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'i' and resid 39 through 52 removed outlier: 8.020A pdb=" N ASP i 75 " --> pdb=" O PRO i 39 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LEU i 73 " --> pdb=" O PRO i 41 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N LEU i 71 " --> pdb=" O PRO i 43 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'j' and resid 40 through 45 removed outlier: 7.163A pdb=" N ILE j 33 " --> pdb=" O LEU j 41 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N TRP j 43 " --> pdb=" O VAL j 31 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL j 31 " --> pdb=" O TRP j 43 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR j 45 " --> pdb=" O THR j 29 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N THR j 29 " --> pdb=" O THR j 45 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'k' and resid 62 through 63 Processing sheet with id=AH1, first strand: chain 'o' and resid 9 through 11 removed outlier: 3.626A pdb=" N ALA o 11 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL o 21 " --> pdb=" O ARG o 35 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ARG o 35 " --> pdb=" O VAL o 21 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG o 51 " --> pdb=" O PHE o 38 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'o' and resid 9 through 11 removed outlier: 3.626A pdb=" N ALA o 11 " --> pdb=" O ARG o 14 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL o 2 " --> pdb=" O THR o 66 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'p' and resid 7 through 13 removed outlier: 7.814A pdb=" N GLN p 8 " --> pdb=" O GLU p 25 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLU p 25 " --> pdb=" O GLN p 8 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL p 21 " --> pdb=" O VAL p 12 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N LYS p 70 " --> pdb=" O LYS p 42 " (cutoff:3.500A) removed outlier: 7.443A pdb=" N HIS p 44 " --> pdb=" O LYS p 70 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N TRP p 72 " --> pdb=" O HIS p 44 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU p 74 " --> pdb=" O HIS p 46 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N SER p 71 " --> pdb=" O CYS p 63 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLU p 59 " --> pdb=" O VAL p 75 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'r' and resid 31 through 32 1903 hydrogen bonds defined for protein. 5424 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3966 hydrogen bonds 6230 hydrogen bond angles 0 basepair planarities 1578 basepair parallelities 2376 stacking parallelities Total time for adding SS restraints: 237.56 Time building geometry restraints manager: 62.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 13387 1.31 - 1.43: 68319 1.43 - 1.56: 61836 1.56 - 1.69: 9179 1.69 - 1.81: 242 Bond restraints: 152963 Sorted by residual: bond pdb=" C1' U 2 887 " pdb=" N1 U 2 887 " ideal model delta sigma weight residual 1.470 1.565 -0.095 1.50e-02 4.44e+03 3.98e+01 bond pdb=" C1' C 5 17 " pdb=" N1 C 5 17 " ideal model delta sigma weight residual 1.470 1.554 -0.084 1.50e-02 4.44e+03 3.10e+01 bond pdb=" C GLY B 195 " pdb=" O GLY B 195 " ideal model delta sigma weight residual 1.230 1.182 0.047 9.40e-03 1.13e+04 2.55e+01 bond pdb=" CA PRO P 52 " pdb=" CB PRO P 52 " ideal model delta sigma weight residual 1.531 1.562 -0.031 6.20e-03 2.60e+04 2.46e+01 bond pdb=" CA VAL d 55 " pdb=" CB VAL d 55 " ideal model delta sigma weight residual 1.539 1.562 -0.023 5.40e-03 3.43e+04 1.76e+01 ... (remaining 152958 not shown) Histogram of bond angle deviations from ideal: 98.97 - 106.05: 25494 106.05 - 113.12: 90841 113.12 - 120.20: 55981 120.20 - 127.28: 46782 127.28 - 134.35: 10216 Bond angle restraints: 229314 Sorted by residual: angle pdb=" C3' A 2 404 " pdb=" O3' A 2 404 " pdb=" P U 2 405 " ideal model delta sigma weight residual 120.20 126.67 -6.47 1.50e+00 4.44e-01 1.86e+01 angle pdb=" C1' U 22473 " pdb=" N1 U 22473 " pdb=" C2 U 22473 " ideal model delta sigma weight residual 117.70 130.12 -12.42 3.00e+00 1.11e-01 1.71e+01 angle pdb=" C3' A 11157 " pdb=" O3' A 11157 " pdb=" P C 11158 " ideal model delta sigma weight residual 120.20 126.30 -6.10 1.50e+00 4.44e-01 1.65e+01 angle pdb=" C4' G 2 242 " pdb=" C3' G 2 242 " pdb=" O3' G 2 242 " ideal model delta sigma weight residual 109.40 115.17 -5.77 1.50e+00 4.44e-01 1.48e+01 angle pdb=" C3' G 2 242 " pdb=" O3' G 2 242 " pdb=" P U 2 243 " ideal model delta sigma weight residual 120.20 125.90 -5.70 1.50e+00 4.44e-01 1.45e+01 ... (remaining 229309 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 86433 35.89 - 71.78: 10341 71.78 - 107.67: 1215 107.67 - 143.55: 16 143.55 - 179.44: 27 Dihedral angle restraints: 98032 sinusoidal: 82703 harmonic: 15329 Sorted by residual: dihedral pdb=" O4' U 21865 " pdb=" C1' U 21865 " pdb=" N1 U 21865 " pdb=" C2 U 21865 " ideal model delta sinusoidal sigma weight residual -160.00 4.29 -164.29 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U 22884 " pdb=" C1' U 22884 " pdb=" N1 U 22884 " pdb=" C2 U 22884 " ideal model delta sinusoidal sigma weight residual 200.00 38.49 161.51 1 1.50e+01 4.44e-03 8.31e+01 dihedral pdb=" O4' C 3 12 " pdb=" C1' C 3 12 " pdb=" N1 C 3 12 " pdb=" C2 C 3 12 " ideal model delta sinusoidal sigma weight residual 200.00 48.10 151.90 1 1.50e+01 4.44e-03 8.03e+01 ... (remaining 98029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 27435 0.069 - 0.138: 1857 0.138 - 0.207: 73 0.207 - 0.276: 18 0.276 - 0.345: 1 Chirality restraints: 29384 Sorted by residual: chirality pdb=" C1' G 11491 " pdb=" O4' G 11491 " pdb=" C2' G 11491 " pdb=" N9 G 11491 " both_signs ideal model delta sigma weight residual False 2.46 2.11 0.35 2.00e-01 2.50e+01 2.98e+00 chirality pdb=" CB ILE l 8 " pdb=" CA ILE l 8 " pdb=" CG1 ILE l 8 " pdb=" CG2 ILE l 8 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C3' G 2 242 " pdb=" C4' G 2 242 " pdb=" O3' G 2 242 " pdb=" C2' G 2 242 " both_signs ideal model delta sigma weight residual False -2.74 -2.48 -0.27 2.00e-01 2.50e+01 1.78e+00 ... (remaining 29381 not shown) Planarity restraints: 11960 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C 1 624 " -0.008 2.00e-02 2.50e+03 2.35e-02 1.24e+01 pdb=" N1 C 1 624 " 0.004 2.00e-02 2.50e+03 pdb=" C2 C 1 624 " 0.061 2.00e-02 2.50e+03 pdb=" O2 C 1 624 " -0.028 2.00e-02 2.50e+03 pdb=" N3 C 1 624 " -0.016 2.00e-02 2.50e+03 pdb=" C4 C 1 624 " -0.002 2.00e-02 2.50e+03 pdb=" N4 C 1 624 " 0.002 2.00e-02 2.50e+03 pdb=" C5 C 1 624 " -0.009 2.00e-02 2.50e+03 pdb=" C6 C 1 624 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE r 40 " 0.017 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C PHE r 40 " -0.058 2.00e-02 2.50e+03 pdb=" O PHE r 40 " 0.021 2.00e-02 2.50e+03 pdb=" N PRO r 41 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 21288 " 0.038 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" N9 G 21288 " -0.051 2.00e-02 2.50e+03 pdb=" C8 G 21288 " -0.000 2.00e-02 2.50e+03 pdb=" N7 G 21288 " -0.005 2.00e-02 2.50e+03 pdb=" C5 G 21288 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G 21288 " 0.007 2.00e-02 2.50e+03 pdb=" O6 G 21288 " 0.008 2.00e-02 2.50e+03 pdb=" N1 G 21288 " 0.004 2.00e-02 2.50e+03 pdb=" C2 G 21288 " -0.004 2.00e-02 2.50e+03 pdb=" N2 G 21288 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G 21288 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G 21288 " 0.014 2.00e-02 2.50e+03 ... (remaining 11957 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 856 2.52 - 3.11: 95299 3.11 - 3.71: 273741 3.71 - 4.30: 385110 4.30 - 4.90: 525866 Nonbonded interactions: 1280872 Sorted by model distance: nonbonded pdb=" OP2 C 21315 " pdb="MG MG 23026 " model vdw 1.922 2.170 nonbonded pdb=" OP2 A 22503 " pdb="MG MG 23021 " model vdw 1.954 2.170 nonbonded pdb=" OP1 G 21332 " pdb="MG MG 23026 " model vdw 1.974 2.170 nonbonded pdb=" OP1 A 22005 " pdb="MG MG 23010 " model vdw 2.008 2.170 nonbonded pdb=" OP2 A 3 58 " pdb="MG MG 3 201 " model vdw 2.011 2.170 ... (remaining 1280867 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.120 Extract box with map and model: 57.380 Check model and map are aligned: 1.470 Set scattering table: 0.940 Process input model: 495.350 Find NCS groups from input model: 2.730 Set up NCS constraints: 0.370 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: 0.030 Load rotamer database and sin/cos tables:2.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 575.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 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 : 0.005 0.095 152963 Z= 0.297 Angle : 0.625 12.422 229314 Z= 0.316 Chirality : 0.037 0.345 29384 Planarity : 0.004 0.054 11960 Dihedral : 22.733 179.443 88139 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.22 % Favored : 95.74 % Rotamer: Outliers : 1.40 % Allowed : 7.50 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.10), residues: 5281 helix: -0.58 (0.11), residues: 1806 sheet: -1.56 (0.15), residues: 976 loop : -2.41 (0.10), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 247 HIS 0.009 0.001 HIS Y 18 PHE 0.014 0.002 PHE e 8 TYR 0.012 0.002 TYR M 64 ARG 0.005 0.001 ARG Q 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1356 time to evaluate : 5.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.7839 (mptt) cc_final: 0.7210 (tppt) REVERT: D 95 MET cc_start: 0.6791 (ptt) cc_final: 0.6415 (ppp) REVERT: D 161 SER cc_start: 0.7218 (t) cc_final: 0.6952 (t) REVERT: D 163 GLU cc_start: 0.8784 (mp0) cc_final: 0.8562 (mp0) REVERT: E 44 HIS cc_start: 0.6570 (t-90) cc_final: 0.6035 (p-80) REVERT: I 38 ILE cc_start: 0.9348 (OUTLIER) cc_final: 0.9054 (mm) REVERT: K 110 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7629 (tm-30) REVERT: M 68 LYS cc_start: 0.8487 (mttt) cc_final: 0.8183 (mttm) REVERT: M 76 LYS cc_start: 0.8282 (mtpp) cc_final: 0.7921 (tttm) REVERT: M 88 LYS cc_start: 0.8451 (tptp) cc_final: 0.8097 (tptt) REVERT: N 28 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8586 (mmtp) REVERT: N 33 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7855 (tm-30) REVERT: O 48 ASP cc_start: 0.7216 (m-30) cc_final: 0.6990 (m-30) REVERT: P 27 ILE cc_start: 0.9277 (mp) cc_final: 0.9064 (mm) REVERT: Q 53 SER cc_start: 0.9034 (m) cc_final: 0.8268 (t) REVERT: Q 65 ASP cc_start: 0.8130 (t0) cc_final: 0.7680 (t70) REVERT: T 8 VAL cc_start: 0.8516 (p) cc_final: 0.8163 (p) REVERT: T 59 GLU cc_start: 0.8353 (pt0) cc_final: 0.7938 (pt0) REVERT: U 25 GLU cc_start: 0.7841 (pt0) cc_final: 0.7610 (pt0) REVERT: W 4 LYS cc_start: 0.8021 (mppt) cc_final: 0.7803 (mtmt) REVERT: X 48 ASN cc_start: 0.8350 (t0) cc_final: 0.8088 (t0) REVERT: Z 7 LYS cc_start: 0.8315 (mtmm) cc_final: 0.7729 (mptt) REVERT: Z 22 THR cc_start: 0.8742 (t) cc_final: 0.8492 (m) REVERT: Z 49 LYS cc_start: 0.8071 (mtpt) cc_final: 0.7760 (ttmm) REVERT: AC 1 MET cc_start: 0.8324 (ttm) cc_final: 0.8104 (ttp) REVERT: AC 37 GLN cc_start: 0.7850 (tt0) cc_final: 0.7565 (tt0) REVERT: a 15 PHE cc_start: 0.6559 (m-80) cc_final: 0.6317 (m-80) REVERT: a 30 ILE cc_start: 0.7757 (OUTLIER) cc_final: 0.7488 (mt) REVERT: a 89 PHE cc_start: 0.6741 (m-80) cc_final: 0.6447 (m-80) REVERT: a 167 HIS cc_start: 0.7655 (t-90) cc_final: 0.7438 (t70) REVERT: b 20 THR cc_start: 0.8095 (p) cc_final: 0.7888 (t) REVERT: b 133 MET cc_start: 0.7663 (mtm) cc_final: 0.6688 (mtp) REVERT: b 139 ASN cc_start: 0.7178 (m-40) cc_final: 0.6795 (m110) REVERT: b 141 MET cc_start: 0.6832 (mmt) cc_final: 0.6200 (mmp) REVERT: b 143 LEU cc_start: 0.7947 (mt) cc_final: 0.7526 (mt) REVERT: b 167 TYR cc_start: 0.7369 (m-80) cc_final: 0.7148 (m-80) REVERT: b 182 ASP cc_start: 0.7357 (t0) cc_final: 0.7153 (t0) REVERT: c 172 VAL cc_start: 0.6897 (OUTLIER) cc_final: 0.6175 (p) REVERT: e 60 VAL cc_start: 0.8764 (t) cc_final: 0.8144 (t) REVERT: e 90 MET cc_start: 0.8163 (mtm) cc_final: 0.7643 (mtt) REVERT: e 92 THR cc_start: 0.8869 (p) cc_final: 0.8512 (t) REVERT: g 1 SER cc_start: 0.8718 (p) cc_final: 0.8345 (t) REVERT: g 20 ASN cc_start: 0.8718 (m110) cc_final: 0.8445 (t0) REVERT: g 37 ASN cc_start: 0.8575 (t0) cc_final: 0.8250 (t0) REVERT: g 110 MET cc_start: 0.8286 (ptp) cc_final: 0.7966 (ptp) REVERT: h 60 LEU cc_start: 0.4624 (mt) cc_final: 0.4288 (mm) REVERT: h 80 HIS cc_start: 0.6331 (t-90) cc_final: 0.5888 (t-90) REVERT: i 9 ARG cc_start: 0.6410 (ttp-170) cc_final: 0.6036 (mtp-110) REVERT: i 46 LYS cc_start: 0.8426 (ptpt) cc_final: 0.8092 (pttp) REVERT: i 63 ASP cc_start: 0.7871 (m-30) cc_final: 0.7634 (m-30) REVERT: j 34 THR cc_start: 0.8671 (p) cc_final: 0.8466 (t) REVERT: j 78 ILE cc_start: 0.8479 (mp) cc_final: 0.8036 (mp) REVERT: j 80 ASN cc_start: 0.8276 (p0) cc_final: 0.7670 (p0) REVERT: k 45 ASN cc_start: 0.6184 (p0) cc_final: 0.5190 (m110) REVERT: k 72 ASN cc_start: 0.6169 (p0) cc_final: 0.5294 (p0) REVERT: l 62 PHE cc_start: 0.7663 (p90) cc_final: 0.7397 (p90) REVERT: l 68 LEU cc_start: 0.8141 (tt) cc_final: 0.7935 (tt) REVERT: m 9 GLU cc_start: 0.8174 (pp20) cc_final: 0.7714 (pp20) REVERT: m 47 LEU cc_start: 0.8173 (tp) cc_final: 0.7828 (tt) REVERT: n 14 PHE cc_start: 0.8543 (m-80) cc_final: 0.7637 (m-80) REVERT: n 16 ARG cc_start: 0.6988 (ptt90) cc_final: 0.6752 (ppt-90) REVERT: n 48 ASP cc_start: 0.8016 (m-30) cc_final: 0.7787 (m-30) REVERT: n 67 ASP cc_start: 0.7649 (m-30) cc_final: 0.7285 (m-30) REVERT: n 79 GLN cc_start: 0.8573 (tt0) cc_final: 0.8325 (tm-30) REVERT: o 5 ARG cc_start: 0.7868 (ptp-170) cc_final: 0.7550 (mtp180) REVERT: o 17 TYR cc_start: 0.7104 (m-80) cc_final: 0.6760 (m-80) REVERT: o 26 ASN cc_start: 0.8900 (m110) cc_final: 0.8518 (m-40) REVERT: o 63 GLN cc_start: 0.8874 (mm-40) cc_final: 0.7931 (mm-40) REVERT: q 27 THR cc_start: 0.7537 (p) cc_final: 0.7288 (p) REVERT: q 29 LYS cc_start: 0.8625 (mtpt) cc_final: 0.8423 (mtpt) REVERT: r 4 LEU cc_start: 0.7865 (tp) cc_final: 0.7620 (tp) REVERT: r 5 LYS cc_start: 0.7980 (mmmm) cc_final: 0.7766 (mptt) REVERT: t 53 LYS cc_start: 0.7674 (tttp) cc_final: 0.7262 (ttpt) outliers start: 61 outliers final: 20 residues processed: 1398 average time/residue: 1.2811 time to fit residues: 3076.2900 Evaluate side-chains 1023 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1000 time to evaluate : 5.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain D residue 20 ASN Chi-restraints excluded: chain I residue 38 ILE Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 92 VAL Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain a residue 30 ILE Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 97 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 101 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 821 optimal weight: 10.0000 chunk 737 optimal weight: 4.9990 chunk 409 optimal weight: 9.9990 chunk 251 optimal weight: 6.9990 chunk 497 optimal weight: 20.0000 chunk 394 optimal weight: 6.9990 chunk 762 optimal weight: 6.9990 chunk 295 optimal weight: 20.0000 chunk 463 optimal weight: 30.0000 chunk 567 optimal weight: 7.9990 chunk 883 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 57 HIS A 85 ASN A 133 ASN A 142 ASN B 67 HIS B 164 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 HIS D 22 ASN D 36 ASN ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 44 HIS E 63 GLN E 114 HIS ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 142 GLN F 18 GLN G 40 HIS ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 104 GLN L 62 ASN L 81 ASN M 38 GLN ** M 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 36 GLN ** O 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 71 ASN P 12 HIS P 86 GLN P 89 HIS P 91 GLN ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN Q 61 ASN R 15 HIS R 59 ASN R 70 HIS ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 44 HIS S 45 GLN S 65 GLN S 68 ASN U 42 HIS U 53 HIS V 5 GLN V 15 ASN W 25 GLN W 45 GLN W 58 ASN Y 5 ASN AB 30 HIS a 57 ASN a 176 ASN b 122 GLN b 175 HIS c 119 HIS ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 GLN d 121 ASN e 14 GLN e 46 GLN f 96 ASN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 ASN ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 5 GLN ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 19 ASN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 8 GLN p 30 HIS p 46 HIS r 55 GLN ** s 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 152963 Z= 0.485 Angle : 0.734 9.779 229314 Z= 0.371 Chirality : 0.042 0.305 29384 Planarity : 0.006 0.048 11960 Dihedral : 23.558 179.890 77676 Min Nonbonded Distance : 1.761 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.70 % Favored : 94.28 % Rotamer: Outliers : 4.53 % Allowed : 15.05 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.11), residues: 5281 helix: 0.31 (0.12), residues: 1813 sheet: -1.28 (0.15), residues: 1022 loop : -2.03 (0.11), residues: 2446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP c 169 HIS 0.013 0.002 HIS A 229 PHE 0.033 0.003 PHE Z 38 TYR 0.027 0.002 TYR D 82 ARG 0.011 0.001 ARG M 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1020 time to evaluate : 5.929 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: B 13 ARG cc_start: 0.8789 (OUTLIER) cc_final: 0.8544 (ptp-170) REVERT: C 7 ASP cc_start: 0.6158 (OUTLIER) cc_final: 0.5610 (m-30) REVERT: D 13 LYS cc_start: 0.7842 (mptt) cc_final: 0.7391 (tppt) REVERT: D 95 MET cc_start: 0.7473 (ptt) cc_final: 0.6858 (ppp) REVERT: D 129 MET cc_start: 0.7459 (tmm) cc_final: 0.6986 (tmm) REVERT: E 38 ASP cc_start: 0.8677 (p0) cc_final: 0.8448 (p0) REVERT: E 44 HIS cc_start: 0.6398 (t70) cc_final: 0.5974 (p-80) REVERT: K 110 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7850 (tm-30) REVERT: K 136 MET cc_start: 0.7007 (tpp) cc_final: 0.6635 (tpp) REVERT: L 110 MET cc_start: 0.8341 (mmm) cc_final: 0.8080 (mmt) REVERT: M 104 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7385 (tp-100) REVERT: M 116 GLN cc_start: 0.8277 (tt0) cc_final: 0.7976 (tp40) REVERT: N 33 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8320 (tm-30) REVERT: N 87 ARG cc_start: 0.7555 (mtp-110) cc_final: 0.7240 (mtp180) REVERT: O 48 ASP cc_start: 0.7442 (m-30) cc_final: 0.7034 (m-30) REVERT: Q 34 ASP cc_start: 0.7903 (t0) cc_final: 0.7422 (t0) REVERT: Q 53 SER cc_start: 0.8969 (m) cc_final: 0.8431 (t) REVERT: Q 57 ASN cc_start: 0.8911 (m-40) cc_final: 0.8612 (m110) REVERT: U 25 GLU cc_start: 0.8026 (pt0) cc_final: 0.7766 (pt0) REVERT: U 64 LYS cc_start: 0.9108 (tttp) cc_final: 0.8820 (ttpp) REVERT: W 4 LYS cc_start: 0.8287 (mppt) cc_final: 0.7920 (mtpt) REVERT: Z 7 LYS cc_start: 0.8325 (mtmm) cc_final: 0.7784 (mptt) REVERT: Z 22 THR cc_start: 0.8951 (t) cc_final: 0.8722 (m) REVERT: Z 38 PHE cc_start: 0.8890 (t80) cc_final: 0.8610 (t80) REVERT: Z 49 LYS cc_start: 0.7996 (mtpt) cc_final: 0.7715 (ttpt) REVERT: AC 1 MET cc_start: 0.8287 (ttm) cc_final: 0.7969 (ttp) REVERT: AC 37 GLN cc_start: 0.8124 (tt0) cc_final: 0.7902 (tt0) REVERT: a 66 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7718 (mt) REVERT: b 133 MET cc_start: 0.7805 (mtm) cc_final: 0.7215 (mtp) REVERT: b 167 TYR cc_start: 0.7193 (m-80) cc_final: 0.6796 (m-80) REVERT: b 182 ASP cc_start: 0.7572 (t0) cc_final: 0.7172 (t0) REVERT: c 125 ASN cc_start: 0.8434 (m110) cc_final: 0.8169 (m110) REVERT: c 151 GLN cc_start: 0.7268 (tp40) cc_final: 0.7024 (tp-100) REVERT: e 17 GLN cc_start: 0.6814 (mt0) cc_final: 0.6527 (mm110) REVERT: e 92 THR cc_start: 0.8939 (p) cc_final: 0.8670 (t) REVERT: f 37 THR cc_start: 0.7437 (p) cc_final: 0.6881 (t) REVERT: g 1 SER cc_start: 0.8752 (p) cc_final: 0.8342 (t) REVERT: g 17 GLN cc_start: 0.8115 (mm110) cc_final: 0.7818 (mm110) REVERT: g 20 ASN cc_start: 0.8943 (m110) cc_final: 0.8461 (t0) REVERT: g 26 MET cc_start: 0.8616 (ptp) cc_final: 0.8351 (ptp) REVERT: g 37 ASN cc_start: 0.8689 (t0) cc_final: 0.8393 (t0) REVERT: g 110 MET cc_start: 0.8320 (ptp) cc_final: 0.8108 (ptp) REVERT: h 18 VAL cc_start: 0.2790 (OUTLIER) cc_final: 0.2585 (p) REVERT: h 59 LYS cc_start: 0.7593 (mmtm) cc_final: 0.7326 (mmtm) REVERT: h 80 HIS cc_start: 0.6402 (t-90) cc_final: 0.6008 (t70) REVERT: i 46 LYS cc_start: 0.8629 (ptpt) cc_final: 0.7961 (pttp) REVERT: j 80 ASN cc_start: 0.8070 (OUTLIER) cc_final: 0.7864 (p0) REVERT: k 39 THR cc_start: 0.5430 (OUTLIER) cc_final: 0.5110 (m) REVERT: m 2 LYS cc_start: 0.6660 (mttm) cc_final: 0.6451 (mttm) REVERT: m 9 GLU cc_start: 0.8132 (pp20) cc_final: 0.7668 (pp20) REVERT: m 88 MET cc_start: 0.8178 (mmp) cc_final: 0.7542 (mmm) REVERT: n 16 ARG cc_start: 0.7465 (ptt90) cc_final: 0.7072 (ppt-90) REVERT: n 48 ASP cc_start: 0.8208 (m-30) cc_final: 0.7972 (m-30) REVERT: n 67 ASP cc_start: 0.7637 (m-30) cc_final: 0.7312 (m-30) REVERT: n 79 GLN cc_start: 0.8595 (tt0) cc_final: 0.8176 (tm-30) REVERT: o 17 TYR cc_start: 0.7486 (m-80) cc_final: 0.7273 (m-80) REVERT: p 51 GLU cc_start: 0.7787 (mp0) cc_final: 0.7467 (mp0) REVERT: p 73 THR cc_start: 0.7666 (p) cc_final: 0.7427 (p) REVERT: q 27 THR cc_start: 0.7841 (p) cc_final: 0.7461 (p) REVERT: r 4 LEU cc_start: 0.7862 (tp) cc_final: 0.7643 (tp) REVERT: r 5 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7792 (mptt) REVERT: r 8 PRO cc_start: 0.6734 (Cg_exo) cc_final: 0.6289 (Cg_endo) REVERT: s 60 GLN cc_start: 0.8526 (mm-40) cc_final: 0.7872 (tp-100) REVERT: s 65 LEU cc_start: 0.8973 (tp) cc_final: 0.8294 (tt) REVERT: s 73 ARG cc_start: 0.8200 (ptm160) cc_final: 0.7689 (mtm-85) outliers start: 198 outliers final: 127 residues processed: 1138 average time/residue: 1.1984 time to fit residues: 2394.3607 Evaluate side-chains 1039 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 905 time to evaluate : 5.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 13 ARG Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 183 GLU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 164 LEU Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 96 TRP Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 7 HIS Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 27 SER Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 11 SER Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 27 LEU Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AC residue 12 ARG Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 116 VAL Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain h residue 18 VAL Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 34 THR Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 39 THR Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 97 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain n residue 21 THR Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 3 ILE Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Chi-restraints excluded: chain t residue 42 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 491 optimal weight: 2.9990 chunk 274 optimal weight: 0.6980 chunk 735 optimal weight: 0.9980 chunk 601 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 885 optimal weight: 10.0000 chunk 956 optimal weight: 8.9990 chunk 788 optimal weight: 1.9990 chunk 877 optimal weight: 10.0000 chunk 301 optimal weight: 10.0000 chunk 710 optimal weight: 20.0000 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 238 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 115 GLN F 18 GLN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 13 HIS ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 31 GLN ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** AB 30 HIS b 175 HIS ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 96 GLN f 96 ASN g 17 GLN g 66 GLN ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 4 ASN ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN p 46 HIS s 19 HIS s 20 ASN s 47 GLN s 51 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 152963 Z= 0.214 Angle : 0.540 10.161 229314 Z= 0.278 Chirality : 0.033 0.264 29384 Planarity : 0.004 0.052 11960 Dihedral : 23.523 179.621 77667 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.75 % Allowed : 17.27 % Favored : 78.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5281 helix: 0.95 (0.12), residues: 1817 sheet: -0.95 (0.16), residues: 1010 loop : -1.72 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP c 169 HIS 0.007 0.001 HIS Y 18 PHE 0.020 0.001 PHE Z 38 TYR 0.017 0.001 TYR l 85 ARG 0.006 0.000 ARG n 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 999 time to evaluate : 5.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 7 ASP cc_start: 0.6051 (OUTLIER) cc_final: 0.5740 (m-30) REVERT: C 165 HIS cc_start: 0.8804 (OUTLIER) cc_final: 0.8571 (t-90) REVERT: D 13 LYS cc_start: 0.7951 (mptt) cc_final: 0.7577 (tppt) REVERT: D 25 MET cc_start: 0.8142 (tpp) cc_final: 0.7926 (mmm) REVERT: D 95 MET cc_start: 0.7161 (ptt) cc_final: 0.6257 (ppp) REVERT: D 129 MET cc_start: 0.7508 (tmm) cc_final: 0.7110 (tmm) REVERT: E 44 HIS cc_start: 0.6465 (t70) cc_final: 0.5871 (p-80) REVERT: G 1 MET cc_start: 0.8345 (ptp) cc_final: 0.7883 (ptp) REVERT: I 56 ASP cc_start: 0.8113 (m-30) cc_final: 0.7849 (m-30) REVERT: K 110 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7800 (tm-30) REVERT: L 110 MET cc_start: 0.8355 (mmm) cc_final: 0.8098 (mmt) REVERT: M 55 GLU cc_start: 0.7473 (mm-30) cc_final: 0.6906 (mm-30) REVERT: M 104 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7314 (tp-100) REVERT: M 116 GLN cc_start: 0.8290 (tt0) cc_final: 0.8030 (tp40) REVERT: N 33 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8262 (tm-30) REVERT: O 48 ASP cc_start: 0.7323 (m-30) cc_final: 0.7021 (m-30) REVERT: P 2 TYR cc_start: 0.8771 (p90) cc_final: 0.8393 (p90) REVERT: Q 34 ASP cc_start: 0.7857 (t0) cc_final: 0.7479 (t0) REVERT: S 14 THR cc_start: 0.8382 (OUTLIER) cc_final: 0.8126 (t) REVERT: U 25 GLU cc_start: 0.7972 (pt0) cc_final: 0.7731 (pt0) REVERT: U 64 LYS cc_start: 0.9048 (tttp) cc_final: 0.8735 (ttpp) REVERT: W 4 LYS cc_start: 0.8149 (mppt) cc_final: 0.7766 (mtpt) REVERT: X 48 ASN cc_start: 0.8503 (t0) cc_final: 0.8218 (t0) REVERT: X 57 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7098 (mm-30) REVERT: Z 7 LYS cc_start: 0.8294 (mtmm) cc_final: 0.7774 (mptt) REVERT: Z 49 LYS cc_start: 0.7959 (mtpt) cc_final: 0.7611 (ttpt) REVERT: AC 37 GLN cc_start: 0.8018 (tt0) cc_final: 0.7666 (tt0) REVERT: b 133 MET cc_start: 0.7734 (mtm) cc_final: 0.6988 (mtp) REVERT: b 167 TYR cc_start: 0.7332 (m-80) cc_final: 0.6913 (m-80) REVERT: b 182 ASP cc_start: 0.7602 (t0) cc_final: 0.7301 (t0) REVERT: c 102 TYR cc_start: 0.8303 (t80) cc_final: 0.8048 (t80) REVERT: c 104 MET cc_start: 0.7363 (ttm) cc_final: 0.6893 (ttm) REVERT: c 125 ASN cc_start: 0.8495 (m110) cc_final: 0.8174 (m110) REVERT: c 151 GLN cc_start: 0.6830 (tp40) cc_final: 0.6621 (tp-100) REVERT: d 70 MET cc_start: 0.7849 (ttp) cc_final: 0.7485 (ttp) REVERT: e 3 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7077 (m-70) REVERT: e 17 GLN cc_start: 0.6681 (mt0) cc_final: 0.6107 (mm110) REVERT: e 82 ASP cc_start: 0.8391 (t0) cc_final: 0.8159 (t0) REVERT: e 92 THR cc_start: 0.9029 (p) cc_final: 0.8715 (t) REVERT: f 37 THR cc_start: 0.7327 (p) cc_final: 0.6739 (t) REVERT: g 1 SER cc_start: 0.8668 (p) cc_final: 0.8250 (t) REVERT: g 20 ASN cc_start: 0.8912 (m110) cc_final: 0.8496 (t0) REVERT: g 37 ASN cc_start: 0.8669 (t0) cc_final: 0.8376 (t0) REVERT: g 110 MET cc_start: 0.8163 (ptp) cc_final: 0.7920 (ptp) REVERT: h 56 MET cc_start: 0.7864 (tmm) cc_final: 0.7297 (tmm) REVERT: h 80 HIS cc_start: 0.6595 (t-90) cc_final: 0.6210 (t70) REVERT: i 46 LYS cc_start: 0.8605 (ptpt) cc_final: 0.8038 (pttp) REVERT: j 80 ASN cc_start: 0.7973 (p0) cc_final: 0.7665 (p0) REVERT: k 45 ASN cc_start: 0.6785 (p0) cc_final: 0.5263 (m110) REVERT: l 62 PHE cc_start: 0.7812 (p90) cc_final: 0.7452 (p90) REVERT: m 46 LYS cc_start: 0.8276 (mmmm) cc_final: 0.8068 (mmtp) REVERT: n 16 ARG cc_start: 0.7322 (ptt90) cc_final: 0.7109 (ptt90) REVERT: n 47 LYS cc_start: 0.8232 (ttmm) cc_final: 0.7899 (ttmt) REVERT: n 48 ASP cc_start: 0.7867 (m-30) cc_final: 0.7632 (m-30) REVERT: n 63 ARG cc_start: 0.8268 (tpt170) cc_final: 0.8001 (tpt170) REVERT: n 67 ASP cc_start: 0.7594 (m-30) cc_final: 0.7209 (m-30) REVERT: n 79 GLN cc_start: 0.8452 (tt0) cc_final: 0.8210 (tm-30) REVERT: o 17 TYR cc_start: 0.7328 (m-80) cc_final: 0.6732 (m-80) REVERT: p 50 ASN cc_start: 0.7265 (OUTLIER) cc_final: 0.6927 (m110) REVERT: p 73 THR cc_start: 0.7576 (OUTLIER) cc_final: 0.7359 (p) REVERT: r 4 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7552 (tp) REVERT: r 5 LYS cc_start: 0.8037 (mmmm) cc_final: 0.7727 (mptt) REVERT: r 8 PRO cc_start: 0.6537 (Cg_exo) cc_final: 0.6126 (Cg_endo) REVERT: r 31 ARG cc_start: 0.6213 (ptm160) cc_final: 0.5985 (ptm160) REVERT: s 60 GLN cc_start: 0.8555 (mm-40) cc_final: 0.8269 (mm-40) REVERT: s 73 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7642 (ptm-80) REVERT: t 53 LYS cc_start: 0.7622 (tttm) cc_final: 0.7170 (ttmm) outliers start: 164 outliers final: 99 residues processed: 1089 average time/residue: 1.2102 time to fit residues: 2326.0897 Evaluate side-chains 1033 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 926 time to evaluate : 5.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 128 MET Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 63 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain k residue 4 ASN Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 50 ASN Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain q residue 43 ILE Chi-restraints excluded: chain q residue 70 THR Chi-restraints excluded: chain r residue 4 LEU Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 874 optimal weight: 10.0000 chunk 665 optimal weight: 2.9990 chunk 459 optimal weight: 30.0000 chunk 97 optimal weight: 10.0000 chunk 422 optimal weight: 10.0000 chunk 594 optimal weight: 10.0000 chunk 888 optimal weight: 8.9990 chunk 940 optimal weight: 20.0000 chunk 464 optimal weight: 20.0000 chunk 841 optimal weight: 10.0000 chunk 253 optimal weight: 2.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN C 9 GLN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 HIS ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 93 ASN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 GLN W 45 GLN W 58 ASN ** b 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 66 GLN ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 125 GLN ** i 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 21 HIS ** j 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 4 ASN ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 9 HIS o 63 GLN p 46 HIS s 19 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 152963 Z= 0.491 Angle : 0.724 10.826 229314 Z= 0.365 Chirality : 0.041 0.315 29384 Planarity : 0.005 0.053 11960 Dihedral : 23.635 179.705 77660 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 5.22 % Allowed : 18.10 % Favored : 76.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.11), residues: 5281 helix: 0.72 (0.12), residues: 1804 sheet: -1.00 (0.16), residues: 1019 loop : -1.80 (0.12), residues: 2458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP c 169 HIS 0.022 0.002 HIS K 13 PHE 0.023 0.002 PHE Z 38 TYR 0.021 0.002 TYR l 85 ARG 0.007 0.001 ARG j 36 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 935 time to evaluate : 5.893 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: C 7 ASP cc_start: 0.6062 (OUTLIER) cc_final: 0.5469 (m-30) REVERT: D 13 LYS cc_start: 0.7934 (mptt) cc_final: 0.7504 (tppt) REVERT: D 129 MET cc_start: 0.7370 (tmm) cc_final: 0.6938 (tmm) REVERT: I 56 ASP cc_start: 0.8036 (m-30) cc_final: 0.7689 (m-30) REVERT: K 106 ASP cc_start: 0.7465 (m-30) cc_final: 0.7033 (m-30) REVERT: K 110 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7861 (tm-30) REVERT: L 110 MET cc_start: 0.8323 (mmm) cc_final: 0.8027 (mmt) REVERT: M 69 ASP cc_start: 0.8824 (m-30) cc_final: 0.8608 (t0) REVERT: M 104 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7356 (tp-100) REVERT: M 116 GLN cc_start: 0.8527 (tt0) cc_final: 0.8208 (tp40) REVERT: O 48 ASP cc_start: 0.7465 (m-30) cc_final: 0.7025 (m-30) REVERT: Q 34 ASP cc_start: 0.8003 (t0) cc_final: 0.7369 (t0) REVERT: U 25 GLU cc_start: 0.8060 (pt0) cc_final: 0.7812 (pt0) REVERT: W 4 LYS cc_start: 0.8370 (mppt) cc_final: 0.7976 (mtpt) REVERT: W 17 GLU cc_start: 0.8192 (tp30) cc_final: 0.7914 (tp30) REVERT: Z 8 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8585 (pp) REVERT: Z 49 LYS cc_start: 0.8000 (mtpt) cc_final: 0.7651 (ttpt) REVERT: AC 37 GLN cc_start: 0.8091 (tt0) cc_final: 0.7801 (tt0) REVERT: a 26 MET cc_start: 0.8598 (mmm) cc_final: 0.8011 (mmp) REVERT: a 99 MET cc_start: 0.7779 (ttm) cc_final: 0.7302 (ttp) REVERT: b 133 MET cc_start: 0.7917 (mtm) cc_final: 0.7318 (mtp) REVERT: b 139 ASN cc_start: 0.7481 (m110) cc_final: 0.7203 (p0) REVERT: b 167 TYR cc_start: 0.7144 (m-80) cc_final: 0.6548 (m-80) REVERT: b 169 GLU cc_start: 0.7873 (tm-30) cc_final: 0.7624 (tp30) REVERT: b 182 ASP cc_start: 0.7653 (t0) cc_final: 0.7280 (t0) REVERT: c 104 MET cc_start: 0.7593 (ttm) cc_final: 0.7065 (ttm) REVERT: c 125 ASN cc_start: 0.8383 (m110) cc_final: 0.8076 (m110) REVERT: d 70 MET cc_start: 0.7804 (ttp) cc_final: 0.7439 (ttp) REVERT: e 3 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7006 (m-70) REVERT: e 17 GLN cc_start: 0.7024 (mt0) cc_final: 0.6658 (mm110) REVERT: e 62 MET cc_start: 0.6604 (mpp) cc_final: 0.6334 (mpp) REVERT: e 82 ASP cc_start: 0.8518 (t0) cc_final: 0.8261 (t0) REVERT: e 92 THR cc_start: 0.9057 (p) cc_final: 0.8841 (t) REVERT: f 37 THR cc_start: 0.7506 (p) cc_final: 0.6946 (t) REVERT: g 1 SER cc_start: 0.8823 (p) cc_final: 0.8367 (t) REVERT: g 20 ASN cc_start: 0.8914 (m110) cc_final: 0.8450 (t0) REVERT: g 26 MET cc_start: 0.8713 (ptp) cc_final: 0.8454 (ptp) REVERT: g 42 GLU cc_start: 0.8761 (tp30) cc_final: 0.8550 (tp30) REVERT: g 110 MET cc_start: 0.8316 (ptp) cc_final: 0.8086 (ptp) REVERT: h 56 MET cc_start: 0.8071 (tmm) cc_final: 0.7360 (tmm) REVERT: h 59 LYS cc_start: 0.7484 (mmtm) cc_final: 0.7215 (mmtm) REVERT: h 80 HIS cc_start: 0.6444 (t-90) cc_final: 0.6081 (t70) REVERT: i 25 ILE cc_start: 0.6857 (OUTLIER) cc_final: 0.6084 (pt) REVERT: i 46 LYS cc_start: 0.8663 (ptpt) cc_final: 0.7952 (pttp) REVERT: j 80 ASN cc_start: 0.8017 (OUTLIER) cc_final: 0.7744 (p0) REVERT: n 48 ASP cc_start: 0.8275 (m-30) cc_final: 0.8005 (m-30) REVERT: n 67 ASP cc_start: 0.7650 (m-30) cc_final: 0.7406 (m-30) REVERT: n 79 GLN cc_start: 0.8526 (tt0) cc_final: 0.8163 (tm-30) REVERT: o 17 TYR cc_start: 0.7599 (m-80) cc_final: 0.7291 (m-80) REVERT: p 73 THR cc_start: 0.7662 (p) cc_final: 0.7440 (p) REVERT: r 5 LYS cc_start: 0.7977 (mmmm) cc_final: 0.7753 (mptt) REVERT: r 8 PRO cc_start: 0.6898 (Cg_exo) cc_final: 0.6537 (Cg_endo) REVERT: r 10 ILE cc_start: 0.7439 (OUTLIER) cc_final: 0.7001 (mt) REVERT: r 31 ARG cc_start: 0.6475 (ptm160) cc_final: 0.6173 (ptm160) REVERT: s 68 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.7874 (ptpp) REVERT: t 53 LYS cc_start: 0.7597 (tttm) cc_final: 0.7190 (ttmm) outliers start: 228 outliers final: 172 residues processed: 1077 average time/residue: 1.1747 time to fit residues: 2235.1021 Evaluate side-chains 1065 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 885 time to evaluate : 5.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 43 ASP Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 43 LYS Chi-restraints excluded: chain E residue 86 LEU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 11 ARG Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 58 ASN Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AC residue 12 ARG Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 89 LEU Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 61 LEU Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain m residue 47 LEU Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 14 ASP Chi-restraints excluded: chain p residue 50 ASN Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain r residue 10 ILE Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 39 ILE Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain s residue 68 LYS Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Chi-restraints excluded: chain t residue 42 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 783 optimal weight: 4.9990 chunk 533 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 700 optimal weight: 4.9990 chunk 388 optimal weight: 10.0000 chunk 802 optimal weight: 9.9990 chunk 650 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 480 optimal weight: 7.9990 chunk 844 optimal weight: 8.9990 chunk 237 optimal weight: 9.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN A 142 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 82 HIS ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN W 45 GLN W 58 ASN a 35 ASN ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 96 ASN ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 GLN k 4 ASN ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN p 46 HIS s 19 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 152963 Z= 0.353 Angle : 0.626 10.809 229314 Z= 0.320 Chirality : 0.038 0.279 29384 Planarity : 0.004 0.048 11960 Dihedral : 23.616 179.637 77660 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 5.31 % Allowed : 18.69 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.11), residues: 5281 helix: 0.94 (0.12), residues: 1801 sheet: -0.91 (0.16), residues: 1026 loop : -1.71 (0.12), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP a 95 HIS 0.011 0.001 HIS K 13 PHE 0.017 0.002 PHE Z 38 TYR 0.025 0.002 TYR c 102 ARG 0.006 0.001 ARG g 87 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 947 time to evaluate : 5.941 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: C 7 ASP cc_start: 0.5953 (OUTLIER) cc_final: 0.5491 (m-30) REVERT: D 13 LYS cc_start: 0.7983 (mptt) cc_final: 0.7562 (tppt) REVERT: D 25 MET cc_start: 0.8091 (tpp) cc_final: 0.7794 (mmm) REVERT: D 95 MET cc_start: 0.7525 (ptt) cc_final: 0.7059 (ppp) REVERT: D 129 MET cc_start: 0.7413 (tmm) cc_final: 0.6982 (tmm) REVERT: E 44 HIS cc_start: 0.6325 (t70) cc_final: 0.6111 (t70) REVERT: G 1 MET cc_start: 0.8108 (ptp) cc_final: 0.7788 (ptp) REVERT: I 56 ASP cc_start: 0.8036 (m-30) cc_final: 0.7684 (m-30) REVERT: K 106 ASP cc_start: 0.7270 (m-30) cc_final: 0.7046 (m-30) REVERT: K 110 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7807 (tm-30) REVERT: L 110 MET cc_start: 0.8328 (mmm) cc_final: 0.8037 (mmt) REVERT: M 43 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7486 (p0) REVERT: M 55 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7146 (mm-30) REVERT: M 69 ASP cc_start: 0.8723 (m-30) cc_final: 0.8517 (t0) REVERT: M 104 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7241 (tp-100) REVERT: M 116 GLN cc_start: 0.8671 (tt0) cc_final: 0.8338 (tp40) REVERT: O 48 ASP cc_start: 0.7383 (m-30) cc_final: 0.7084 (m-30) REVERT: Q 82 MET cc_start: 0.7251 (mtt) cc_final: 0.6915 (mtt) REVERT: U 25 GLU cc_start: 0.8039 (pt0) cc_final: 0.7781 (pt0) REVERT: U 64 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8726 (ttpp) REVERT: W 4 LYS cc_start: 0.8321 (mppt) cc_final: 0.7909 (mtpt) REVERT: Z 8 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8526 (pp) REVERT: Z 49 LYS cc_start: 0.8006 (mtpt) cc_final: 0.7681 (ttpt) REVERT: AC 37 GLN cc_start: 0.8053 (tt0) cc_final: 0.7738 (tt0) REVERT: b 66 THR cc_start: 0.6990 (OUTLIER) cc_final: 0.6752 (p) REVERT: b 133 MET cc_start: 0.7801 (mtm) cc_final: 0.7149 (mtp) REVERT: b 167 TYR cc_start: 0.7116 (m-80) cc_final: 0.6455 (m-80) REVERT: b 169 GLU cc_start: 0.7904 (tm-30) cc_final: 0.6888 (tm-30) REVERT: b 182 ASP cc_start: 0.7621 (t0) cc_final: 0.7256 (t0) REVERT: c 104 MET cc_start: 0.7595 (ttm) cc_final: 0.6989 (ttm) REVERT: c 125 ASN cc_start: 0.8389 (m110) cc_final: 0.8185 (m110) REVERT: e 3 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7098 (m-70) REVERT: e 17 GLN cc_start: 0.7047 (mt0) cc_final: 0.6660 (mm110) REVERT: e 62 MET cc_start: 0.6730 (mpp) cc_final: 0.6478 (mpp) REVERT: e 82 ASP cc_start: 0.8523 (t0) cc_final: 0.8242 (t0) REVERT: f 37 THR cc_start: 0.7455 (p) cc_final: 0.6893 (t) REVERT: g 1 SER cc_start: 0.8757 (p) cc_final: 0.8286 (t) REVERT: g 20 ASN cc_start: 0.8946 (m110) cc_final: 0.8439 (t0) REVERT: g 110 MET cc_start: 0.8263 (ptp) cc_final: 0.7999 (ptp) REVERT: h 56 MET cc_start: 0.8177 (tmm) cc_final: 0.7679 (tmm) REVERT: h 59 LYS cc_start: 0.7613 (mmtm) cc_final: 0.7385 (mmtm) REVERT: h 80 HIS cc_start: 0.6458 (t-90) cc_final: 0.6093 (t70) REVERT: i 25 ILE cc_start: 0.6991 (OUTLIER) cc_final: 0.6306 (pt) REVERT: i 46 LYS cc_start: 0.8655 (ptpt) cc_final: 0.7987 (pttp) REVERT: j 74 LYS cc_start: 0.8821 (tttp) cc_final: 0.8580 (pttt) REVERT: j 80 ASN cc_start: 0.7971 (OUTLIER) cc_final: 0.7693 (p0) REVERT: k 4 ASN cc_start: 0.8604 (m110) cc_final: 0.8379 (m110) REVERT: k 43 LYS cc_start: 0.5808 (OUTLIER) cc_final: 0.5244 (mtmm) REVERT: k 45 ASN cc_start: 0.6919 (p0) cc_final: 0.6693 (p0) REVERT: k 61 GLU cc_start: 0.7789 (mp0) cc_final: 0.7581 (mp0) REVERT: k 66 ILE cc_start: 0.8514 (OUTLIER) cc_final: 0.7999 (tp) REVERT: k 87 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7367 (tttm) REVERT: m 22 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8123 (tttt) REVERT: m 46 LYS cc_start: 0.8235 (mmmm) cc_final: 0.7986 (mmtp) REVERT: n 48 ASP cc_start: 0.8144 (m-30) cc_final: 0.7840 (m-30) REVERT: n 79 GLN cc_start: 0.8500 (tt0) cc_final: 0.8169 (tm-30) REVERT: p 39 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7156 (mmp-170) REVERT: p 73 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7468 (p) REVERT: r 8 PRO cc_start: 0.6854 (Cg_exo) cc_final: 0.6458 (Cg_endo) REVERT: r 31 ARG cc_start: 0.6640 (ptm160) cc_final: 0.6294 (ptm160) REVERT: s 59 ARG cc_start: 0.8489 (ttp-110) cc_final: 0.7748 (ttp-110) REVERT: s 73 ARG cc_start: 0.8265 (ptm160) cc_final: 0.7716 (ptm-80) REVERT: t 53 LYS cc_start: 0.7533 (tttm) cc_final: 0.7143 (ttmm) outliers start: 232 outliers final: 176 residues processed: 1091 average time/residue: 1.1791 time to fit residues: 2273.3631 Evaluate side-chains 1103 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 912 time to evaluate : 5.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 7 ASP Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 165 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 86 MET Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AB residue 58 ILE Chi-restraints excluded: chain a residue 18 GLN Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 77 ASN Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 50 THR Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 64 GLN Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain k residue 3 VAL Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 43 LYS Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 44 ILE Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain m residue 22 LYS Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 26 ASN Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 73 THR Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 316 optimal weight: 2.9990 chunk 846 optimal weight: 10.0000 chunk 185 optimal weight: 1.9990 chunk 552 optimal weight: 10.0000 chunk 232 optimal weight: 2.9990 chunk 941 optimal weight: 20.0000 chunk 781 optimal weight: 4.9990 chunk 435 optimal weight: 5.9990 chunk 78 optimal weight: 7.9990 chunk 311 optimal weight: 20.0000 chunk 494 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 43 GLN ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN W 25 GLN W 45 GLN W 58 ASN a 35 ASN ** b 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 64 GLN ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN p 46 HIS s 47 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 152963 Z= 0.281 Angle : 0.582 11.533 229314 Z= 0.299 Chirality : 0.035 0.271 29384 Planarity : 0.004 0.052 11960 Dihedral : 23.588 179.393 77658 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 5.38 % Allowed : 19.49 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.11), residues: 5281 helix: 1.11 (0.12), residues: 1804 sheet: -0.85 (0.16), residues: 1044 loop : -1.60 (0.12), residues: 2433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 169 HIS 0.009 0.001 HIS K 13 PHE 0.021 0.002 PHE s 50 TYR 0.038 0.002 TYR M 64 ARG 0.007 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1201 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 966 time to evaluate : 5.567 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: C 165 HIS cc_start: 0.8762 (OUTLIER) cc_final: 0.8517 (t-170) REVERT: D 13 LYS cc_start: 0.8074 (mptt) cc_final: 0.7734 (tppt) REVERT: D 30 VAL cc_start: 0.7810 (m) cc_final: 0.7502 (m) REVERT: D 95 MET cc_start: 0.7366 (ptt) cc_final: 0.7040 (ppp) REVERT: D 129 MET cc_start: 0.7389 (tmm) cc_final: 0.7083 (tmm) REVERT: E 44 HIS cc_start: 0.6341 (t70) cc_final: 0.6120 (t70) REVERT: G 1 MET cc_start: 0.8089 (ptp) cc_final: 0.7731 (ptp) REVERT: I 56 ASP cc_start: 0.8008 (m-30) cc_final: 0.7639 (m-30) REVERT: K 106 ASP cc_start: 0.7135 (m-30) cc_final: 0.6891 (m-30) REVERT: L 110 MET cc_start: 0.8303 (mmm) cc_final: 0.8021 (mmt) REVERT: M 43 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7603 (p0) REVERT: M 55 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7135 (mm-30) REVERT: M 69 ASP cc_start: 0.8757 (m-30) cc_final: 0.8522 (t0) REVERT: M 104 GLN cc_start: 0.7539 (OUTLIER) cc_final: 0.7212 (tp-100) REVERT: M 116 GLN cc_start: 0.8616 (tt0) cc_final: 0.8308 (tp40) REVERT: O 48 ASP cc_start: 0.7339 (m-30) cc_final: 0.7055 (m-30) REVERT: U 25 GLU cc_start: 0.7992 (pt0) cc_final: 0.7739 (pt0) REVERT: U 64 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8735 (ttpp) REVERT: W 4 LYS cc_start: 0.8293 (mppt) cc_final: 0.7885 (mtpt) REVERT: W 36 GLN cc_start: 0.8319 (mp10) cc_final: 0.8118 (mp10) REVERT: W 45 GLN cc_start: 0.8372 (tt0) cc_final: 0.8019 (tt0) REVERT: W 49 ASP cc_start: 0.8389 (m-30) cc_final: 0.8000 (m-30) REVERT: X 48 ASN cc_start: 0.8606 (t0) cc_final: 0.8313 (t0) REVERT: Z 7 LYS cc_start: 0.8251 (mttp) cc_final: 0.7834 (mptt) REVERT: Z 8 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8483 (pp) REVERT: Z 49 LYS cc_start: 0.8015 (mtpt) cc_final: 0.7655 (ttpt) REVERT: AC 37 GLN cc_start: 0.7993 (tt0) cc_final: 0.7759 (tt0) REVERT: a 26 MET cc_start: 0.8605 (mmm) cc_final: 0.8170 (mmp) REVERT: b 66 THR cc_start: 0.7174 (OUTLIER) cc_final: 0.6743 (p) REVERT: b 133 MET cc_start: 0.7716 (mtm) cc_final: 0.7082 (mtp) REVERT: b 167 TYR cc_start: 0.7161 (m-80) cc_final: 0.6528 (m-80) REVERT: b 169 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7260 (tm-30) REVERT: b 182 ASP cc_start: 0.7590 (t0) cc_final: 0.7225 (t0) REVERT: c 102 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7991 (t80) REVERT: c 104 MET cc_start: 0.7600 (ttm) cc_final: 0.6998 (ttm) REVERT: c 125 ASN cc_start: 0.8362 (m110) cc_final: 0.7953 (m-40) REVERT: e 3 HIS cc_start: 0.7819 (OUTLIER) cc_final: 0.7097 (m-70) REVERT: e 17 GLN cc_start: 0.6996 (mt0) cc_final: 0.6421 (mm110) REVERT: e 82 ASP cc_start: 0.8508 (t0) cc_final: 0.8222 (t0) REVERT: f 37 THR cc_start: 0.7526 (p) cc_final: 0.6973 (t) REVERT: g 1 SER cc_start: 0.8720 (p) cc_final: 0.8232 (t) REVERT: g 20 ASN cc_start: 0.8938 (m110) cc_final: 0.8461 (t0) REVERT: g 26 MET cc_start: 0.8649 (ptp) cc_final: 0.8423 (ptp) REVERT: g 42 GLU cc_start: 0.8701 (tp30) cc_final: 0.8489 (tp30) REVERT: g 110 MET cc_start: 0.8239 (ptp) cc_final: 0.7980 (ptp) REVERT: h 56 MET cc_start: 0.7992 (tmm) cc_final: 0.7581 (tmm) REVERT: h 59 LYS cc_start: 0.7585 (mmtm) cc_final: 0.7370 (mmtm) REVERT: h 80 HIS cc_start: 0.6484 (t-90) cc_final: 0.6121 (t70) REVERT: i 25 ILE cc_start: 0.6887 (OUTLIER) cc_final: 0.6239 (pt) REVERT: i 46 LYS cc_start: 0.8638 (ptpt) cc_final: 0.7999 (pttp) REVERT: j 17 ASP cc_start: 0.7213 (m-30) cc_final: 0.6961 (m-30) REVERT: j 74 LYS cc_start: 0.8811 (tttp) cc_final: 0.8572 (pttt) REVERT: j 80 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7592 (p0) REVERT: k 4 ASN cc_start: 0.8544 (m110) cc_final: 0.8301 (m110) REVERT: k 45 ASN cc_start: 0.6888 (p0) cc_final: 0.5488 (m110) REVERT: k 61 GLU cc_start: 0.7834 (mp0) cc_final: 0.7626 (mp0) REVERT: k 66 ILE cc_start: 0.8482 (OUTLIER) cc_final: 0.7930 (tp) REVERT: m 22 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.8065 (tttt) REVERT: m 29 ILE cc_start: 0.8554 (mt) cc_final: 0.8215 (mm) REVERT: m 46 LYS cc_start: 0.8255 (mmmm) cc_final: 0.7978 (mmtp) REVERT: n 47 LYS cc_start: 0.8208 (ttmm) cc_final: 0.7991 (tttt) REVERT: n 48 ASP cc_start: 0.8111 (m-30) cc_final: 0.7802 (m-30) REVERT: n 79 GLN cc_start: 0.8410 (tt0) cc_final: 0.8155 (tm-30) REVERT: o 17 TYR cc_start: 0.7517 (m-80) cc_final: 0.7047 (m-80) REVERT: o 31 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.6793 (ttp-170) REVERT: p 39 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7188 (mmp-170) REVERT: r 31 ARG cc_start: 0.6583 (ptm160) cc_final: 0.6201 (ptm160) REVERT: t 53 LYS cc_start: 0.7512 (tttm) cc_final: 0.7123 (ttmm) outliers start: 235 outliers final: 176 residues processed: 1106 average time/residue: 1.1680 time to fit residues: 2283.1400 Evaluate side-chains 1109 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 919 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 50 THR Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain V residue 1 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AB residue 58 ILE Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 79 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 102 TYR Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain h residue 119 LYS Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 51 PHE Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain m residue 22 LYS Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 31 ARG Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 68 SER Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 14 ASP Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 27 THR Chi-restraints excluded: chain q residue 66 LEU Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 907 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 536 optimal weight: 8.9990 chunk 687 optimal weight: 6.9990 chunk 532 optimal weight: 8.9990 chunk 792 optimal weight: 3.9990 chunk 525 optimal weight: 50.0000 chunk 937 optimal weight: 20.0000 chunk 586 optimal weight: 10.0000 chunk 571 optimal weight: 7.9990 chunk 432 optimal weight: 8.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN ** T 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 25 GLN W 58 ASN a 35 ASN ** b 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN p 46 HIS s 19 HIS s 47 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 152963 Z= 0.407 Angle : 0.666 11.709 229314 Z= 0.339 Chirality : 0.040 0.282 29384 Planarity : 0.005 0.078 11960 Dihedral : 23.644 179.454 77658 Min Nonbonded Distance : 1.803 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 5.61 % Allowed : 20.11 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.11), residues: 5281 helix: 0.94 (0.12), residues: 1801 sheet: -0.88 (0.16), residues: 1035 loop : -1.67 (0.12), residues: 2445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP D 96 HIS 0.009 0.001 HIS C 165 PHE 0.029 0.002 PHE s 50 TYR 0.037 0.002 TYR M 64 ARG 0.009 0.001 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1166 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 921 time to evaluate : 5.984 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: C 165 HIS cc_start: 0.8814 (OUTLIER) cc_final: 0.8584 (t-170) REVERT: D 13 LYS cc_start: 0.8112 (mptt) cc_final: 0.7734 (tppt) REVERT: D 30 VAL cc_start: 0.7654 (m) cc_final: 0.7342 (m) REVERT: D 95 MET cc_start: 0.7464 (OUTLIER) cc_final: 0.7166 (ppp) REVERT: D 129 MET cc_start: 0.7456 (tmm) cc_final: 0.7110 (tmm) REVERT: E 44 HIS cc_start: 0.6328 (t70) cc_final: 0.6128 (t70) REVERT: I 56 ASP cc_start: 0.8028 (m-30) cc_final: 0.7646 (m-30) REVERT: K 106 ASP cc_start: 0.7241 (m-30) cc_final: 0.7026 (m-30) REVERT: M 43 ASN cc_start: 0.8010 (OUTLIER) cc_final: 0.7542 (p0) REVERT: M 55 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7214 (mm-30) REVERT: M 69 ASP cc_start: 0.8747 (m-30) cc_final: 0.8540 (t0) REVERT: M 104 GLN cc_start: 0.7585 (OUTLIER) cc_final: 0.7259 (tp-100) REVERT: M 116 GLN cc_start: 0.8619 (tt0) cc_final: 0.8351 (tp40) REVERT: O 48 ASP cc_start: 0.7457 (m-30) cc_final: 0.7028 (m-30) REVERT: U 25 GLU cc_start: 0.8034 (pt0) cc_final: 0.7794 (pt0) REVERT: U 64 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8728 (ttpp) REVERT: W 4 LYS cc_start: 0.8353 (mppt) cc_final: 0.7940 (mtpt) REVERT: W 17 GLU cc_start: 0.8116 (tp30) cc_final: 0.7899 (tp30) REVERT: W 49 ASP cc_start: 0.8392 (m-30) cc_final: 0.8176 (m-30) REVERT: Z 7 LYS cc_start: 0.8369 (mttp) cc_final: 0.7968 (mptt) REVERT: Z 8 ILE cc_start: 0.8783 (OUTLIER) cc_final: 0.8556 (pp) REVERT: Z 49 LYS cc_start: 0.8036 (mtpt) cc_final: 0.7681 (ttpt) REVERT: AC 37 GLN cc_start: 0.7989 (tt0) cc_final: 0.7661 (tt0) REVERT: b 114 LEU cc_start: 0.8228 (mm) cc_final: 0.8023 (mt) REVERT: b 133 MET cc_start: 0.7787 (mtm) cc_final: 0.7302 (mtp) REVERT: b 167 TYR cc_start: 0.7122 (m-80) cc_final: 0.6620 (m-80) REVERT: b 169 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7302 (tm-30) REVERT: b 182 ASP cc_start: 0.7516 (t0) cc_final: 0.7194 (t0) REVERT: c 102 TYR cc_start: 0.8298 (t80) cc_final: 0.7886 (t80) REVERT: c 104 MET cc_start: 0.7667 (ttm) cc_final: 0.7022 (ttm) REVERT: c 125 ASN cc_start: 0.8160 (m110) cc_final: 0.7842 (m-40) REVERT: d 70 MET cc_start: 0.7705 (ttp) cc_final: 0.7326 (ttp) REVERT: e 3 HIS cc_start: 0.7945 (OUTLIER) cc_final: 0.7550 (m-70) REVERT: e 17 GLN cc_start: 0.7010 (mt0) cc_final: 0.6489 (mm110) REVERT: e 76 THR cc_start: 0.7967 (OUTLIER) cc_final: 0.7708 (t) REVERT: e 82 ASP cc_start: 0.8532 (t0) cc_final: 0.8231 (t0) REVERT: f 37 THR cc_start: 0.7486 (p) cc_final: 0.6920 (t) REVERT: g 1 SER cc_start: 0.8762 (p) cc_final: 0.8269 (t) REVERT: g 20 ASN cc_start: 0.8971 (m110) cc_final: 0.8486 (t0) REVERT: g 110 MET cc_start: 0.8294 (ptp) cc_final: 0.8053 (ptp) REVERT: h 56 MET cc_start: 0.7998 (tmm) cc_final: 0.7561 (tmm) REVERT: h 80 HIS cc_start: 0.6512 (t-90) cc_final: 0.6171 (t70) REVERT: i 25 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6286 (pt) REVERT: i 46 LYS cc_start: 0.8677 (ptpt) cc_final: 0.8121 (pttp) REVERT: i 49 PHE cc_start: 0.7315 (OUTLIER) cc_final: 0.7107 (m-80) REVERT: j 74 LYS cc_start: 0.8827 (tttp) cc_final: 0.8589 (pttt) REVERT: j 80 ASN cc_start: 0.7929 (OUTLIER) cc_final: 0.7675 (p0) REVERT: k 66 ILE cc_start: 0.8498 (OUTLIER) cc_final: 0.8050 (tp) REVERT: k 87 LYS cc_start: 0.7927 (OUTLIER) cc_final: 0.7394 (tttm) REVERT: m 29 ILE cc_start: 0.8574 (mt) cc_final: 0.8228 (mm) REVERT: m 46 LYS cc_start: 0.8311 (mmmm) cc_final: 0.8018 (mmtp) REVERT: m 88 MET cc_start: 0.8124 (mmp) cc_final: 0.7545 (mmm) REVERT: n 48 ASP cc_start: 0.8162 (m-30) cc_final: 0.7938 (m-30) REVERT: n 79 GLN cc_start: 0.8511 (tt0) cc_final: 0.8160 (tm-30) REVERT: o 17 TYR cc_start: 0.7509 (m-80) cc_final: 0.6919 (m-80) REVERT: o 31 ARG cc_start: 0.8313 (OUTLIER) cc_final: 0.6855 (ttp-170) REVERT: p 39 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7238 (mmp-170) REVERT: p 61 ARG cc_start: 0.8020 (OUTLIER) cc_final: 0.7230 (ttm170) REVERT: r 31 ARG cc_start: 0.6667 (ptm160) cc_final: 0.6262 (ptm160) REVERT: r 34 SER cc_start: 0.7996 (OUTLIER) cc_final: 0.7602 (t) REVERT: r 55 GLN cc_start: 0.7346 (tp40) cc_final: 0.6847 (pt0) REVERT: t 53 LYS cc_start: 0.7528 (tttm) cc_final: 0.7230 (ttmt) outliers start: 245 outliers final: 207 residues processed: 1067 average time/residue: 1.1752 time to fit residues: 2222.0937 Evaluate side-chains 1125 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 901 time to evaluate : 5.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 86 CYS Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 126 ASN Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 7 HIS Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 25 GLU Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain V residue 1 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain W residue 58 ASN Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 5 LYS Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 25 THR Chi-restraints excluded: chain Y residue 42 ILE Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 1 MET Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AB residue 30 HIS Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 79 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 129 THR Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 57 LYS Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 123 LEU Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain d residue 163 ILE Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain f residue 3 ARG Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 59 GLU Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain h residue 114 LYS Chi-restraints excluded: chain h residue 117 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 7 ASN Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 44 ILE Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 101 THR Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 31 ARG Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 68 SER Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 14 ASP Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 61 ARG Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain r residue 9 PHE Chi-restraints excluded: chain r residue 12 LEU Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 580 optimal weight: 7.9990 chunk 374 optimal weight: 5.9990 chunk 560 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 184 optimal weight: 4.9990 chunk 181 optimal weight: 0.9990 chunk 596 optimal weight: 8.9990 chunk 638 optimal weight: 5.9990 chunk 463 optimal weight: 30.0000 chunk 87 optimal weight: 8.9990 chunk 737 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 HIS ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 ASN T 12 GLN W 58 ASN a 35 ASN ** b 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 77 ASN ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 56 HIS ** i 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN p 46 HIS s 19 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 152963 Z= 0.278 Angle : 0.587 11.781 229314 Z= 0.301 Chirality : 0.036 0.273 29384 Planarity : 0.004 0.048 11960 Dihedral : 23.624 179.572 77658 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 5.17 % Allowed : 20.89 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.11), residues: 5281 helix: 1.12 (0.12), residues: 1803 sheet: -0.77 (0.16), residues: 1026 loop : -1.59 (0.12), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP c 169 HIS 0.008 0.001 HIS A 141 PHE 0.020 0.002 PHE F 47 TYR 0.037 0.002 TYR M 64 ARG 0.008 0.000 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 947 time to evaluate : 5.962 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: C 165 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8537 (t-170) REVERT: D 13 LYS cc_start: 0.8133 (mptt) cc_final: 0.7758 (tppt) REVERT: D 30 VAL cc_start: 0.7821 (m) cc_final: 0.7555 (m) REVERT: D 95 MET cc_start: 0.7329 (ptt) cc_final: 0.7072 (ppp) REVERT: D 129 MET cc_start: 0.7400 (tmm) cc_final: 0.6887 (tmm) REVERT: G 1 MET cc_start: 0.8044 (ptp) cc_final: 0.7451 (ptp) REVERT: I 56 ASP cc_start: 0.8055 (m-30) cc_final: 0.7686 (m-30) REVERT: K 106 ASP cc_start: 0.7250 (m-30) cc_final: 0.7036 (m-30) REVERT: L 110 MET cc_start: 0.8304 (mmm) cc_final: 0.8019 (mmt) REVERT: M 43 ASN cc_start: 0.8072 (OUTLIER) cc_final: 0.7695 (p0) REVERT: M 55 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7215 (mm-30) REVERT: M 69 ASP cc_start: 0.8752 (m-30) cc_final: 0.8535 (t0) REVERT: M 104 GLN cc_start: 0.7536 (OUTLIER) cc_final: 0.7214 (tp-100) REVERT: M 116 GLN cc_start: 0.8606 (tt0) cc_final: 0.8339 (tp40) REVERT: O 48 ASP cc_start: 0.7334 (m-30) cc_final: 0.6937 (m-30) REVERT: T 59 GLU cc_start: 0.8662 (pt0) cc_final: 0.8450 (pt0) REVERT: U 25 GLU cc_start: 0.8000 (pt0) cc_final: 0.7739 (pt0) REVERT: U 64 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8743 (ttpp) REVERT: W 4 LYS cc_start: 0.8325 (mppt) cc_final: 0.7891 (mtpt) REVERT: W 17 GLU cc_start: 0.8058 (tp30) cc_final: 0.7841 (tp30) REVERT: W 36 GLN cc_start: 0.8348 (mp10) cc_final: 0.8139 (mp10) REVERT: W 45 GLN cc_start: 0.8381 (tt0) cc_final: 0.8065 (tp-100) REVERT: W 49 ASP cc_start: 0.8449 (m-30) cc_final: 0.7910 (m-30) REVERT: X 48 ASN cc_start: 0.8615 (t0) cc_final: 0.8325 (t0) REVERT: Z 7 LYS cc_start: 0.8303 (mttp) cc_final: 0.7903 (mptt) REVERT: Z 8 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8486 (pp) REVERT: Z 49 LYS cc_start: 0.8014 (mtpt) cc_final: 0.7648 (ttpt) REVERT: AC 37 GLN cc_start: 0.8027 (tt0) cc_final: 0.7719 (tt0) REVERT: b 66 THR cc_start: 0.7056 (OUTLIER) cc_final: 0.6703 (p) REVERT: b 114 LEU cc_start: 0.8212 (mm) cc_final: 0.7992 (mt) REVERT: b 133 MET cc_start: 0.7742 (mtm) cc_final: 0.7129 (mtp) REVERT: b 167 TYR cc_start: 0.7096 (m-80) cc_final: 0.6507 (m-80) REVERT: b 169 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7254 (tm-30) REVERT: b 182 ASP cc_start: 0.7580 (t0) cc_final: 0.7239 (t0) REVERT: c 104 MET cc_start: 0.7648 (ttm) cc_final: 0.7013 (ttm) REVERT: d 13 LYS cc_start: 0.8575 (mmmt) cc_final: 0.7674 (mmtm) REVERT: d 70 MET cc_start: 0.7818 (ttp) cc_final: 0.7468 (ttp) REVERT: e 3 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.7122 (m-70) REVERT: e 17 GLN cc_start: 0.7016 (mt0) cc_final: 0.6617 (mm110) REVERT: e 76 THR cc_start: 0.7972 (OUTLIER) cc_final: 0.7698 (t) REVERT: e 82 ASP cc_start: 0.8517 (t0) cc_final: 0.8210 (t0) REVERT: f 37 THR cc_start: 0.7480 (p) cc_final: 0.6900 (t) REVERT: g 1 SER cc_start: 0.8630 (p) cc_final: 0.8172 (t) REVERT: g 20 ASN cc_start: 0.8954 (m110) cc_final: 0.8433 (t0) REVERT: g 110 MET cc_start: 0.8249 (ptp) cc_final: 0.7974 (ptp) REVERT: h 56 MET cc_start: 0.7948 (tmm) cc_final: 0.7567 (tpp) REVERT: h 80 HIS cc_start: 0.6501 (t-90) cc_final: 0.6147 (t70) REVERT: i 46 LYS cc_start: 0.8682 (ptpt) cc_final: 0.8121 (pttp) REVERT: i 49 PHE cc_start: 0.7338 (OUTLIER) cc_final: 0.7074 (m-80) REVERT: j 17 ASP cc_start: 0.7107 (m-30) cc_final: 0.6885 (m-30) REVERT: j 74 LYS cc_start: 0.8843 (tttp) cc_final: 0.8579 (pttt) REVERT: j 80 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7583 (p0) REVERT: k 52 CYS cc_start: 0.6990 (OUTLIER) cc_final: 0.6127 (t) REVERT: k 61 GLU cc_start: 0.7791 (mp0) cc_final: 0.7574 (mp0) REVERT: k 66 ILE cc_start: 0.8548 (OUTLIER) cc_final: 0.7937 (tp) REVERT: k 87 LYS cc_start: 0.7926 (OUTLIER) cc_final: 0.7399 (tttm) REVERT: m 46 LYS cc_start: 0.8215 (mmmm) cc_final: 0.7951 (mmtp) REVERT: m 88 MET cc_start: 0.8030 (mmp) cc_final: 0.7507 (mmm) REVERT: n 48 ASP cc_start: 0.8139 (m-30) cc_final: 0.7834 (m-30) REVERT: n 79 GLN cc_start: 0.8481 (tt0) cc_final: 0.8171 (tm-30) REVERT: o 1 MET cc_start: 0.7595 (ppp) cc_final: 0.7269 (ppp) REVERT: o 17 TYR cc_start: 0.7490 (m-80) cc_final: 0.7002 (m-80) REVERT: o 31 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.6772 (ttp-170) REVERT: p 39 ARG cc_start: 0.8333 (OUTLIER) cc_final: 0.7234 (mmp-170) REVERT: p 56 ASP cc_start: 0.8290 (OUTLIER) cc_final: 0.6502 (m-30) REVERT: p 61 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.7144 (ttm170) REVERT: r 34 SER cc_start: 0.7928 (OUTLIER) cc_final: 0.7569 (t) REVERT: r 55 GLN cc_start: 0.7352 (tp40) cc_final: 0.6870 (pt0) REVERT: s 59 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7579 (mtm-85) REVERT: t 53 LYS cc_start: 0.7503 (tttm) cc_final: 0.7197 (ttmt) outliers start: 226 outliers final: 187 residues processed: 1084 average time/residue: 1.2598 time to fit residues: 2438.2679 Evaluate side-chains 1111 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 906 time to evaluate : 5.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 165 HIS Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 25 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 71 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 64 LYS Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain V residue 1 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AB residue 30 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 79 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 128 LEU Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 128 MET Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 20 GLN Chi-restraints excluded: chain i residue 27 GLU Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 51 VAL Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain m residue 22 LYS Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 26 ASN Chi-restraints excluded: chain o residue 31 ARG Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 68 SER Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 14 ASP Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 61 ARG Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 853 optimal weight: 10.0000 chunk 898 optimal weight: 10.0000 chunk 819 optimal weight: 10.0000 chunk 873 optimal weight: 10.0000 chunk 526 optimal weight: 40.0000 chunk 380 optimal weight: 10.0000 chunk 686 optimal weight: 0.9980 chunk 268 optimal weight: 5.9990 chunk 789 optimal weight: 2.9990 chunk 826 optimal weight: 10.0000 chunk 870 optimal weight: 10.0000 overall best weight: 5.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN a 35 ASN ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 152963 Z= 0.419 Angle : 0.683 11.557 229314 Z= 0.347 Chirality : 0.040 0.310 29384 Planarity : 0.005 0.054 11960 Dihedral : 23.672 179.100 77658 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.89 % Favored : 93.11 % Rotamer: Outliers : 5.35 % Allowed : 20.98 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.11), residues: 5281 helix: 0.90 (0.12), residues: 1802 sheet: -0.86 (0.16), residues: 1015 loop : -1.69 (0.12), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 96 HIS 0.009 0.001 HIS C 165 PHE 0.025 0.002 PHE Z 38 TYR 0.042 0.002 TYR M 64 ARG 0.009 0.001 ARG d 68 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 234 poor density : 911 time to evaluate : 5.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 LYS cc_start: 0.8004 (mptt) cc_final: 0.7737 (tppt) REVERT: D 30 VAL cc_start: 0.7711 (OUTLIER) cc_final: 0.7331 (m) REVERT: D 95 MET cc_start: 0.7446 (OUTLIER) cc_final: 0.7176 (ppp) REVERT: D 129 MET cc_start: 0.7383 (OUTLIER) cc_final: 0.7009 (tmm) REVERT: G 1 MET cc_start: 0.8009 (ptp) cc_final: 0.7644 (ptp) REVERT: I 56 ASP cc_start: 0.8073 (m-30) cc_final: 0.7668 (m-30) REVERT: K 106 ASP cc_start: 0.7228 (m-30) cc_final: 0.6978 (m-30) REVERT: M 43 ASN cc_start: 0.8095 (OUTLIER) cc_final: 0.7637 (p0) REVERT: M 104 GLN cc_start: 0.7598 (OUTLIER) cc_final: 0.7271 (tp-100) REVERT: M 116 GLN cc_start: 0.8572 (tt0) cc_final: 0.8359 (tp40) REVERT: O 48 ASP cc_start: 0.7465 (m-30) cc_final: 0.7031 (m-30) REVERT: T 59 GLU cc_start: 0.8719 (pt0) cc_final: 0.8512 (pt0) REVERT: U 25 GLU cc_start: 0.8018 (pt0) cc_final: 0.7773 (pt0) REVERT: W 4 LYS cc_start: 0.8379 (mppt) cc_final: 0.7944 (mtpt) REVERT: W 17 GLU cc_start: 0.8155 (tp30) cc_final: 0.7929 (tp30) REVERT: Z 7 LYS cc_start: 0.8336 (mttp) cc_final: 0.7931 (mptt) REVERT: Z 8 ILE cc_start: 0.8779 (OUTLIER) cc_final: 0.8537 (pp) REVERT: Z 49 LYS cc_start: 0.8030 (mtpt) cc_final: 0.7670 (ttpt) REVERT: AC 37 GLN cc_start: 0.7986 (tt0) cc_final: 0.7658 (tt0) REVERT: b 109 GLU cc_start: 0.7101 (pm20) cc_final: 0.6788 (pp20) REVERT: b 133 MET cc_start: 0.7871 (mtm) cc_final: 0.7404 (mtp) REVERT: b 167 TYR cc_start: 0.7118 (m-80) cc_final: 0.6659 (m-80) REVERT: b 169 GLU cc_start: 0.8021 (tm-30) cc_final: 0.7308 (tm-30) REVERT: b 182 ASP cc_start: 0.7524 (t0) cc_final: 0.7206 (t0) REVERT: c 104 MET cc_start: 0.7753 (ttm) cc_final: 0.7084 (ttm) REVERT: d 13 LYS cc_start: 0.8620 (mmmt) cc_final: 0.7700 (mmtm) REVERT: d 70 MET cc_start: 0.7809 (ttp) cc_final: 0.7419 (ttp) REVERT: e 3 HIS cc_start: 0.7965 (OUTLIER) cc_final: 0.7118 (m-70) REVERT: e 17 GLN cc_start: 0.7216 (mt0) cc_final: 0.6691 (mm110) REVERT: e 82 ASP cc_start: 0.8524 (t0) cc_final: 0.8209 (t0) REVERT: g 1 SER cc_start: 0.8650 (p) cc_final: 0.8206 (t) REVERT: g 20 ASN cc_start: 0.8970 (m110) cc_final: 0.8540 (t0) REVERT: g 110 MET cc_start: 0.8256 (ptp) cc_final: 0.8018 (ptp) REVERT: h 56 MET cc_start: 0.7986 (tmm) cc_final: 0.7353 (tpp) REVERT: h 59 LYS cc_start: 0.7438 (mmtm) cc_final: 0.7181 (mmtm) REVERT: h 62 LEU cc_start: 0.8291 (OUTLIER) cc_final: 0.8083 (pp) REVERT: h 80 HIS cc_start: 0.6443 (t-90) cc_final: 0.6069 (t70) REVERT: i 46 LYS cc_start: 0.8666 (ptpt) cc_final: 0.8125 (pttp) REVERT: i 49 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.7163 (m-80) REVERT: j 80 ASN cc_start: 0.7915 (OUTLIER) cc_final: 0.7576 (p0) REVERT: k 52 CYS cc_start: 0.7177 (OUTLIER) cc_final: 0.6409 (t) REVERT: k 66 ILE cc_start: 0.8517 (OUTLIER) cc_final: 0.8046 (tp) REVERT: k 87 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7432 (tttm) REVERT: l 22 TYR cc_start: 0.7511 (t80) cc_final: 0.7154 (t80) REVERT: l 55 LEU cc_start: 0.7678 (mt) cc_final: 0.7238 (pp) REVERT: l 67 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7721 (t0) REVERT: m 46 LYS cc_start: 0.8283 (mmmm) cc_final: 0.7991 (mmtp) REVERT: n 48 ASP cc_start: 0.8177 (m-30) cc_final: 0.7949 (m-30) REVERT: n 79 GLN cc_start: 0.8520 (tt0) cc_final: 0.8154 (tm-30) REVERT: o 17 TYR cc_start: 0.7430 (m-80) cc_final: 0.6915 (m-80) REVERT: o 31 ARG cc_start: 0.8329 (OUTLIER) cc_final: 0.6898 (ttp-170) REVERT: p 39 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7293 (mmp-170) REVERT: p 61 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7105 (ttm170) REVERT: r 34 SER cc_start: 0.7977 (OUTLIER) cc_final: 0.7642 (t) REVERT: r 55 GLN cc_start: 0.7381 (tp40) cc_final: 0.6885 (pt0) REVERT: s 59 ARG cc_start: 0.8037 (mtm-85) cc_final: 0.7587 (mtm-85) REVERT: t 53 LYS cc_start: 0.7525 (tttm) cc_final: 0.7231 (ttmt) outliers start: 234 outliers final: 198 residues processed: 1055 average time/residue: 1.1702 time to fit residues: 2185.2367 Evaluate side-chains 1110 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 894 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 103 ASP Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 55 ASP Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 69 VAL Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain N residue 114 ASN Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 7 HIS Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain V residue 1 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AB residue 30 HIS Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 79 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 128 MET Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 192 TYR Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 87 SER Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain f residue 3 ARG Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 112 ASP Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 20 GLN Chi-restraints excluded: chain i residue 27 GLU Chi-restraints excluded: chain i residue 49 PHE Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 97 VAL Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain m residue 22 LYS Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain n residue 56 LEU Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 26 ASN Chi-restraints excluded: chain o residue 31 ARG Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 68 SER Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 14 ASP Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 61 ARG Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 573 optimal weight: 7.9990 chunk 924 optimal weight: 20.0000 chunk 564 optimal weight: 6.9990 chunk 438 optimal weight: 7.9990 chunk 642 optimal weight: 6.9990 chunk 969 optimal weight: 20.0000 chunk 892 optimal weight: 8.9990 chunk 771 optimal weight: 0.6980 chunk 80 optimal weight: 8.9990 chunk 596 optimal weight: 8.9990 chunk 473 optimal weight: 7.9990 overall best weight: 6.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN a 35 ASN c 73 ASN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 74 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 152963 Z= 0.425 Angle : 0.690 12.301 229314 Z= 0.351 Chirality : 0.041 0.397 29384 Planarity : 0.005 0.056 11960 Dihedral : 23.741 179.956 77658 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 5.15 % Allowed : 21.60 % Favored : 73.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.11), residues: 5281 helix: 0.78 (0.12), residues: 1802 sheet: -0.86 (0.16), residues: 1006 loop : -1.70 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP D 96 HIS 0.008 0.001 HIS C 165 PHE 0.026 0.002 PHE Z 38 TYR 0.043 0.002 TYR M 64 ARG 0.010 0.001 ARG q 60 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10562 Ramachandran restraints generated. 5281 Oldfield, 0 Emsley, 5281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 909 time to evaluate : 5.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 30 VAL cc_start: 0.7796 (OUTLIER) cc_final: 0.7458 (m) REVERT: D 95 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.6958 (ppp) REVERT: D 129 MET cc_start: 0.7380 (OUTLIER) cc_final: 0.6995 (tmm) REVERT: G 1 MET cc_start: 0.8034 (ptp) cc_final: 0.7674 (ptp) REVERT: I 56 ASP cc_start: 0.8002 (m-30) cc_final: 0.7599 (m-30) REVERT: K 106 ASP cc_start: 0.7264 (m-30) cc_final: 0.6982 (m-30) REVERT: M 43 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7639 (p0) REVERT: M 104 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7269 (tp-100) REVERT: M 116 GLN cc_start: 0.8629 (tt0) cc_final: 0.8358 (tp40) REVERT: O 48 ASP cc_start: 0.7439 (m-30) cc_final: 0.7026 (m-30) REVERT: T 59 GLU cc_start: 0.8710 (pt0) cc_final: 0.8502 (pt0) REVERT: U 25 GLU cc_start: 0.8021 (pt0) cc_final: 0.7782 (pt0) REVERT: W 17 GLU cc_start: 0.8183 (tp30) cc_final: 0.7961 (tp30) REVERT: Z 7 LYS cc_start: 0.8356 (mttp) cc_final: 0.7956 (mptt) REVERT: Z 8 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8522 (pp) REVERT: Z 49 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7646 (ttpt) REVERT: AC 37 GLN cc_start: 0.8004 (tt0) cc_final: 0.7695 (tt0) REVERT: a 168 GLU cc_start: 0.7849 (tm-30) cc_final: 0.6946 (tm-30) REVERT: b 109 GLU cc_start: 0.7184 (pm20) cc_final: 0.6542 (pp20) REVERT: b 133 MET cc_start: 0.7863 (mtm) cc_final: 0.7543 (mtp) REVERT: b 167 TYR cc_start: 0.7030 (m-80) cc_final: 0.6774 (m-80) REVERT: b 169 GLU cc_start: 0.8020 (tm-30) cc_final: 0.7309 (tm-30) REVERT: b 182 ASP cc_start: 0.7623 (t0) cc_final: 0.7311 (t0) REVERT: b 183 TYR cc_start: 0.8429 (t80) cc_final: 0.8220 (t80) REVERT: c 104 MET cc_start: 0.7800 (ttm) cc_final: 0.7047 (ttm) REVERT: d 13 LYS cc_start: 0.8609 (mmmt) cc_final: 0.7693 (mmtm) REVERT: d 70 MET cc_start: 0.7853 (ttp) cc_final: 0.7457 (ttp) REVERT: e 3 HIS cc_start: 0.7977 (OUTLIER) cc_final: 0.7115 (m-70) REVERT: e 82 ASP cc_start: 0.8526 (t0) cc_final: 0.8211 (t0) REVERT: g 1 SER cc_start: 0.8673 (p) cc_final: 0.8234 (t) REVERT: g 20 ASN cc_start: 0.8987 (m110) cc_final: 0.8547 (t0) REVERT: g 110 MET cc_start: 0.8260 (ptp) cc_final: 0.8026 (ptp) REVERT: h 56 MET cc_start: 0.7895 (tmm) cc_final: 0.7387 (tmm) REVERT: h 80 HIS cc_start: 0.6447 (t-90) cc_final: 0.5902 (t70) REVERT: i 25 ILE cc_start: 0.6845 (OUTLIER) cc_final: 0.6117 (pt) REVERT: i 46 LYS cc_start: 0.8654 (ptpt) cc_final: 0.8116 (pttp) REVERT: j 80 ASN cc_start: 0.7959 (OUTLIER) cc_final: 0.7697 (p0) REVERT: k 52 CYS cc_start: 0.6912 (OUTLIER) cc_final: 0.6251 (t) REVERT: k 66 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8018 (tp) REVERT: k 87 LYS cc_start: 0.7871 (OUTLIER) cc_final: 0.7541 (tptp) REVERT: l 22 TYR cc_start: 0.7479 (t80) cc_final: 0.7190 (t80) REVERT: l 67 ASP cc_start: 0.8239 (OUTLIER) cc_final: 0.7769 (t0) REVERT: m 5 MET cc_start: 0.7384 (tpp) cc_final: 0.7054 (ttm) REVERT: m 46 LYS cc_start: 0.8334 (mmmm) cc_final: 0.8057 (mmtp) REVERT: m 88 MET cc_start: 0.8133 (mmp) cc_final: 0.7881 (mmp) REVERT: n 48 ASP cc_start: 0.8161 (m-30) cc_final: 0.7920 (m-30) REVERT: n 79 GLN cc_start: 0.8509 (tt0) cc_final: 0.8147 (tm-30) REVERT: o 1 MET cc_start: 0.7407 (ppp) cc_final: 0.7083 (ppp) REVERT: o 17 TYR cc_start: 0.7579 (m-80) cc_final: 0.7107 (m-80) REVERT: o 31 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.6941 (ttp-170) REVERT: p 39 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.7311 (mmp-170) REVERT: p 61 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7107 (ttm170) REVERT: r 34 SER cc_start: 0.7974 (OUTLIER) cc_final: 0.7609 (t) REVERT: r 55 GLN cc_start: 0.7392 (tp40) cc_final: 0.6915 (pt0) REVERT: t 53 LYS cc_start: 0.7517 (tttm) cc_final: 0.7224 (ttmt) outliers start: 225 outliers final: 196 residues processed: 1044 average time/residue: 1.1463 time to fit residues: 2121.2354 Evaluate side-chains 1103 residues out of total 4407 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 890 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 19 VAL Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 50 THR Chi-restraints excluded: chain A residue 52 HIS Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain A residue 249 VAL Chi-restraints excluded: chain B residue 18 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 91 THR Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 200 ASP Chi-restraints excluded: chain C residue 4 VAL Chi-restraints excluded: chain C residue 150 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain D residue 5 ASP Chi-restraints excluded: chain D residue 7 TYR Chi-restraints excluded: chain D residue 16 MET Chi-restraints excluded: chain D residue 27 VAL Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 37 MET Chi-restraints excluded: chain D residue 95 MET Chi-restraints excluded: chain D residue 129 MET Chi-restraints excluded: chain D residue 132 ARG Chi-restraints excluded: chain D residue 153 ILE Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 74 MET Chi-restraints excluded: chain E residue 78 VAL Chi-restraints excluded: chain E residue 105 SER Chi-restraints excluded: chain E residue 154 GLU Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain G residue 57 LEU Chi-restraints excluded: chain G residue 88 THR Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 141 ASP Chi-restraints excluded: chain I residue 21 CYS Chi-restraints excluded: chain I residue 29 HIS Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 80 ASP Chi-restraints excluded: chain I residue 104 THR Chi-restraints excluded: chain J residue 27 LEU Chi-restraints excluded: chain J residue 118 THR Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 7 THR Chi-restraints excluded: chain K residue 28 PHE Chi-restraints excluded: chain K residue 93 VAL Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain K residue 132 THR Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain L residue 48 VAL Chi-restraints excluded: chain L residue 57 THR Chi-restraints excluded: chain L residue 60 VAL Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain M residue 36 TYR Chi-restraints excluded: chain M residue 38 GLN Chi-restraints excluded: chain M residue 40 ILE Chi-restraints excluded: chain M residue 43 ASN Chi-restraints excluded: chain M residue 45 SER Chi-restraints excluded: chain M residue 49 VAL Chi-restraints excluded: chain M residue 65 THR Chi-restraints excluded: chain M residue 93 ASP Chi-restraints excluded: chain M residue 104 GLN Chi-restraints excluded: chain N residue 72 VAL Chi-restraints excluded: chain N residue 75 THR Chi-restraints excluded: chain N residue 80 VAL Chi-restraints excluded: chain O residue 30 VAL Chi-restraints excluded: chain O residue 73 ILE Chi-restraints excluded: chain O residue 76 SER Chi-restraints excluded: chain P residue 22 LEU Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 41 ILE Chi-restraints excluded: chain Q residue 3 THR Chi-restraints excluded: chain Q residue 4 ILE Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 106 VAL Chi-restraints excluded: chain Q residue 108 SER Chi-restraints excluded: chain R residue 92 ASN Chi-restraints excluded: chain S residue 14 THR Chi-restraints excluded: chain S residue 57 ILE Chi-restraints excluded: chain S residue 82 VAL Chi-restraints excluded: chain T residue 3 THR Chi-restraints excluded: chain T residue 43 ASP Chi-restraints excluded: chain T residue 49 ASN Chi-restraints excluded: chain T residue 61 LEU Chi-restraints excluded: chain T residue 83 LYS Chi-restraints excluded: chain U residue 26 SER Chi-restraints excluded: chain U residue 54 THR Chi-restraints excluded: chain U residue 66 GLU Chi-restraints excluded: chain V residue 1 SER Chi-restraints excluded: chain V residue 7 THR Chi-restraints excluded: chain V residue 39 VAL Chi-restraints excluded: chain V residue 57 VAL Chi-restraints excluded: chain V residue 58 ILE Chi-restraints excluded: chain W residue 56 LEU Chi-restraints excluded: chain X residue 3 THR Chi-restraints excluded: chain X residue 38 GLU Chi-restraints excluded: chain Y residue 24 VAL Chi-restraints excluded: chain Y residue 54 ILE Chi-restraints excluded: chain Z residue 8 ILE Chi-restraints excluded: chain AA residue 24 THR Chi-restraints excluded: chain AB residue 30 HIS Chi-restraints excluded: chain AB residue 58 ILE Chi-restraints excluded: chain a residue 13 VAL Chi-restraints excluded: chain a residue 66 ILE Chi-restraints excluded: chain a residue 79 VAL Chi-restraints excluded: chain a residue 124 THR Chi-restraints excluded: chain a residue 163 ILE Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain b residue 66 THR Chi-restraints excluded: chain b residue 90 VAL Chi-restraints excluded: chain b residue 123 LEU Chi-restraints excluded: chain b residue 127 VAL Chi-restraints excluded: chain b residue 128 MET Chi-restraints excluded: chain b residue 148 ILE Chi-restraints excluded: chain b residue 189 HIS Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 57 LYS Chi-restraints excluded: chain c residue 141 VAL Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 193 ASP Chi-restraints excluded: chain d residue 14 LEU Chi-restraints excluded: chain d residue 15 ILE Chi-restraints excluded: chain d residue 17 VAL Chi-restraints excluded: chain d residue 20 VAL Chi-restraints excluded: chain d residue 23 THR Chi-restraints excluded: chain d residue 79 THR Chi-restraints excluded: chain d residue 84 VAL Chi-restraints excluded: chain d residue 99 SER Chi-restraints excluded: chain d residue 104 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 143 LEU Chi-restraints excluded: chain d residue 147 ASN Chi-restraints excluded: chain e residue 3 HIS Chi-restraints excluded: chain e residue 13 ASP Chi-restraints excluded: chain e residue 22 ILE Chi-restraints excluded: chain e residue 74 LEU Chi-restraints excluded: chain e residue 76 THR Chi-restraints excluded: chain e residue 92 THR Chi-restraints excluded: chain e residue 94 HIS Chi-restraints excluded: chain e residue 97 THR Chi-restraints excluded: chain f residue 14 ASP Chi-restraints excluded: chain f residue 30 MET Chi-restraints excluded: chain g residue 11 THR Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain h residue 46 VAL Chi-restraints excluded: chain h residue 62 LEU Chi-restraints excluded: chain i residue 15 HIS Chi-restraints excluded: chain i residue 20 GLN Chi-restraints excluded: chain i residue 25 ILE Chi-restraints excluded: chain i residue 27 GLU Chi-restraints excluded: chain i residue 60 ASP Chi-restraints excluded: chain i residue 66 GLU Chi-restraints excluded: chain j residue 58 THR Chi-restraints excluded: chain j residue 73 VAL Chi-restraints excluded: chain j residue 80 ASN Chi-restraints excluded: chain j residue 85 VAL Chi-restraints excluded: chain k residue 40 THR Chi-restraints excluded: chain k residue 52 CYS Chi-restraints excluded: chain k residue 54 VAL Chi-restraints excluded: chain k residue 66 ILE Chi-restraints excluded: chain k residue 79 ILE Chi-restraints excluded: chain k residue 81 ILE Chi-restraints excluded: chain k residue 87 LYS Chi-restraints excluded: chain k residue 101 LEU Chi-restraints excluded: chain k residue 106 VAL Chi-restraints excluded: chain l residue 24 VAL Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 67 ASP Chi-restraints excluded: chain m residue 92 ILE Chi-restraints excluded: chain m residue 97 LYS Chi-restraints excluded: chain n residue 26 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 3 THR Chi-restraints excluded: chain o residue 19 VAL Chi-restraints excluded: chain o residue 21 VAL Chi-restraints excluded: chain o residue 24 SER Chi-restraints excluded: chain o residue 26 ASN Chi-restraints excluded: chain o residue 31 ARG Chi-restraints excluded: chain o residue 55 ASP Chi-restraints excluded: chain o residue 57 ILE Chi-restraints excluded: chain o residue 68 SER Chi-restraints excluded: chain p residue 6 THR Chi-restraints excluded: chain p residue 14 ASP Chi-restraints excluded: chain p residue 27 PHE Chi-restraints excluded: chain p residue 39 ARG Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 56 ASP Chi-restraints excluded: chain p residue 61 ARG Chi-restraints excluded: chain p residue 75 VAL Chi-restraints excluded: chain q residue 67 LEU Chi-restraints excluded: chain r residue 14 LEU Chi-restraints excluded: chain r residue 18 VAL Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 42 ASN Chi-restraints excluded: chain r residue 52 ASN Chi-restraints excluded: chain r residue 54 ARG Chi-restraints excluded: chain r residue 62 THR Chi-restraints excluded: chain r residue 66 VAL Chi-restraints excluded: chain r residue 76 THR Chi-restraints excluded: chain r residue 78 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 13 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 973 random chunks: chunk 613 optimal weight: 10.0000 chunk 822 optimal weight: 10.0000 chunk 236 optimal weight: 0.7980 chunk 711 optimal weight: 7.9990 chunk 113 optimal weight: 0.7980 chunk 214 optimal weight: 0.9980 chunk 773 optimal weight: 5.9990 chunk 323 optimal weight: 10.0000 chunk 793 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 131 ASN ** K 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 62 ASN ** Q 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN Z 25 ASN f 96 ASN ** g 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 27 GLN ** n 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 18 GLN ** s 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.076492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.054180 restraints weight = 534207.233| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.26 r_work: 0.2976 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.3593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 152963 Z= 0.176 Angle : 0.556 11.986 229314 Z= 0.286 Chirality : 0.034 0.446 29384 Planarity : 0.004 0.052 11960 Dihedral : 23.651 179.423 77658 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.03 % Allowed : 22.67 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.11), residues: 5281 helix: 1.17 (0.12), residues: 1803 sheet: -0.80 (0.16), residues: 1063 loop : -1.51 (0.12), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 169 HIS 0.008 0.001 HIS Y 18 PHE 0.020 0.001 PHE E 51 TYR 0.039 0.002 TYR M 64 ARG 0.008 0.000 ARG e 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 37448.42 seconds wall clock time: 653 minutes 43.60 seconds (39223.60 seconds total)