Starting phenix.real_space_refine on Wed Mar 20 17:44:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpo_16155/03_2024/8bpo_16155.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpo_16155/03_2024/8bpo_16155.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpo_16155/03_2024/8bpo_16155.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpo_16155/03_2024/8bpo_16155.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpo_16155/03_2024/8bpo_16155.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bpo_16155/03_2024/8bpo_16155.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 5 6.06 5 P 3812 5.49 5 Mg 214 5.21 5 S 286 5.16 5 C 75206 2.51 5 N 26849 2.21 5 O 36954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A2 ASP 33": "OD1" <-> "OD2" Residue "A2 TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 ASP 51": "OD1" <-> "OD2" Residue "A2 TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 GLU 109": "OE1" <-> "OE2" Residue "A2 GLU 117": "OE1" <-> "OE2" Residue "A2 TYR 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A2 ASP 176": "OD1" <-> "OD2" Residue "A2 TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 147": "OD1" <-> "OD2" Residue "B2 TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 GLU 182": "OE1" <-> "OE2" Residue "B2 ASP 214": "OD1" <-> "OD2" Residue "B2 TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 ASP 295": "OD1" <-> "OD2" Residue "B2 TYR 307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B2 PHE 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C2 GLU 145": "OE1" <-> "OE2" Residue "C2 GLU 146": "OE1" <-> "OE2" Residue "C2 GLU 149": "OE1" <-> "OE2" Residue "C2 TYR 211": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ASP 116": "OD1" <-> "OD2" Residue "D2 GLU 124": "OE1" <-> "OE2" Residue "D2 GLU 129": "OE1" <-> "OE2" Residue "D2 PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ASP 168": "OD1" <-> "OD2" Residue "D2 TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D2 ASP 215": "OD1" <-> "OD2" Residue "D2 PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 TYR 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E2 GLU 244": "OE1" <-> "OE2" Residue "E2 ASP 252": "OD1" <-> "OD2" Residue "F2 GLU 51": "OE1" <-> "OE2" Residue "F2 GLU 59": "OE1" <-> "OE2" Residue "F2 GLU 67": "OE1" <-> "OE2" Residue "F2 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 TYR 181": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 187": "OE1" <-> "OE2" Residue "F2 ASP 188": "OD1" <-> "OD2" Residue "F2 TYR 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F2 GLU 228": "OE1" <-> "OE2" Residue "G2 ASP 103": "OD1" <-> "OD2" Residue "G2 TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 PHE 136": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 ASP 141": "OD1" <-> "OD2" Residue "G2 TYR 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G2 ASP 284": "OD1" <-> "OD2" Residue "G2 GLU 285": "OE1" <-> "OE2" Residue "H2 ASP 37": "OD1" <-> "OD2" Residue "H2 ASP 58": "OD1" <-> "OD2" Residue "H2 TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I2 TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I2 ASP 28": "OD1" <-> "OD2" Residue "I2 ASP 55": "OD1" <-> "OD2" Residue "I2 ASP 183": "OD1" <-> "OD2" Residue "I2 ASP 193": "OD1" <-> "OD2" Residue "J2 PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J2 GLU 160": "OE1" <-> "OE2" Residue "K2 TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 GLU 143": "OE1" <-> "OE2" Residue "K2 PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K2 PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L2 ASP 39": "OD1" <-> "OD2" Residue "L2 GLU 96": "OE1" <-> "OE2" Residue "M2 ASP 17": "OD1" <-> "OD2" Residue "M2 TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M2 TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M2 TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M2 TYR 119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M2 PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M2 ASP 136": "OD1" <-> "OD2" Residue "M2 TYR 203": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N2 TYR 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N2 TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N2 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N2 GLU 162": "OE1" <-> "OE2" Residue "N2 TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O2 ASP 108": "OD1" <-> "OD2" Residue "O2 GLU 115": "OE1" <-> "OE2" Residue "P2 ASP 129": "OD1" <-> "OD2" Residue "P2 TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q2 GLU 28": "OE1" <-> "OE2" Residue "Q2 ASP 116": "OD1" <-> "OD2" Residue "Q2 GLU 140": "OE1" <-> "OE2" Residue "R2 ASP 147": "OD1" <-> "OD2" Residue "R2 PHE 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ASP 38": "OD1" <-> "OD2" Residue "S2 TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S2 ASP 113": "OD1" <-> "OD2" Residue "S2 TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T2 ASP 24": "OD1" <-> "OD2" Residue "T2 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T2 TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U2 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U2 ASP 92": "OD1" <-> "OD2" Residue "U2 PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U2 ASP 100": "OD1" <-> "OD2" Residue "V2 TYR 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V2 GLU 37": "OE1" <-> "OE2" Residue "V2 PHE 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V2 TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W2 ASP 72": "OD1" <-> "OD2" Residue "W2 TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W2 PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W2 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W2 GLU 133": "OE1" <-> "OE2" Residue "W2 TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W2 ASP 145": "OD1" <-> "OD2" Residue "X2 PHE 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X2 TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X2 ASP 53": "OD1" <-> "OD2" Residue "X2 TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y2 ASP 30": "OD1" <-> "OD2" Residue "Y2 ASP 47": "OD1" <-> "OD2" Residue "Y2 TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y2 ASP 103": "OD1" <-> "OD2" Residue "Z2 TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z2 TYR 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z2 GLU 135": "OE1" <-> "OE2" Residue "a2 GLU 30": "OE1" <-> "OE2" Residue "a2 TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 TYR 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b2 GLU 61": "OE1" <-> "OE2" Residue "b2 TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c2 GLU 48": "OE1" <-> "OE2" Residue "c2 ASP 61": "OD1" <-> "OD2" Residue "c2 TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c2 TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c2 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d2 PHE 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d2 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d2 TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d2 GLU 98": "OE1" <-> "OE2" Residue "e2 TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e2 GLU 23": "OE1" <-> "OE2" Residue "e2 TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f2 GLU 99": "OE1" <-> "OE2" Residue "g2 GLU 67": "OE1" <-> "OE2" Residue "g2 TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i2 PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j2 PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j2 GLU 68": "OE1" <-> "OE2" Residue "k2 PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n2 TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o2 TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o2 PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o2 TYR 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p2 TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p2 ASP 56": "OD1" <-> "OD2" Residue "q2 PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q2 PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q2 PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r2 ASP 150": "OD1" <-> "OD2" Residue "s2 TYR 886": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s2 ASP 933": "OD1" <-> "OD2" Residue "s2 GLU 944": "OE1" <-> "OE2" Residue "s2 TYR 1188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s2 TYR 1307": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t2 PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t2 ASP 163": "OD1" <-> "OD2" Residue "t2 GLU 214": "OE1" <-> "OE2" Residue "t2 PHE 247": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t2 ASP 254": "OD1" <-> "OD2" Residue "t2 GLU 269": "OE1" <-> "OE2" Residue "t2 PHE 343": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t2 GLU 348": "OE1" <-> "OE2" Residue "t2 PHE 353": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t2 PHE 355": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 143326 Number of models: 1 Model: "" Number of chains: 64 Chain: "A1" Number of atoms: 75972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3543, 75972 Classifications: {'RNA': 3543} Modifications used: {'rna2p_pur': 358, 'rna2p_pyr': 216, 'rna3p_pur': 1588, 'rna3p_pyr': 1381} Link IDs: {'rna2p': 574, 'rna3p': 2968} Chain breaks: 27 Chain: "B1" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "C1" Number of atoms: 3208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3208 Classifications: {'RNA': 151} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 15, 'rna3p_pur': 59, 'rna3p_pyr': 63} Link IDs: {'rna2p': 28, 'rna3p': 122} Chain breaks: 1 Chain: "D1" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 150 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 1, 'TRANS': 27} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 81 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'UNK:plan-1': 27} Unresolved non-hydrogen planarities: 27 Chain: "A2" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1898 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 14, 'TRANS': 233} Chain: "B2" Number of atoms: 3172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3172 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 15, 'TRANS': 378} Chain: "C2" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D2" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 2391 Classifications: {'peptide': 293} Link IDs: {'PTRANS': 9, 'TRANS': 283} Chain: "E2" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1729 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 201} Chain breaks: 3 Chain: "F2" Number of atoms: 1875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1875 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "G2" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 1879 Classifications: {'peptide': 233} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 219} Chain breaks: 1 Chain: "H2" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I2" Number of atoms: 1664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1664 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 193} Chain breaks: 1 Chain: "J2" Number of atoms: 1362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1362 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} Chain: "K2" Number of atoms: 1702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1702 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "L2" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "M2" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "N2" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1630 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "O2" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "P2" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1514 Classifications: {'peptide': 187} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "Q2" Number of atoms: 1294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1294 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 3, 'TRANS': 151} Chain: "R2" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1462 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 164} Chain: "S2" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "T2" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 834 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 2, 'TRANS': 99} Chain: "U2" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "V2" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "W2" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 967 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "X2" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Y2" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "Z2" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "a2" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 3, 'TRANS': 100} Chain breaks: 1 Chain: "b2" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 761 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 2, 'TRANS': 95} Chain: "c2" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "d2" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "e2" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "f2" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "g2" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "h2" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "i2" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "j2" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "k2" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 447 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "l2" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "m2" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 239 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Chain: "n2" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "o2" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "p2" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 124, 994 Classifications: {'peptide': 124} Link IDs: {'PTRANS': 5, 'TRANS': 118} Chain: "q2" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1507 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain: "r2" Number of atoms: 1160 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1160 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "s2" Number of atoms: 3050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 395, 3050 Classifications: {'peptide': 395} Link IDs: {'PTRANS': 11, 'TRANS': 383} Chain breaks: 8 Chain: "t2" Number of atoms: 3262 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3262 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain breaks: 1 Chain: "u2" Number of atoms: 82 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 82 Classifications: {'peptide': 11} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 10} 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: "A1" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 194 Unusual residues: {' MG': 194} Classifications: {'undetermined': 194} Link IDs: {None: 193} Chain: "B1" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "C1" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Unusual residues: {' MG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f2" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "l2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "n2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o2" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0KM9 SG CYSf2 46 100.786 170.915 208.286 1.00 73.74 S ATOM A0KMQ SG CYSf2 49 101.178 174.551 207.034 1.00 71.53 S ATOM A0KU1 SG CYSf2 83 102.814 174.096 209.867 1.00 52.71 S ATOM A0KUL SG CYSf2 86 98.833 173.463 210.015 1.00 65.87 S ATOM A0MKC SG CYSi2 19 127.551 123.898 185.971 1.00 39.15 S ATOM A0ML4 SG CYSi2 22 128.936 121.610 183.245 1.00 38.23 S ATOM A0MNN SG CYSi2 34 125.501 123.232 182.823 1.00 39.01 S ATOM A0MO6 SG CYSi2 37 126.053 120.514 185.435 1.00 34.59 S ATOM A0NWR SG CYSl2 70 104.092 138.329 73.775 1.00 35.96 S ATOM A0NXH SG CYSl2 73 107.338 139.603 75.231 1.00 44.98 S ATOM A0NZZ SG CYSl2 84 107.402 138.295 71.695 1.00 42.28 S ATOM A0O17 SG CYSl2 89 107.076 135.950 74.567 1.00 51.50 S ATOM A0ODC SG CYSn2 12 59.205 69.020 149.020 1.00 48.66 S ATOM A0OE0 SG CYSn2 15 56.949 66.051 149.633 1.00 58.47 S ATOM A0OR1 SG CYSn2 72 55.606 69.726 150.083 1.00 61.62 S ATOM A0OS2 SG CYSn2 77 58.221 68.010 152.422 1.00 58.77 S ATOM A0P6S SG CYSo2 39 88.048 176.644 198.069 1.00 49.67 S ATOM A0P7F SG CYSo2 42 89.933 179.393 199.059 1.00 48.87 S ATOM A0PAT SG CYSo2 57 91.219 176.932 196.872 1.00 47.14 S Time building chain proxies: 55.67, per 1000 atoms: 0.39 Number of scatterers: 143326 At special positions: 0 Unit cell: (237.094, 235.436, 274.399, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 5 29.99 S 286 16.00 P 3812 15.00 Mg 214 11.99 O 36954 8.00 N 26849 7.00 C 75206 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYSs21005 " - pdb=" SG CYSs21063 " 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: 55.19 Conformation dependent library (CDL) restraints added in 8.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZNf2 201 " pdb="ZN ZNf2 201 " - pdb=" SG CYSf2 46 " pdb="ZN ZNf2 201 " - pdb=" SG CYSf2 49 " pdb="ZN ZNf2 201 " - pdb=" SG CYSf2 83 " pdb="ZN ZNf2 201 " - pdb=" SG CYSf2 86 " pdb=" ZNi2 101 " pdb="ZN ZNi2 101 " - pdb=" SG CYSi2 37 " pdb="ZN ZNi2 101 " - pdb=" SG CYSi2 22 " pdb="ZN ZNi2 101 " - pdb=" SG CYSi2 19 " pdb="ZN ZNi2 101 " - pdb=" SG CYSi2 34 " pdb=" ZNl2 200 " pdb="ZN ZNl2 200 " - pdb=" SG CYSl2 73 " pdb="ZN ZNl2 200 " - pdb=" SG CYSl2 89 " pdb="ZN ZNl2 200 " - pdb=" SG CYSl2 84 " pdb="ZN ZNl2 200 " - pdb=" SG CYSl2 70 " pdb=" ZNn2 200 " pdb="ZN ZNn2 200 " - pdb=" SG CYSn2 77 " pdb="ZN ZNn2 200 " - pdb=" SG CYSn2 12 " pdb="ZN ZNn2 200 " - pdb=" SG CYSn2 15 " pdb="ZN ZNn2 200 " - pdb=" SG CYSn2 72 " pdb=" ZNo2 100 " pdb="ZN ZNo2 100 " - pdb=" SG CYSo2 42 " pdb="ZN ZNo2 100 " - pdb=" SG CYSo2 39 " pdb="ZN ZNo2 100 " - pdb=" SG CYSo2 57 " Number of angles added : 24 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14242 Finding SS restraints... Secondary structure from input PDB file: 288 helices and 78 sheets defined 42.3% alpha, 14.5% beta 1151 base pairs and 2066 stacking pairs defined. Time for finding SS restraints: 48.71 Creating SS restraints... Processing helix chain 'D1' and resid 3 through 15 removed outlier: 3.652A pdb=" N UNKD1 11 " --> pdb=" O UNKD1 7 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N UNKD1 12 " --> pdb=" O UNKD1 8 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEUD1 13 " --> pdb=" O UNKD1 9 " (cutoff:3.500A) Processing helix chain 'A2' and resid 5 through 10 Processing helix chain 'A2' and resid 33 through 39 Processing helix chain 'A2' and resid 173 through 177 removed outlier: 3.754A pdb=" N LYSA2 177 " --> pdb=" O ARGA2 174 " (cutoff:3.500A) Processing helix chain 'A2' and resid 181 through 191 removed outlier: 3.741A pdb=" N ALAA2 185 " --> pdb=" O LYSA2 181 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ALAA2 191 " --> pdb=" O HISA2 187 " (cutoff:3.500A) Processing helix chain 'A2' and resid 200 through 204 Processing helix chain 'B2' and resid 111 through 117 removed outlier: 3.845A pdb=" N ARGB2 117 " --> pdb=" O GLUB2 113 " (cutoff:3.500A) Processing helix chain 'B2' and resid 133 through 137 removed outlier: 3.741A pdb=" N TRPB2 137 " --> pdb=" O CYSB2 134 " (cutoff:3.500A) Processing helix chain 'B2' and resid 139 through 157 removed outlier: 3.738A pdb=" N GLNB2 145 " --> pdb=" O ALAB2 141 " (cutoff:3.500A) Processing helix chain 'B2' and resid 167 through 171 removed outlier: 3.656A pdb=" N LEUB2 170 " --> pdb=" O GLNB2 167 " (cutoff:3.500A) Processing helix chain 'B2' and resid 189 through 198 Processing helix chain 'B2' and resid 230 through 235 Processing helix chain 'B2' and resid 381 through 390 Processing helix chain 'C2' and resid 25 through 30 Processing helix chain 'C2' and resid 33 through 45 Processing helix chain 'C2' and resid 46 through 49 removed outlier: 3.509A pdb=" N ARGC2 49 " --> pdb=" O LYSC2 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 46 through 49' Processing helix chain 'C2' and resid 116 through 130 Processing helix chain 'C2' and resid 133 through 139 removed outlier: 3.625A pdb=" N VALC2 137 " --> pdb=" O LEUC2 133 " (cutoff:3.500A) Processing helix chain 'C2' and resid 163 through 174 removed outlier: 3.649A pdb=" N ALAC2 167 " --> pdb=" O LYSC2 163 " (cutoff:3.500A) Processing helix chain 'C2' and resid 176 through 186 removed outlier: 3.908A pdb=" N ILEC2 180 " --> pdb=" O ALAC2 176 " (cutoff:3.500A) Processing helix chain 'C2' and resid 192 through 198 removed outlier: 3.633A pdb=" N LYSC2 195 " --> pdb=" O GLYC2 192 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASNC2 198 " --> pdb=" O LYSC2 195 " (cutoff:3.500A) Processing helix chain 'C2' and resid 216 through 222 Processing helix chain 'C2' and resid 236 through 241 Processing helix chain 'C2' and resid 242 through 245 removed outlier: 3.761A pdb=" N HISC2 245 " --> pdb=" O PROC2 242 " (cutoff:3.500A) No H-bonds generated for 'chain 'C2' and resid 242 through 245' Processing helix chain 'C2' and resid 254 through 258 Processing helix chain 'C2' and resid 259 through 264 Processing helix chain 'C2' and resid 288 through 294 Processing helix chain 'C2' and resid 295 through 300 removed outlier: 3.509A pdb=" N ARGC2 300 " --> pdb=" O PROC2 296 " (cutoff:3.500A) Processing helix chain 'C2' and resid 321 through 329 Processing helix chain 'C2' and resid 331 through 338 Processing helix chain 'C2' and resid 340 through 361 removed outlier: 3.500A pdb=" N GLUC2 352 " --> pdb=" O LYSC2 348 " (cutoff:3.500A) Processing helix chain 'D2' and resid 9 through 15 Processing helix chain 'D2' and resid 20 through 25 Processing helix chain 'D2' and resid 29 through 38 removed outlier: 3.950A pdb=" N ARGD2 35 " --> pdb=" O TYRD2 31 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ILED2 38 " --> pdb=" O LYSD2 34 " (cutoff:3.500A) Processing helix chain 'D2' and resid 40 through 44 removed outlier: 3.610A pdb=" N TYRD2 44 " --> pdb=" O LYSD2 41 " (cutoff:3.500A) Processing helix chain 'D2' and resid 82 through 87 removed outlier: 3.820A pdb=" N TYRD2 86 " --> pdb=" O GLUD2 82 " (cutoff:3.500A) Processing helix chain 'D2' and resid 94 through 114 Processing helix chain 'D2' and resid 157 through 170 Processing helix chain 'D2' and resid 191 through 200 removed outlier: 3.624A pdb=" N HISD2 195 " --> pdb=" O ASND2 191 " (cutoff:3.500A) Processing helix chain 'D2' and resid 201 through 215 Processing helix chain 'D2' and resid 215 through 223 Processing helix chain 'D2' and resid 223 through 229 removed outlier: 4.163A pdb=" N ILED2 227 " --> pdb=" O PHED2 223 " (cutoff:3.500A) Processing helix chain 'D2' and resid 235 through 250 Processing helix chain 'D2' and resid 272 through 293 removed outlier: 3.507A pdb=" N VALD2 280 " --> pdb=" O LYSD2 276 " (cutoff:3.500A) Processing helix chain 'E2' and resid 60 through 69 Processing helix chain 'E2' and resid 70 through 73 Processing helix chain 'E2' and resid 135 through 139 Processing helix chain 'E2' and resid 216 through 221 Processing helix chain 'E2' and resid 246 through 265 removed outlier: 4.009A pdb=" N GLNE2 259 " --> pdb=" O ALAE2 255 " (cutoff:3.500A) Proline residue: E2 262 - end of helix Processing helix chain 'E2' and resid 269 through 276 Processing helix chain 'F2' and resid 24 through 78 removed outlier: 3.717A pdb=" N ILEF2 29 " --> pdb=" O ALAF2 25 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYSF2 58 " --> pdb=" O LYSF2 54 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N GLUF2 67 " --> pdb=" O METF2 63 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILEF2 68 " --> pdb=" O TYRF2 64 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALAF2 77 " --> pdb=" O METF2 73 " (cutoff:3.500A) Processing helix chain 'F2' and resid 101 through 111 Processing helix chain 'F2' and resid 125 through 133 removed outlier: 3.861A pdb=" N METF2 131 " --> pdb=" O ALAF2 127 " (cutoff:3.500A) Processing helix chain 'F2' and resid 135 through 137 No H-bonds generated for 'chain 'F2' and resid 135 through 137' Processing helix chain 'F2' and resid 145 through 157 Processing helix chain 'F2' and resid 170 through 179 removed outlier: 4.065A pdb=" N ILEF2 174 " --> pdb=" O ASPF2 170 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N SERF2 177 " --> pdb=" O LEUF2 173 " (cutoff:3.500A) Processing helix chain 'F2' and resid 180 through 182 No H-bonds generated for 'chain 'F2' and resid 180 through 182' Processing helix chain 'F2' and resid 185 through 195 Processing helix chain 'F2' and resid 199 through 207 removed outlier: 3.672A pdb=" N LEUF2 207 " --> pdb=" O ALAF2 203 " (cutoff:3.500A) Processing helix chain 'F2' and resid 225 through 229 Processing helix chain 'F2' and resid 238 through 247 removed outlier: 3.729A pdb=" N LEUF2 242 " --> pdb=" O GLNF2 238 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARGF2 245 " --> pdb=" O ARGF2 241 " (cutoff:3.500A) Processing helix chain 'G2' and resid 104 through 108 removed outlier: 3.845A pdb=" N VALG2 108 " --> pdb=" O THRG2 105 " (cutoff:3.500A) Processing helix chain 'G2' and resid 111 through 127 removed outlier: 4.176A pdb=" N LYSG2 125 " --> pdb=" O ALAG2 121 " (cutoff:3.500A) Processing helix chain 'G2' and resid 130 through 135 Processing helix chain 'G2' and resid 141 through 153 removed outlier: 3.908A pdb=" N THRG2 146 " --> pdb=" O ARGG2 142 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLNG2 147 " --> pdb=" O GLNG2 143 " (cutoff:3.500A) Processing helix chain 'G2' and resid 159 through 176 removed outlier: 3.638A pdb=" N LYSG2 164 " --> pdb=" O LYSG2 160 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALAG2 176 " --> pdb=" O GLUG2 172 " (cutoff:3.500A) Processing helix chain 'G2' and resid 192 through 202 Processing helix chain 'G2' and resid 216 through 220 Processing helix chain 'G2' and resid 222 through 231 Processing helix chain 'G2' and resid 239 through 244 Processing helix chain 'G2' and resid 264 through 277 removed outlier: 3.849A pdb=" N ALAG2 274 " --> pdb=" O LYSG2 270 " (cutoff:3.500A) Processing helix chain 'G2' and resid 282 through 287 Processing helix chain 'G2' and resid 296 through 318 removed outlier: 3.750A pdb=" N ILEG2 303 " --> pdb=" O SERG2 299 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LEUG2 314 " --> pdb=" O LYSG2 310 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEUG2 318 " --> pdb=" O LEUG2 314 " (cutoff:3.500A) Processing helix chain 'H2' and resid 63 through 68 removed outlier: 3.514A pdb=" N ALAH2 68 " --> pdb=" O ARGH2 64 " (cutoff:3.500A) Processing helix chain 'H2' and resid 68 through 86 removed outlier: 3.894A pdb=" N THRH2 72 " --> pdb=" O ALAH2 68 " (cutoff:3.500A) Processing helix chain 'H2' and resid 107 through 109 No H-bonds generated for 'chain 'H2' and resid 107 through 109' Processing helix chain 'H2' and resid 116 through 120 removed outlier: 3.597A pdb=" N GLYH2 119 " --> pdb=" O ASNH2 116 " (cutoff:3.500A) Processing helix chain 'H2' and resid 150 through 165 removed outlier: 3.762A pdb=" N THRH2 165 " --> pdb=" O ILEH2 161 " (cutoff:3.500A) Processing helix chain 'I2' and resid 42 through 46 removed outlier: 3.895A pdb=" N GLUI2 45 " --> pdb=" O LYSI2 42 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N PHEI2 46 " --> pdb=" O VALI2 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'I2' and resid 42 through 46' Processing helix chain 'I2' and resid 62 through 81 removed outlier: 3.659A pdb=" N LYSI2 78 " --> pdb=" O LYSI2 74 " (cutoff:3.500A) Processing helix chain 'I2' and resid 144 through 156 Processing helix chain 'I2' and resid 157 through 159 No H-bonds generated for 'chain 'I2' and resid 157 through 159' Processing helix chain 'I2' and resid 177 through 187 removed outlier: 4.589A pdb=" N GLUI2 182 " --> pdb=" O ALAI2 178 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N ASPI2 183 " --> pdb=" O ASPI2 179 " (cutoff:3.500A) Processing helix chain 'I2' and resid 205 through 214 removed outlier: 3.834A pdb=" N TRPI2 209 " --> pdb=" O PROI2 205 " (cutoff:3.500A) Processing helix chain 'J2' and resid 10 through 14 removed outlier: 3.643A pdb=" N GLUJ2 14 " --> pdb=" O PROJ2 11 " (cutoff:3.500A) Processing helix chain 'J2' and resid 30 through 45 removed outlier: 3.767A pdb=" N THRJ2 34 " --> pdb=" O GLYJ2 30 " (cutoff:3.500A) Processing helix chain 'J2' and resid 76 through 90 removed outlier: 4.018A pdb=" N GLUJ2 80 " --> pdb=" O GLYJ2 76 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLUJ2 81 " --> pdb=" O ALAJ2 77 " (cutoff:3.500A) Processing helix chain 'J2' and resid 97 through 99 No H-bonds generated for 'chain 'J2' and resid 97 through 99' Processing helix chain 'J2' and resid 111 through 116 Processing helix chain 'J2' and resid 138 through 143 removed outlier: 3.579A pdb=" N ILEJ2 141 " --> pdb=" O GLYJ2 138 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALAJ2 142 " --> pdb=" O PHEJ2 139 " (cutoff:3.500A) Processing helix chain 'J2' and resid 158 through 170 removed outlier: 3.510A pdb=" N TYRJ2 170 " --> pdb=" O PHEJ2 166 " (cutoff:3.500A) Processing helix chain 'K2' and resid 27 through 46 removed outlier: 3.516A pdb=" N ILEK2 33 " --> pdb=" O PROK2 29 " (cutoff:3.500A) Processing helix chain 'K2' and resid 77 through 85 Processing helix chain 'K2' and resid 87 through 92 removed outlier: 4.382A pdb=" N ARGK2 92 " --> pdb=" O LYSK2 88 " (cutoff:3.500A) Processing helix chain 'K2' and resid 93 through 95 No H-bonds generated for 'chain 'K2' and resid 93 through 95' Processing helix chain 'K2' and resid 107 through 123 Processing helix chain 'K2' and resid 140 through 145 removed outlier: 3.579A pdb=" N LEUK2 144 " --> pdb=" O SERK2 140 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYSK2 145 " --> pdb=" O ALAK2 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'K2' and resid 140 through 145' Processing helix chain 'K2' and resid 170 through 175 Processing helix chain 'K2' and resid 177 through 191 Processing helix chain 'K2' and resid 191 through 208 removed outlier: 3.795A pdb=" N GLUK2 208 " --> pdb=" O GLUK2 204 " (cutoff:3.500A) Processing helix chain 'L2' and resid 69 through 81 Processing helix chain 'L2' and resid 81 through 89 removed outlier: 3.693A pdb=" N LYSL2 85 " --> pdb=" O ASPL2 81 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALAL2 87 " --> pdb=" O ASNL2 83 " (cutoff:3.500A) Processing helix chain 'L2' and resid 89 through 104 removed outlier: 3.506A pdb=" N LYSL2 93 " --> pdb=" O THRL2 89 " (cutoff:3.500A) Processing helix chain 'L2' and resid 105 through 139 Processing helix chain 'M2' and resid 3 through 11 Processing helix chain 'M2' and resid 16 through 32 Processing helix chain 'M2' and resid 44 through 52 Processing helix chain 'M2' and resid 83 through 88 removed outlier: 3.699A pdb=" N HISM2 87 " --> pdb=" O PROM2 84 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N GLYM2 88 " --> pdb=" O VALM2 85 " (cutoff:3.500A) Processing helix chain 'M2' and resid 97 through 110 removed outlier: 3.685A pdb=" N HISM2 109 " --> pdb=" O ARGM2 105 " (cutoff:3.500A) Processing helix chain 'M2' and resid 139 through 144 Processing helix chain 'M2' and resid 153 through 157 removed outlier: 3.706A pdb=" N LYSM2 157 " --> pdb=" O PROM2 154 " (cutoff:3.500A) Processing helix chain 'M2' and resid 165 through 170 Processing helix chain 'M2' and resid 180 through 184 removed outlier: 3.680A pdb=" N THRM2 183 " --> pdb=" O PHEM2 180 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ILEM2 184 " --> pdb=" O HISM2 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'M2' and resid 180 through 184' Processing helix chain 'M2' and resid 187 through 196 Processing helix chain 'N2' and resid 15 through 29 removed outlier: 3.513A pdb=" N LYSN2 25 " --> pdb=" O ALAN2 21 " (cutoff:3.500A) Processing helix chain 'N2' and resid 37 through 40 Processing helix chain 'N2' and resid 46 through 60 removed outlier: 3.568A pdb=" N LYSN2 60 " --> pdb=" O ALAN2 56 " (cutoff:3.500A) Processing helix chain 'N2' and resid 75 through 86 Processing helix chain 'N2' and resid 92 through 101 removed outlier: 3.558A pdb=" N ARGN2 101 " --> pdb=" O ALAN2 97 " (cutoff:3.500A) Processing helix chain 'N2' and resid 124 through 129 Processing helix chain 'N2' and resid 138 through 144 Processing helix chain 'N2' and resid 149 through 185 removed outlier: 3.760A pdb=" N ILEN2 166 " --> pdb=" O GLUN2 162 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N HISN2 167 " --> pdb=" O LYSN2 163 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYSN2 183 " --> pdb=" O LYSN2 179 " (cutoff:3.500A) Processing helix chain 'N2' and resid 189 through 198 removed outlier: 3.560A pdb=" N ASPN2 194 " --> pdb=" O SERN2 190 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N VALN2 195 " --> pdb=" O LYSN2 191 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N LEUN2 196 " --> pdb=" O PHEN2 192 " (cutoff:3.500A) Processing helix chain 'O2' and resid 10 through 12 No H-bonds generated for 'chain 'O2' and resid 10 through 12' Processing helix chain 'O2' and resid 25 through 37 Processing helix chain 'O2' and resid 40 through 53 Processing helix chain 'O2' and resid 70 through 76 removed outlier: 3.769A pdb=" N ALAO2 73 " --> pdb=" O CYSO2 70 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYSO2 74 " --> pdb=" O ALAO2 71 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLNO2 75 " --> pdb=" O GLNO2 72 " (cutoff:3.500A) Processing helix chain 'O2' and resid 84 through 106 removed outlier: 3.692A pdb=" N LEUO2 91 " --> pdb=" O SERO2 87 " (cutoff:3.500A) Processing helix chain 'O2' and resid 132 through 134 No H-bonds generated for 'chain 'O2' and resid 132 through 134' Processing helix chain 'P2' and resid 22 through 39 removed outlier: 3.551A pdb=" N ARGP2 37 " --> pdb=" O ARGP2 33 " (cutoff:3.500A) Processing helix chain 'P2' and resid 41 through 53 removed outlier: 4.098A pdb=" N GLNP2 45 " --> pdb=" O SERP2 41 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N METP2 53 " --> pdb=" O LYSP2 49 " (cutoff:3.500A) Processing helix chain 'P2' and resid 54 through 58 Processing helix chain 'P2' and resid 63 through 71 Processing helix chain 'P2' and resid 106 through 117 Processing helix chain 'P2' and resid 122 through 130 Processing helix chain 'P2' and resid 142 through 152 removed outlier: 4.288A pdb=" N ARGP2 146 " --> pdb=" O ARGP2 143 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N GLUP2 147 " --> pdb=" O LYSP2 144 " (cutoff:3.500A) removed outlier: 6.137A pdb=" N VALP2 148 " --> pdb=" O GLYP2 145 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHEP2 152 " --> pdb=" O TYRP2 149 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 4 through 16 removed outlier: 3.513A pdb=" N ARGQ2 9 " --> pdb=" O ARGQ2 5 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 28 through 33 removed outlier: 3.533A pdb=" N ILEQ2 32 " --> pdb=" O GLUQ2 28 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 37 through 47 removed outlier: 3.558A pdb=" N LYSQ2 43 " --> pdb=" O GLNQ2 39 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 60 through 73 removed outlier: 3.598A pdb=" N LYSQ2 72 " --> pdb=" O LEUQ2 68 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 84 through 89 Processing helix chain 'Q2' and resid 90 through 112 Processing helix chain 'Q2' and resid 116 through 129 removed outlier: 3.660A pdb=" N LEUQ2 125 " --> pdb=" O HISQ2 121 " (cutoff:3.500A) Processing helix chain 'Q2' and resid 134 through 153 removed outlier: 3.554A pdb=" N ARGQ2 151 " --> pdb=" O ALAQ2 147 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LYSQ2 152 " --> pdb=" O ASPQ2 148 " (cutoff:3.500A) Processing helix chain 'R2' and resid 36 through 52 Processing helix chain 'R2' and resid 101 through 118 Processing helix chain 'R2' and resid 139 through 144 Processing helix chain 'S2' and resid 54 through 58 removed outlier: 3.539A pdb=" N HISS2 58 " --> pdb=" O LYSS2 55 " (cutoff:3.500A) Processing helix chain 'S2' and resid 100 through 118 removed outlier: 3.918A pdb=" N SERS2 104 " --> pdb=" O LYSS2 100 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N PHES2 105 " --> pdb=" O SERS2 101 " (cutoff:3.500A) Processing helix chain 'T2' and resid 25 through 32 removed outlier: 3.635A pdb=" N VALT2 29 " --> pdb=" O CYST2 25 " (cutoff:3.500A) Processing helix chain 'T2' and resid 35 through 47 removed outlier: 3.725A pdb=" N PHET2 39 " --> pdb=" O ASPT2 35 " (cutoff:3.500A) Processing helix chain 'T2' and resid 53 through 58 removed outlier: 3.879A pdb=" N LEUT2 56 " --> pdb=" O ALAT2 53 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLYT2 57 " --> pdb=" O GLYT2 54 " (cutoff:3.500A) Processing helix chain 'T2' and resid 79 through 94 removed outlier: 4.093A pdb=" N LEUT2 83 " --> pdb=" O SERT2 79 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYST2 84 " --> pdb=" O LYST2 80 " (cutoff:3.500A) Processing helix chain 'U2' and resid 122 through 127 Processing helix chain 'U2' and resid 129 through 136 removed outlier: 3.860A pdb=" N ASNU2 135 " --> pdb=" O ARGU2 131 " (cutoff:3.500A) Processing helix chain 'V2' and resid 33 through 42 Processing helix chain 'V2' and resid 45 through 49 Processing helix chain 'V2' and resid 52 through 60 Processing helix chain 'W2' and resid 83 through 94 removed outlier: 3.501A pdb=" N LYSW2 88 " --> pdb=" O GLUW2 84 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYSW2 89 " --> pdb=" O SERW2 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASNW2 93 " --> pdb=" O LYSW2 89 " (cutoff:3.500A) Processing helix chain 'W2' and resid 105 through 117 removed outlier: 3.576A pdb=" N LYSW2 115 " --> pdb=" O GLNW2 111 " (cutoff:3.500A) Processing helix chain 'W2' and resid 145 through 154 removed outlier: 3.893A pdb=" N LYSW2 152 " --> pdb=" O ASPW2 148 " (cutoff:3.500A) Processing helix chain 'X2' and resid 10 through 20 Processing helix chain 'X2' and resid 22 through 30 removed outlier: 3.770A pdb=" N LYSX2 28 " --> pdb=" O HISX2 24 " (cutoff:3.500A) Processing helix chain 'X2' and resid 35 through 43 removed outlier: 3.631A pdb=" N GLNX2 40 " --> pdb=" O LYSX2 36 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYSX2 41 " --> pdb=" O GLUX2 37 " (cutoff:3.500A) Processing helix chain 'X2' and resid 100 through 102 No H-bonds generated for 'chain 'X2' and resid 100 through 102' Processing helix chain 'X2' and resid 112 through 134 removed outlier: 3.714A pdb=" N LYSX2 117 " --> pdb=" O LYSX2 113 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 58 through 66 removed outlier: 3.539A pdb=" N ALAY2 63 " --> pdb=" O LYSY2 59 " (cutoff:3.500A) Processing helix chain 'Y2' and resid 97 through 102 removed outlier: 3.820A pdb=" N VALY2 100 " --> pdb=" O ASNY2 97 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N PHEY2 101 " --> pdb=" O LYSY2 98 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ARGY2 102 " --> pdb=" O ASPY2 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y2' and resid 97 through 102' Processing helix chain 'Y2' and resid 103 through 123 removed outlier: 3.514A pdb=" N LYSY2 117 " --> pdb=" O GLUY2 113 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 2 through 6 Processing helix chain 'Z2' and resid 7 through 11 Processing helix chain 'Z2' and resid 41 through 49 Processing helix chain 'Z2' and resid 76 through 81 removed outlier: 5.059A pdb=" N TRPZ2 79 " --> pdb=" O ASPZ2 76 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEUZ2 81 " --> pdb=" O LEUZ2 78 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 83 through 93 removed outlier: 3.539A pdb=" N ARGZ2 87 " --> pdb=" O SERZ2 83 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASNZ2 89 " --> pdb=" O GLNZ2 85 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALAZ2 90 " --> pdb=" O THRZ2 86 " (cutoff:3.500A) Processing helix chain 'Z2' and resid 103 through 107 Processing helix chain 'Z2' and resid 130 through 141 Processing helix chain 'a2' and resid 11 through 17 removed outlier: 3.745A pdb=" N HISa2 17 " --> pdb=" O SERa2 13 " (cutoff:3.500A) Processing helix chain 'a2' and resid 36 through 49 Processing helix chain 'a2' and resid 53 through 76 removed outlier: 3.588A pdb=" N ALAa2 59 " --> pdb=" O LYSa2 55 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYSa2 63 " --> pdb=" O ALAa2 59 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALAa2 69 " --> pdb=" O METa2 65 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLUa2 70 " --> pdb=" O ALAa2 66 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALAa2 74 " --> pdb=" O GLUa2 70 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEUa2 75 " --> pdb=" O ALAa2 71 " (cutoff:3.500A) Processing helix chain 'a2' and resid 90 through 100 Processing helix chain 'a2' and resid 105 through 114 Processing helix chain 'b2' and resid 11 through 25 removed outlier: 4.100A pdb=" N SERb2 16 " --> pdb=" O GLUb2 12 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LYSb2 23 " --> pdb=" O GLNb2 19 " (cutoff:3.500A) Processing helix chain 'b2' and resid 31 through 40 removed outlier: 3.560A pdb=" N METb2 37 " --> pdb=" O GLNb2 33 " (cutoff:3.500A) Processing helix chain 'b2' and resid 55 through 68 removed outlier: 4.895A pdb=" N GLUb2 61 " --> pdb=" O LYSb2 57 " (cutoff:3.500A) Processing helix chain 'b2' and resid 77 through 85 Processing helix chain 'c2' and resid 29 through 34 removed outlier: 3.894A pdb=" N HISc2 34 " --> pdb=" O HISc2 30 " (cutoff:3.500A) Processing helix chain 'c2' and resid 37 through 39 No H-bonds generated for 'chain 'c2' and resid 37 through 39' Processing helix chain 'c2' and resid 40 through 57 Processing helix chain 'c2' and resid 65 through 73 Processing helix chain 'd2' and resid 57 through 61 removed outlier: 3.740A pdb=" N TYRd2 60 " --> pdb=" O ASNd2 57 " (cutoff:3.500A) Processing helix chain 'd2' and resid 81 through 86 removed outlier: 3.625A pdb=" N GLUd2 86 " --> pdb=" O LYSd2 83 " (cutoff:3.500A) Processing helix chain 'd2' and resid 88 through 92 removed outlier: 3.866A pdb=" N ASNd2 92 " --> pdb=" O LEUd2 89 " (cutoff:3.500A) Processing helix chain 'd2' and resid 104 through 118 removed outlier: 3.683A pdb=" N ALAd2 110 " --> pdb=" O LYSd2 106 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLNd2 117 " --> pdb=" O GLUd2 113 " (cutoff:3.500A) Processing helix chain 'e2' and resid 35 through 39 removed outlier: 3.608A pdb=" N GLUe2 38 " --> pdb=" O ALAe2 35 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THRe2 39 " --> pdb=" O ARGe2 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'e2' and resid 35 through 39' Processing helix chain 'e2' and resid 93 through 97 removed outlier: 3.606A pdb=" N ILEe2 97 " --> pdb=" O ALAe2 94 " (cutoff:3.500A) Processing helix chain 'f2' and resid 60 through 66 removed outlier: 3.671A pdb=" N METf2 65 " --> pdb=" O LYSf2 62 " (cutoff:3.500A) Processing helix chain 'f2' and resid 68 through 72 Processing helix chain 'f2' and resid 83 through 115 removed outlier: 3.538A pdb=" N ARGf2 90 " --> pdb=" O CYSf2 86 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARGf2 93 " --> pdb=" O ASPf2 89 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N GLUf2 98 " --> pdb=" O ALAf2 94 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLNf2 114 " --> pdb=" O GLNf2 110 " (cutoff:3.500A) Processing helix chain 'g2' and resid 13 through 38 Processing helix chain 'g2' and resid 40 through 45 Processing helix chain 'g2' and resid 45 through 73 removed outlier: 4.161A pdb=" N VALg2 49 " --> pdb=" O SERg2 45 " (cutoff:3.500A) Processing helix chain 'g2' and resid 88 through 93 Processing helix chain 'g2' and resid 96 through 101 Processing helix chain 'g2' and resid 104 through 114 Processing helix chain 'h2' and resid 25 through 30 removed outlier: 3.574A pdb=" N ARGh2 30 " --> pdb=" O SERh2 27 " (cutoff:3.500A) Processing helix chain 'h2' and resid 34 through 49 removed outlier: 3.563A pdb=" N PHEh2 39 " --> pdb=" O LYSh2 35 " (cutoff:3.500A) Processing helix chain 'h2' and resid 51 through 63 removed outlier: 3.702A pdb=" N VALh2 63 " --> pdb=" O GLUh2 59 " (cutoff:3.500A) Processing helix chain 'h2' and resid 65 through 78 Processing helix chain 'h2' and resid 79 through 102 removed outlier: 3.684A pdb=" N LEUh2 94 " --> pdb=" O LEUh2 90 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALAh2 101 " --> pdb=" O METh2 97 " (cutoff:3.500A) Processing helix chain 'i2' and resid 6 through 11 removed outlier: 3.544A pdb=" N GLYi2 9 " --> pdb=" O SERi2 6 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYSi2 10 " --> pdb=" O SERi2 7 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARGi2 11 " --> pdb=" O PHEi2 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'i2' and resid 6 through 11' Processing helix chain 'i2' and resid 50 through 55 Processing helix chain 'i2' and resid 66 through 74 removed outlier: 3.503A pdb=" N ARGi2 72 " --> pdb=" O LYSi2 68 " (cutoff:3.500A) Processing helix chain 'i2' and resid 75 through 77 No H-bonds generated for 'chain 'i2' and resid 75 through 77' Processing helix chain 'j2' and resid 8 through 16 removed outlier: 3.660A pdb=" N LEUj2 13 " --> pdb=" O LYSj2 9 " (cutoff:3.500A) Processing helix chain 'j2' and resid 49 through 60 removed outlier: 3.623A pdb=" N GLUj2 54 " --> pdb=" O LYSj2 50 " (cutoff:3.500A) Processing helix chain 'k2' and resid 6 through 19 Processing helix chain 'k2' and resid 24 through 30 removed outlier: 3.602A pdb=" N ILEk2 27 " --> pdb=" O PROk2 24 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TRPk2 28 " --> pdb=" O GLNk2 25 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N METk2 29 " --> pdb=" O TRPk2 26 " (cutoff:3.500A) Processing helix chain 'l2' and resid 53 through 65 removed outlier: 3.951A pdb=" N LEUl2 59 " --> pdb=" O SERl2 55 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALAl2 60 " --> pdb=" O LEUl2 56 " (cutoff:3.500A) Processing helix chain 'm2' and resid 2 through 25 Processing helix chain 'n2' and resid 35 through 45 Processing helix chain 'o2' and resid 9 through 15 Processing helix chain 'o2' and resid 19 through 35 removed outlier: 4.206A pdb=" N LYSo2 28 " --> pdb=" O LYSo2 24 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILEo2 29 " --> pdb=" O METo2 25 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N HISo2 34 " --> pdb=" O GLUo2 30 " (cutoff:3.500A) Processing helix chain 'o2' and resid 73 through 92 removed outlier: 3.679A pdb=" N THRo2 78 " --> pdb=" O THRo2 74 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VALo2 79 " --> pdb=" O SERo2 75 " (cutoff:3.500A) Processing helix chain 'p2' and resid 3 through 11 removed outlier: 3.547A pdb=" N VALp2 9 " --> pdb=" O LEUp2 5 " (cutoff:3.500A) Processing helix chain 'p2' and resid 87 through 99 removed outlier: 3.624A pdb=" N ARGp2 94 " --> pdb=" O LEUp2 90 " (cutoff:3.500A) Processing helix chain 'p2' and resid 103 through 105 No H-bonds generated for 'chain 'p2' and resid 103 through 105' Processing helix chain 'p2' and resid 106 through 121 Processing helix chain 'q2' and resid 6 through 22 removed outlier: 3.945A pdb=" N SERq2 11 " --> pdb=" O ALAq2 7 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N PHEq2 14 " --> pdb=" O LYSq2 10 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEUq2 15 " --> pdb=" O SERq2 11 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEUq2 20 " --> pdb=" O LYSq2 16 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASPq2 22 " --> pdb=" O ILEq2 18 " (cutoff:3.500A) Processing helix chain 'q2' and resid 36 through 47 removed outlier: 4.020A pdb=" N GLNq2 42 " --> pdb=" O LYSq2 38 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N SERq2 46 " --> pdb=" O GLNq2 42 " (cutoff:3.500A) Processing helix chain 'q2' and resid 57 through 66 removed outlier: 3.705A pdb=" N ARGq2 66 " --> pdb=" O ARGq2 62 " (cutoff:3.500A) Processing helix chain 'q2' and resid 78 through 82 removed outlier: 3.835A pdb=" N ILEq2 82 " --> pdb=" O LEUq2 79 " (cutoff:3.500A) Processing helix chain 'q2' and resid 96 through 103 removed outlier: 3.649A pdb=" N LEUq2 102 " --> pdb=" O ILEq2 98 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEUq2 103 " --> pdb=" O ARGq2 99 " (cutoff:3.500A) Processing helix chain 'q2' and resid 134 through 138 removed outlier: 4.032A pdb=" N PHEq2 137 " --> pdb=" O LYSq2 134 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHEq2 138 " --> pdb=" O THRq2 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'q2' and resid 134 through 138' Processing helix chain 'q2' and resid 168 through 171 removed outlier: 4.147A pdb=" N GLUq2 171 " --> pdb=" O GLYq2 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'q2' and resid 168 through 171' Processing helix chain 'q2' and resid 172 through 179 removed outlier: 3.642A pdb=" N LEUq2 178 " --> pdb=" O LEUq2 174 " (cutoff:3.500A) Processing helix chain 'r2' and resid 28 through 33 removed outlier: 3.616A pdb=" N ILEr2 32 " --> pdb=" O LEUr2 28 " (cutoff:3.500A) Processing helix chain 'r2' and resid 38 through 49 removed outlier: 3.975A pdb=" N ASPr2 45 " --> pdb=" O LYSr2 41 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALAr2 47 " --> pdb=" O GLYr2 43 " (cutoff:3.500A) Processing helix chain 'r2' and resid 78 through 85 Processing helix chain 'r2' and resid 109 through 120 Processing helix chain 'r2' and resid 124 through 137 removed outlier: 4.319A pdb=" N ILEr2 132 " --> pdb=" O THRr2 128 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N GLNr2 137 " --> pdb=" O LEUr2 133 " (cutoff:3.500A) Processing helix chain 'r2' and resid 146 through 148 No H-bonds generated for 'chain 'r2' and resid 146 through 148' Processing helix chain 'r2' and resid 149 through 154 removed outlier: 3.948A pdb=" N ASPr2 153 " --> pdb=" O HISr2 149 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASPr2 154 " --> pdb=" O ASPr2 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'r2' and resid 149 through 154' Processing helix chain 's2' and resid 860 through 891 Processing helix chain 's2' and resid 901 through 919 Processing helix chain 's2' and resid 927 through 944 Processing helix chain 's2' and resid 947 through 958 Processing helix chain 's2' and resid 958 through 968 removed outlier: 3.757A pdb=" N ALAs2 962 " --> pdb=" O GLYs2 958 " (cutoff:3.500A) Processing helix chain 's2' and resid 969 through 971 No H-bonds generated for 'chain 's2' and resid 969 through 971' Processing helix chain 's2' and resid 983 through 999 Processing helix chain 's2' and resid 1001 through 1011 Processing helix chain 's2' and resid 1012 through 1027 removed outlier: 3.650A pdb=" N PHEs21016 " --> pdb=" O ASNs21012 " (cutoff:3.500A) Processing helix chain 's2' and resid 1048 through 1067 Processing helix chain 's2' and resid 1094 through 1110 Processing helix chain 's2' and resid 1110 through 1122 Processing helix chain 's2' and resid 1130 through 1150 Processing helix chain 's2' and resid 1171 through 1178 Processing helix chain 's2' and resid 1179 through 1181 No H-bonds generated for 'chain 's2' and resid 1179 through 1181' Processing helix chain 's2' and resid 1182 through 1192 Processing helix chain 's2' and resid 1211 through 1230 Processing helix chain 's2' and resid 1230 through 1239 Processing helix chain 's2' and resid 1242 through 1261 Processing helix chain 's2' and resid 1263 through 1279 Processing helix chain 's2' and resid 1281 through 1290 Processing helix chain 's2' and resid 1296 through 1302 Processing helix chain 's2' and resid 1305 through 1310 Processing helix chain 's2' and resid 1310 through 1325 Proline residue: s21319 - end of helix Processing helix chain 's2' and resid 1328 through 1339 Processing helix chain 's2' and resid 1341 through 1354 Processing helix chain 't2' and resid 13 through 34 removed outlier: 5.525A pdb=" N PHEt2 31 " --> pdb=" O ARGt2 27 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLUt2 32 " --> pdb=" O ASPt2 28 " (cutoff:3.500A) Processing helix chain 't2' and resid 34 through 39 removed outlier: 3.760A pdb=" N ASPt2 38 " --> pdb=" O HISt2 34 " (cutoff:3.500A) Processing helix chain 't2' and resid 41 through 62 Processing helix chain 't2' and resid 67 through 79 Processing helix chain 't2' and resid 89 through 99 Processing helix chain 't2' and resid 102 through 117 Processing helix chain 't2' and resid 118 through 133 Processing helix chain 't2' and resid 135 through 149 removed outlier: 4.312A pdb=" N ARGt2 147 " --> pdb=" O SERt2 143 " (cutoff:3.500A) Processing helix chain 't2' and resid 153 through 175 Processing helix chain 't2' and resid 178 through 196 Processing helix chain 't2' and resid 199 through 217 removed outlier: 3.710A pdb=" N SERt2 203 " --> pdb=" O ASNt2 199 " (cutoff:3.500A) Processing helix chain 't2' and resid 223 through 237 removed outlier: 4.108A pdb=" N HISt2 227 " --> pdb=" O ASNt2 223 " (cutoff:3.500A) Processing helix chain 't2' and resid 239 through 254 Processing helix chain 't2' and resid 258 through 281 Processing helix chain 't2' and resid 282 through 284 No H-bonds generated for 'chain 't2' and resid 282 through 284' Processing helix chain 't2' and resid 285 through 295 Processing helix chain 't2' and resid 297 through 305 Proline residue: t2 303 - end of helix Processing helix chain 't2' and resid 323 through 327 removed outlier: 3.540A pdb=" N LEUt2 327 " --> pdb=" O LEUt2 324 " (cutoff:3.500A) Processing helix chain 't2' and resid 412 through 415 Processing helix chain 't2' and resid 424 through 428 Processing sheet with id=AA1, first strand: chain 'D1' and resid 26 through 27 Processing sheet with id=AA2, first strand: chain 'A2' and resid 71 through 77 removed outlier: 6.273A pdb=" N LEUA2 58 " --> pdb=" O ILEA2 48 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILEA2 48 " --> pdb=" O LEUA2 58 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N LYSA2 60 " --> pdb=" O LYSA2 46 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ARGA2 64 " --> pdb=" O LYSA2 42 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYSA2 42 " --> pdb=" O ARGA2 64 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A2' and resid 101 through 103 removed outlier: 6.675A pdb=" N ARGA2 147 " --> pdb=" O ILEA2 137 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N HISA2 139 " --> pdb=" O LYSA2 145 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LYSA2 145 " --> pdb=" O HISA2 139 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A2' and resid 224 through 225 Processing sheet with id=AA5, first strand: chain 'B2' and resid 42 through 43 removed outlier: 5.115A pdb=" N ILEB2 160 " --> pdb=" O VALB2 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYB2 88 " --> pdb=" O LEUB2 163 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HISB2 165 " --> pdb=" O VALB2 86 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VALB2 86 " --> pdb=" O HISB2 165 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N VALB2 87 " --> pdb=" O PHEB2 106 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N PHEB2 106 " --> pdb=" O VALB2 87 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ILEB2 89 " --> pdb=" O THRB2 104 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N THRB2 104 " --> pdb=" O ILEB2 89 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N GLYB2 91 " --> pdb=" O PHEB2 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B2' and resid 42 through 43 removed outlier: 5.115A pdb=" N ILEB2 160 " --> pdb=" O VALB2 185 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLYB2 88 " --> pdb=" O LEUB2 163 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HISB2 165 " --> pdb=" O VALB2 86 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N VALB2 86 " --> pdb=" O HISB2 165 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B2' and resid 365 through 368 removed outlier: 6.839A pdb=" N LEUB2 365 " --> pdb=" O GLUB2 59 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLUB2 59 " --> pdb=" O LEUB2 365 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N VALB2 344 " --> pdb=" O VALB2 222 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N VALB2 222 " --> pdb=" O VALB2 344 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N ILEB2 217 " --> pdb=" O ASNB2 281 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYSB2 283 " --> pdb=" O LYSB2 334 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N METB2 332 " --> pdb=" O TYRB2 285 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ILEB2 287 " --> pdb=" O PHEB2 330 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N PHEB2 330 " --> pdb=" O ILEB2 287 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLYB2 52 " --> pdb=" O ILEB2 78 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLUB2 80 " --> pdb=" O LYSB2 50 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N LYSB2 50 " --> pdb=" O GLUB2 80 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B2' and resid 228 through 229 Processing sheet with id=AA9, first strand: chain 'B2' and resid 292 through 294 removed outlier: 3.887A pdb=" N LEUB2 292 " --> pdb=" O ILEB2 299 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C2' and resid 17 through 23 removed outlier: 4.866A pdb=" N LYSC2 20 " --> pdb=" O VALC2 10 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N VALC2 153 " --> pdb=" O SERC2 9 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N LEUC2 152 " --> pdb=" O TRPC2 252 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THRC2 253 " --> pdb=" O ILEC2 210 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C2' and resid 64 through 66 removed outlier: 3.516A pdb=" N ARGC2 78 " --> pdb=" O GLUC2 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C2' and resid 188 through 189 Processing sheet with id=AB4, first strand: chain 'D2' and resid 71 through 79 removed outlier: 4.622A pdb=" N ASPD2 72 " --> pdb=" O ARGD2 68 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARGD2 68 " --> pdb=" O ASPD2 72 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N ILED2 74 " --> pdb=" O TYRD2 66 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYRD2 66 " --> pdb=" O ILED2 74 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N CYSD2 76 " --> pdb=" O ILED2 64 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N METD2 51 " --> pdb=" O ASPD2 147 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D2' and resid 183 through 184 Processing sheet with id=AB6, first strand: chain 'E2' and resid 51 through 53 removed outlier: 3.676A pdb=" N VALE2 53 " --> pdb=" O ILEE2 56 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E2' and resid 94 through 98 Processing sheet with id=AB8, first strand: chain 'E2' and resid 190 through 192 removed outlier: 3.748A pdb=" N LYSE2 163 " --> pdb=" O ILEE2 155 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THRE2 151 " --> pdb=" O PHEE2 167 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ILEE2 152 " --> pdb=" O THRE2 200 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F2' and resid 80 through 82 Processing sheet with id=AC1, first strand: chain 'F2' and resid 210 through 211 removed outlier: 4.047A pdb=" N ASNF2 118 " --> pdb=" O ARGF2 93 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N ILEF2 139 " --> pdb=" O GLYF2 233 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F2' and resid 158 through 161 Processing sheet with id=AC3, first strand: chain 'G2' and resid 128 through 129 Processing sheet with id=AC4, first strand: chain 'G2' and resid 190 through 191 removed outlier: 6.366A pdb=" N VALG2 208 " --> pdb=" O CYSG2 235 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LEUG2 237 " --> pdb=" O VALG2 208 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ILEG2 210 " --> pdb=" O LEUG2 237 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H2' and resid 3 through 11 removed outlier: 7.168A pdb=" N ILEH2 4 " --> pdb=" O TRPH2 61 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H2' and resid 17 through 20 Processing sheet with id=AC7, first strand: chain 'H2' and resid 133 through 136 removed outlier: 5.965A pdb=" N ARGH2 93 " --> pdb=" O VALH2 181 " (cutoff:3.500A) removed outlier: 5.143A pdb=" N VALH2 181 " --> pdb=" O ARGH2 93 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VALH2 95 " --> pdb=" O ILEH2 179 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ILEH2 179 " --> pdb=" O VALH2 95 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H2' and resid 102 through 106 Processing sheet with id=AC9, first strand: chain 'I2' and resid 35 through 37 removed outlier: 6.590A pdb=" N METI2 52 " --> pdb=" O ILEI2 135 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SERI2 137 " --> pdb=" O GLYI2 50 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLYI2 50 " --> pdb=" O SERI2 137 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ARGI2 139 " --> pdb=" O LEUI2 48 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEUI2 48 " --> pdb=" O ARGI2 139 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I2' and resid 58 through 61 removed outlier: 6.819A pdb=" N ILEI2 97 " --> pdb=" O GLNI2 123 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N THRI2 125 " --> pdb=" O HISI2 95 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N HISI2 95 " --> pdb=" O THRI2 125 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I2' and resid 190 through 193 removed outlier: 3.968A pdb=" N GLYI2 196 " --> pdb=" O ASPI2 193 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J2' and resid 49 through 52 removed outlier: 6.859A pdb=" N VALJ2 133 " --> pdb=" O ARGJ2 18 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEUJ2 20 " --> pdb=" O TYRJ2 131 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N TYRJ2 131 " --> pdb=" O LEUJ2 20 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEUJ2 22 " --> pdb=" O ASPJ2 129 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ASPJ2 129 " --> pdb=" O LEUJ2 22 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'J2' and resid 93 through 95 Processing sheet with id=AD5, first strand: chain 'K2' and resid 22 through 24 Processing sheet with id=AD6, first strand: chain 'K2' and resid 58 through 60 Processing sheet with id=AD7, first strand: chain 'K2' and resid 124 through 126 Processing sheet with id=AD8, first strand: chain 'L2' and resid 45 through 51 removed outlier: 4.921A pdb=" N ARGL2 46 " --> pdb=" O GLYL2 40 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N GLYL2 40 " --> pdb=" O ARGL2 46 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ARGL2 35 " --> pdb=" O ILEL2 31 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ASPL2 39 " --> pdb=" O ILEL2 27 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ILEL2 27 " --> pdb=" O ASPL2 39 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYSL2 23 " --> pdb=" O VALL2 15 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ARGL2 11 " --> pdb=" O ILEL2 27 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N VALL2 12 " --> pdb=" O THRL2 58 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'M2' and resid 36 through 39 removed outlier: 4.518A pdb=" N ILEM2 61 " --> pdb=" O ALAM2 39 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLYM2 122 " --> pdb=" O PHEM2 129 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N GLUM2 131 " --> pdb=" O TRPM2 120 " (cutoff:3.500A) removed outlier: 5.626A pdb=" N TRPM2 120 " --> pdb=" O GLUM2 131 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ILEM2 133 " --> pdb=" O SERM2 118 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N SERM2 118 " --> pdb=" O ILEM2 133 " (cutoff:3.500A) removed outlier: 8.467A pdb=" N ILEM2 135 " --> pdb=" O LEUM2 116 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N LEUM2 116 " --> pdb=" O ILEM2 135 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'N2' and resid 7 through 10 removed outlier: 6.392A pdb=" N LEUN2 7 " --> pdb=" O VALN2 34 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N VALN2 36 " --> pdb=" O LEUN2 7 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEUN2 9 " --> pdb=" O VALN2 36 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N VALN2 33 " --> pdb=" O LYSN2 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'N2' and resid 42 through 44 Processing sheet with id=AE3, first strand: chain 'O2' and resid 14 through 22 removed outlier: 3.733A pdb=" N ASNO2 21 " --> pdb=" O CYSO2 144 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N CYSO2 144 " --> pdb=" O ASNO2 21 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N HISO2 145 " --> pdb=" O VALO2 119 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N VALO2 119 " --> pdb=" O HISO2 145 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLUO2 147 " --> pdb=" O ILEO2 117 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILEO2 117 " --> pdb=" O GLUO2 147 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILEO2 149 " --> pdb=" O GLUO2 115 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O2' and resid 58 through 59 Processing sheet with id=AE5, first strand: chain 'O2' and resid 128 through 130 Processing sheet with id=AE6, first strand: chain 'P2' and resid 61 through 62 removed outlier: 6.229A pdb=" N LEUP2 61 " --> pdb=" O THRP2 87 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'P2' and resid 119 through 121 removed outlier: 6.362A pdb=" N VALP2 100 " --> pdb=" O LEUP2 121 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N THRP2 79 " --> pdb=" O VALP2 137 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N LEUP2 139 " --> pdb=" O THRP2 79 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VALP2 81 " --> pdb=" O LEUP2 139 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q2' and resid 22 through 24 Processing sheet with id=AE9, first strand: chain 'R2' and resid 59 through 66 removed outlier: 6.568A pdb=" N VALR2 13 " --> pdb=" O VALR2 62 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N CYSR2 64 " --> pdb=" O LYSR2 11 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYSR2 11 " --> pdb=" O CYSR2 64 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N GLNR2 66 " --> pdb=" O GLUR2 9 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N GLUR2 9 " --> pdb=" O GLNR2 66 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'R2' and resid 90 through 99 removed outlier: 4.217A pdb=" N ASNR2 77 " --> pdb=" O ILER2 132 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYSR2 128 " --> pdb=" O TRPR2 81 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'S2' and resid 83 through 92 removed outlier: 3.564A pdb=" N ASNS2 66 " --> pdb=" O GLYS2 73 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VALS2 75 " --> pdb=" O VALS2 64 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N VALS2 64 " --> pdb=" O VALS2 75 " (cutoff:3.500A) removed outlier: 8.058A pdb=" N ASNS2 77 " --> pdb=" O GLYS2 62 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N GLYS2 62 " --> pdb=" O ASNS2 77 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'T2' and resid 61 through 66 removed outlier: 3.512A pdb=" N LYST2 69 " --> pdb=" O SERT2 66 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEUT2 112 " --> pdb=" O ASPT2 24 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'U2' and resid 20 through 21 Processing sheet with id=AF5, first strand: chain 'U2' and resid 25 through 28 removed outlier: 6.855A pdb=" N METU2 62 " --> pdb=" O ILEU2 40 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N VALU2 42 " --> pdb=" O METU2 60 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N METU2 60 " --> pdb=" O VALU2 42 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N ALAU2 102 " --> pdb=" O ILEU2 82 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N GLYU2 103 " --> pdb=" O VALU2 25 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ASNU2 27 " --> pdb=" O GLYU2 103 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N ILEU2 105 " --> pdb=" O ASNU2 27 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'U2' and resid 88 through 89 removed outlier: 6.628A pdb=" N PHEU2 95 " --> pdb=" O ARGV2 20 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N ALAV2 22 " --> pdb=" O PHEU2 95 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N TYRU2 97 " --> pdb=" O ALAV2 22 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ARGV2 23 " --> pdb=" O LYSV2 27 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N LYSV2 27 " --> pdb=" O ARGV2 23 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'U2' and resid 120 through 121 Processing sheet with id=AF8, first strand: chain 'V2' and resid 4 through 5 Processing sheet with id=AF9, first strand: chain 'W2' and resid 77 through 80 removed outlier: 3.565A pdb=" N PHEW2 79 " --> pdb=" O ILEW2 99 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N LYSW2 134 " --> pdb=" O VALW2 100 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LYSW2 135 " --> pdb=" O THRW2 126 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N THRW2 126 " --> pdb=" O LYSW2 135 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TYRW2 137 " --> pdb=" O VALW2 124 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N VALW2 124 " --> pdb=" O TYRW2 137 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ARGW2 139 " --> pdb=" O ALAW2 122 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'X2' and resid 31 through 33 Processing sheet with id=AG2, first strand: chain 'X2' and resid 94 through 99 removed outlier: 6.052A pdb=" N VALX2 85 " --> pdb=" O VALX2 97 " (cutoff:3.500A) removed outlier: 11.268A pdb=" N ILEX2 99 " --> pdb=" O GLUX2 83 " (cutoff:3.500A) removed outlier: 10.206A pdb=" N GLUX2 83 " --> pdb=" O ILEX2 99 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N GLUX2 83 " --> pdb=" O VALX2 70 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VALX2 70 " --> pdb=" O GLUX2 83 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N VALX2 85 " --> pdb=" O GLYX2 68 " (cutoff:3.500A) removed outlier: 10.074A pdb=" N GLYX2 68 " --> pdb=" O VALX2 85 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N GLUX2 54 " --> pdb=" O THRX2 107 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'Y2' and resid 69 through 76 removed outlier: 6.620A pdb=" N LYSY2 69 " --> pdb=" O ASPY2 47 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N ALAY2 44 " --> pdb=" O ILEY2 25 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ILEY2 25 " --> pdb=" O ALAY2 44 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILEY2 46 " --> pdb=" O ALAY2 23 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ALAY2 23 " --> pdb=" O ILEY2 46 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYSY2 9 " --> pdb=" O ILEY2 25 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VALY2 10 " --> pdb=" O THRY2 83 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'Z2' and resid 72 through 74 removed outlier: 6.004A pdb=" N VALZ2 73 " --> pdb=" O LEUZ2 112 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'Z2' and resid 100 through 102 removed outlier: 6.457A pdb=" N ILEZ2 101 " --> pdb=" O LYSZ2 125 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b2' and resid 26 through 29 removed outlier: 6.465A pdb=" N LYSb2 26 " --> pdb=" O ILEb2 97 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N LEUb2 45 " --> pdb=" O ILEb2 96 " (cutoff:3.500A) removed outlier: 6.064A pdb=" N VALb2 46 " --> pdb=" O HISb2 72 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'c2' and resid 21 through 28 removed outlier: 4.771A pdb=" N ASPc2 61 " --> pdb=" O LEUc2 102 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'd2' and resid 75 through 79 Processing sheet with id=AG9, first strand: chain 'e2' and resid 7 through 16 removed outlier: 5.855A pdb=" N PHEe2 11 " --> pdb=" O LYSe2 29 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LYSe2 29 " --> pdb=" O PHEe2 11 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLYe2 13 " --> pdb=" O LEUe2 27 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N THRe2 25 " --> pdb=" O LYSe2 15 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N HISe2 24 " --> pdb=" O PHEe2 88 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N PHEe2 88 " --> pdb=" O HISe2 24 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N METe2 83 " --> pdb=" O HISe2 78 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARGe2 76 " --> pdb=" O ARGe2 85 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N LYSe2 87 " --> pdb=" O VALe2 74 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VALe2 74 " --> pdb=" O LYSe2 87 " (cutoff:3.500A) removed outlier: 8.636A pdb=" N GLYe2 62 " --> pdb=" O THRe2 57 " (cutoff:3.500A) removed outlier: 9.258A pdb=" N THRe2 57 " --> pdb=" O GLYe2 62 " (cutoff:3.500A) removed outlier: 10.278A pdb=" N ASNe2 55 " --> pdb=" O PROe2 64 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N LYSe2 66 " --> pdb=" O ALAe2 53 " (cutoff:3.500A) removed outlier: 5.216A pdb=" N VALe2 50 " --> pdb=" O ARGe2 100 " (cutoff:3.500A) removed outlier: 7.220A pdb=" N ARGe2 100 " --> pdb=" O VALe2 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f2' and resid 20 through 24 Processing sheet with id=AH2, first strand: chain 'i2' and resid 16 through 18 removed outlier: 3.531A pdb=" N THRi2 33 " --> pdb=" O HISi2 28 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'j2' and resid 3 through 5 removed outlier: 4.485A pdb=" N VALj2 46 " --> pdb=" O ILEj2 5 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASNj2 31 " --> pdb=" O ASNj2 28 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASNj2 28 " --> pdb=" O ASNj2 31 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SERj2 22 " --> pdb=" O ARGj2 37 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N VALj2 23 " --> pdb=" O LYSj2 67 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'l2' and resid 76 through 77 Processing sheet with id=AH5, first strand: chain 'n2' and resid 3 through 4 Processing sheet with id=AH6, first strand: chain 'n2' and resid 7 through 11 removed outlier: 3.987A pdb=" N ILEn2 66 " --> pdb=" O ILEn2 85 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'o2' and resid 47 through 51 removed outlier: 6.935A pdb=" N ILEo2 54 " --> pdb=" O ARGo2 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'p2' and resid 17 through 20 removed outlier: 3.566A pdb=" N ILEp2 18 " --> pdb=" O TYRp2 25 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'p2' and resid 49 through 53 Processing sheet with id=AI1, first strand: chain 'q2' and resid 29 through 31 removed outlier: 6.706A pdb=" N ILEq2 29 " --> pdb=" O GLNq2 190 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILEq2 188 " --> pdb=" O GLYq2 31 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'q2' and resid 51 through 54 Processing sheet with id=AI3, first strand: chain 'r2' and resid 11 through 13 removed outlier: 4.073A pdb=" N ILEr2 64 " --> pdb=" O LYSr2 11 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEUr2 62 " --> pdb=" O VALr2 13 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 't2' and resid 320 through 321 removed outlier: 6.099A pdb=" N GLUt2 320 " --> pdb=" O VALt2 336 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEUt2 338 " --> pdb=" O GLUt2 320 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N VALt2 341 " --> pdb=" O VALt2 358 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N VALt2 358 " --> pdb=" O VALt2 341 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N PHEt2 343 " --> pdb=" O GLYt2 356 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ALAt2 366 " --> pdb=" O VALt2 408 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VALt2 410 " --> pdb=" O ALAt2 366 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N METt2 368 " --> pdb=" O VALt2 410 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASNt2 390 " --> pdb=" O ARGt2 409 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLYt2 330 " --> pdb=" O LEUt2 391 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 't2' and resid 320 through 321 removed outlier: 6.099A pdb=" N GLUt2 320 " --> pdb=" O VALt2 336 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N LEUt2 338 " --> pdb=" O GLUt2 320 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 't2' and resid 432 through 436 2482 hydrogen bonds defined for protein. 7047 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3006 hydrogen bonds 5102 hydrogen bond angles 0 basepair planarities 1151 basepair parallelities 2066 stacking parallelities Total time for adding SS restraints: 282.08 Time building geometry restraints manager: 59.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 15208 1.31 - 1.44: 63647 1.44 - 1.57: 66974 1.57 - 1.70: 7599 1.70 - 1.82: 452 Bond restraints: 153880 Sorted by residual: bond pdb=" CA ARGQ2 60 " pdb=" C ARGQ2 60 " ideal model delta sigma weight residual 1.522 1.605 -0.083 1.31e-02 5.83e+03 4.03e+01 bond pdb=" C LEUs21231 " pdb=" N PROs21232 " ideal model delta sigma weight residual 1.335 1.397 -0.061 1.36e-02 5.41e+03 2.03e+01 bond pdb=" C ALAK2 47 " pdb=" N PROK2 48 " ideal model delta sigma weight residual 1.336 1.376 -0.040 9.80e-03 1.04e+04 1.70e+01 bond pdb=" C LEUq2 79 " pdb=" N PROq2 80 " ideal model delta sigma weight residual 1.337 1.382 -0.046 1.11e-02 8.12e+03 1.69e+01 bond pdb=" C HISr2 147 " pdb=" N PROr2 148 " ideal model delta sigma weight residual 1.336 1.380 -0.044 1.08e-02 8.57e+03 1.65e+01 ... (remaining 153875 not shown) Histogram of bond angle deviations from ideal: 96.16 - 104.18: 14573 104.18 - 112.21: 85682 112.21 - 120.24: 68861 120.24 - 128.27: 51210 128.27 - 136.30: 5853 Bond angle restraints: 226179 Sorted by residual: angle pdb=" C LEUJ2 22 " pdb=" N ASNJ2 23 " pdb=" CA ASNJ2 23 " ideal model delta sigma weight residual 122.21 112.77 9.44 1.62e+00 3.81e-01 3.40e+01 angle pdb=" O3' CA1 245 " pdb=" C3' CA1 245 " pdb=" C2' CA1 245 " ideal model delta sigma weight residual 109.50 117.94 -8.44 1.50e+00 4.44e-01 3.16e+01 angle pdb=" C LEUp2 32 " pdb=" N LYSp2 33 " pdb=" CA LYSp2 33 " ideal model delta sigma weight residual 121.54 132.13 -10.59 1.91e+00 2.74e-01 3.07e+01 angle pdb=" O3' AA12502 " pdb=" C3' AA12502 " pdb=" C2' AA12502 " ideal model delta sigma weight residual 109.50 117.79 -8.29 1.50e+00 4.44e-01 3.05e+01 angle pdb=" CG ARGM2 44 " pdb=" CD ARGM2 44 " pdb=" NE ARGM2 44 " ideal model delta sigma weight residual 112.00 124.04 -12.04 2.20e+00 2.07e-01 2.99e+01 ... (remaining 226174 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 88486 35.99 - 71.98: 9481 71.98 - 107.96: 1239 107.96 - 143.95: 26 143.95 - 179.94: 78 Dihedral angle restraints: 99310 sinusoidal: 77246 harmonic: 22064 Sorted by residual: dihedral pdb=" C5' AA12502 " pdb=" C4' AA12502 " pdb=" C3' AA12502 " pdb=" O3' AA12502 " ideal model delta sinusoidal sigma weight residual 147.00 74.61 72.39 1 8.00e+00 1.56e-02 1.05e+02 dihedral pdb=" C5' CA1 245 " pdb=" C4' CA1 245 " pdb=" C3' CA1 245 " pdb=" O3' CA1 245 " ideal model delta sinusoidal sigma weight residual 147.00 77.15 69.85 1 8.00e+00 1.56e-02 9.83e+01 dihedral pdb=" C4' GA12546 " pdb=" C3' GA12546 " pdb=" C2' GA12546 " pdb=" C1' GA12546 " ideal model delta sinusoidal sigma weight residual -35.00 32.61 -67.61 1 8.00e+00 1.56e-02 9.29e+01 ... (remaining 99307 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 27138 0.105 - 0.211: 920 0.211 - 0.316: 62 0.316 - 0.421: 19 0.421 - 0.527: 3 Chirality restraints: 28142 Sorted by residual: chirality pdb=" C3' CA1 245 " pdb=" C4' CA1 245 " pdb=" O3' CA1 245 " pdb=" C2' CA1 245 " both_signs ideal model delta sigma weight residual False -2.74 -2.22 -0.53 2.00e-01 2.50e+01 6.93e+00 chirality pdb=" C3' AA12502 " pdb=" C4' AA12502 " pdb=" O3' AA12502 " pdb=" C2' AA12502 " both_signs ideal model delta sigma weight residual False -2.74 -2.27 -0.47 2.00e-01 2.50e+01 5.61e+00 chirality pdb=" CB THRM2 80 " pdb=" CA THRM2 80 " pdb=" OG1 THRM2 80 " pdb=" CG2 THRM2 80 " both_signs ideal model delta sigma weight residual False 2.55 2.11 0.45 2.00e-01 2.50e+01 4.97e+00 ... (remaining 28139 not shown) Planarity restraints: 14420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' CA12867 " 0.000 2.00e-02 2.50e+03 3.07e-02 2.12e+01 pdb=" N1 CA12867 " -0.005 2.00e-02 2.50e+03 pdb=" C2 CA12867 " -0.071 2.00e-02 2.50e+03 pdb=" O2 CA12867 " 0.050 2.00e-02 2.50e+03 pdb=" N3 CA12867 " 0.004 2.00e-02 2.50e+03 pdb=" C4 CA12867 " -0.018 2.00e-02 2.50e+03 pdb=" N4 CA12867 " 0.012 2.00e-02 2.50e+03 pdb=" C5 CA12867 " 0.012 2.00e-02 2.50e+03 pdb=" C6 CA12867 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GA1 978 " -0.055 2.00e-02 2.50e+03 2.44e-02 1.78e+01 pdb=" N9 GA1 978 " 0.061 2.00e-02 2.50e+03 pdb=" C8 GA1 978 " 0.003 2.00e-02 2.50e+03 pdb=" N7 GA1 978 " -0.001 2.00e-02 2.50e+03 pdb=" C5 GA1 978 " -0.004 2.00e-02 2.50e+03 pdb=" C6 GA1 978 " -0.009 2.00e-02 2.50e+03 pdb=" O6 GA1 978 " -0.011 2.00e-02 2.50e+03 pdb=" N1 GA1 978 " -0.007 2.00e-02 2.50e+03 pdb=" C2 GA1 978 " 0.007 2.00e-02 2.50e+03 pdb=" N2 GA1 978 " 0.006 2.00e-02 2.50e+03 pdb=" N3 GA1 978 " 0.003 2.00e-02 2.50e+03 pdb=" C4 GA1 978 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' GA12884 " -0.009 2.00e-02 2.50e+03 2.23e-02 1.49e+01 pdb=" N9 GA12884 " 0.009 2.00e-02 2.50e+03 pdb=" C8 GA12884 " -0.005 2.00e-02 2.50e+03 pdb=" N7 GA12884 " -0.005 2.00e-02 2.50e+03 pdb=" C5 GA12884 " 0.000 2.00e-02 2.50e+03 pdb=" C6 GA12884 " 0.016 2.00e-02 2.50e+03 pdb=" O6 GA12884 " -0.016 2.00e-02 2.50e+03 pdb=" N1 GA12884 " -0.003 2.00e-02 2.50e+03 pdb=" C2 GA12884 " 0.060 2.00e-02 2.50e+03 pdb=" N2 GA12884 " -0.041 2.00e-02 2.50e+03 pdb=" N3 GA12884 " -0.003 2.00e-02 2.50e+03 pdb=" C4 GA12884 " -0.002 2.00e-02 2.50e+03 ... (remaining 14417 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 842 2.51 - 3.11: 88815 3.11 - 3.70: 265036 3.70 - 4.30: 391316 4.30 - 4.90: 541801 Nonbonded interactions: 1287810 Sorted by model distance: nonbonded pdb="MG MGA15128 " pdb="MG MGA15264 " model vdw 1.912 1.300 nonbonded pdb=" OP1 AA11534 " pdb="MG MGA15106 " model vdw 2.017 2.170 nonbonded pdb=" O6 GA11321 " pdb="MG MGA15185 " model vdw 2.035 2.170 nonbonded pdb=" OP1 AA14394 " pdb="MG MGA15185 " model vdw 2.039 2.170 nonbonded pdb=" OP2 CA12411 " pdb="MG MGA15142 " model vdw 2.045 2.170 ... (remaining 1287805 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: 5.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 28.710 Check model and map are aligned: 1.760 Set scattering table: 0.950 Process input model: 563.700 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.350 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 615.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 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 : 0.004 0.106 153880 Z= 0.232 Angle : 0.852 14.957 226179 Z= 0.443 Chirality : 0.044 0.527 28142 Planarity : 0.007 0.099 14420 Dihedral : 23.105 179.939 85065 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.60 % Rotamer: Outliers : 0.03 % Allowed : 0.25 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.09), residues: 7480 helix: -1.50 (0.08), residues: 2859 sheet: -0.83 (0.16), residues: 1015 loop : -1.22 (0.09), residues: 3606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.002 TRPt2 182 HIS 0.014 0.002 HISt2 227 PHE 0.025 0.002 PHEq2 14 TYR 0.056 0.002 TYRt2 113 ARG 0.016 0.001 ARGH2 56 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1469 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1467 time to evaluate : 7.591 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: D2 128 ASP cc_start: 0.7139 (m-30) cc_final: 0.6829 (m-30) REVERT: E2 117 ARG cc_start: 0.8248 (ptp90) cc_final: 0.7683 (ptm-80) REVERT: G2 164 LYS cc_start: 0.7230 (mtmt) cc_final: 0.6998 (mtmp) REVERT: G2 206 GLN cc_start: 0.8191 (mt0) cc_final: 0.7710 (mt0) REVERT: I2 101 LYS cc_start: 0.7178 (ptmt) cc_final: 0.6947 (mppt) REVERT: J2 38 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7625 (ttpm) REVERT: J2 92 TYR cc_start: 0.7760 (m-80) cc_final: 0.7207 (m-80) REVERT: J2 163 MET cc_start: 0.8498 (mtt) cc_final: 0.8245 (mtt) REVERT: K2 42 ARG cc_start: 0.8584 (ttt90) cc_final: 0.8302 (ttp-170) REVERT: M2 189 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7812 (ttm110) REVERT: N2 159 LYS cc_start: 0.8527 (ttpp) cc_final: 0.7841 (ttpt) REVERT: N2 180 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7955 (tm-30) REVERT: N2 186 GLU cc_start: 0.6610 (tm-30) cc_final: 0.6382 (tt0) REVERT: P2 92 VAL cc_start: 0.7050 (p) cc_final: 0.6820 (m) REVERT: R2 108 GLN cc_start: 0.8533 (tt0) cc_final: 0.8316 (tt0) REVERT: R2 143 LYS cc_start: 0.8817 (mtpp) cc_final: 0.8593 (mtpm) REVERT: T2 38 ASN cc_start: 0.5052 (t0) cc_final: 0.4795 (t0) REVERT: T2 47 ILE cc_start: 0.7010 (mp) cc_final: 0.6703 (mp) REVERT: U2 71 GLU cc_start: 0.8075 (pm20) cc_final: 0.7637 (pm20) REVERT: X2 61 HIS cc_start: 0.8497 (t-90) cc_final: 0.8250 (t-170) REVERT: a2 63 LYS cc_start: 0.7419 (tttm) cc_final: 0.7188 (mtpp) REVERT: g2 103 LYS cc_start: 0.8177 (ptpp) cc_final: 0.7954 (pttm) REVERT: g2 111 GLU cc_start: 0.8436 (mt-10) cc_final: 0.8218 (tt0) REVERT: h2 59 GLU cc_start: 0.8262 (mm-30) cc_final: 0.8050 (mm-30) REVERT: j2 55 LYS cc_start: 0.7409 (mtmt) cc_final: 0.7013 (pttt) REVERT: o2 77 VAL cc_start: 0.8157 (t) cc_final: 0.7915 (t) REVERT: t2 56 GLN cc_start: 0.5359 (mt0) cc_final: 0.4935 (mt0) REVERT: t2 72 MET cc_start: 0.3505 (ptm) cc_final: 0.2565 (ptm) outliers start: 2 outliers final: 1 residues processed: 1467 average time/residue: 2.3887 time to fit residues: 4875.6882 Evaluate side-chains 1045 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1044 time to evaluate : 9.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain t2 residue 390 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 945 optimal weight: 3.9990 chunk 848 optimal weight: 8.9990 chunk 471 optimal weight: 3.9990 chunk 289 optimal weight: 7.9990 chunk 572 optimal weight: 9.9990 chunk 453 optimal weight: 8.9990 chunk 877 optimal weight: 9.9990 chunk 339 optimal weight: 20.0000 chunk 533 optimal weight: 8.9990 chunk 653 optimal weight: 7.9990 chunk 1017 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 42 HIS B2 138 GLN B2 145 GLN B2 158 GLN C2 119 GLN C2 203 GLN D2 191 ASN D2 195 HIS E2 170 GLN E2 185 ASN F2 57 HIS F2 79 ASN G2 96 GLN G2 119 GLN G2 194 ASN H2 102 ASN H2 106 GLN H2 108 ASN H2 140 GLN H2 149 ASN I2 147 HIS I2 177 ASN J2 167 GLN K2 15 HIS L2 33 GLN L2 48 GLN ** M2 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O2 25 HIS O2 56 GLN O2 118 GLN P2 8 ASN P2 77 ASN P2 188 ASN Q2 30 ASN ** Q2 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 58 HIS R2 37 HIS ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 69 GLN U2 36 ASN W2 108 GLN W2 125 ASN W2 151 ASN X2 86 GLN Z2 66 ASN Z2 120 GLN ** b2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 40 GLN d2 52 GLN d2 92 ASN d2 126 ASN f2 100 GLN f2 114 GLN g2 20 GLN g2 63 GLN g2 65 GLN g2 68 ASN g2 108 GLN h2 26 HIS k2 17 GLN k2 25 GLN k2 33 ASN l2 64 ASN l2 93 ASN p2 41 ASN q2 12 ASN q2 58 ASN q2 195 ASN r2 115 GLN r2 137 GLN s21268 HIS s21327 ASN s21330 GLN t2 34 HIS t2 227 HIS ** t2 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t2 374 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.135 153880 Z= 0.525 Angle : 0.810 17.586 226179 Z= 0.414 Chirality : 0.049 0.554 28142 Planarity : 0.007 0.121 14420 Dihedral : 24.319 179.867 69036 Min Nonbonded Distance : 1.629 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 4.26 % Allowed : 11.90 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.09), residues: 7480 helix: -0.47 (0.09), residues: 2877 sheet: -0.66 (0.16), residues: 1021 loop : -0.94 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRPM2 120 HIS 0.017 0.002 HISK2 67 PHE 0.027 0.003 PHED2 13 TYR 0.046 0.003 TYRF2 138 ARG 0.013 0.001 ARGB2 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1114 time to evaluate : 7.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 245 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7840 (tmt170) REVERT: B2 56 ILE cc_start: 0.9078 (OUTLIER) cc_final: 0.8877 (mp) REVERT: B2 169 ARG cc_start: 0.8229 (ptt90) cc_final: 0.7966 (ppt170) REVERT: B2 203 GLN cc_start: 0.8020 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: C2 14 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.7395 (mtpp) REVERT: C2 16 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7715 (mp0) REVERT: D2 212 MET cc_start: 0.7892 (ttm) cc_final: 0.7514 (mtp) REVERT: E2 49 ASN cc_start: 0.7830 (p0) cc_final: 0.7621 (p0) REVERT: E2 117 ARG cc_start: 0.8393 (ptp90) cc_final: 0.7857 (ptt-90) REVERT: F2 138 TYR cc_start: 0.8715 (OUTLIER) cc_final: 0.8462 (m-80) REVERT: G2 96 GLN cc_start: 0.8353 (OUTLIER) cc_final: 0.8137 (mm-40) REVERT: G2 143 GLN cc_start: 0.7688 (OUTLIER) cc_final: 0.6879 (pp30) REVERT: G2 164 LYS cc_start: 0.7597 (mtmt) cc_final: 0.7361 (mtpm) REVERT: H2 80 MET cc_start: 0.8452 (mtp) cc_final: 0.8073 (mtp) REVERT: I2 128 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8434 (mtm180) REVERT: I2 142 LEU cc_start: 0.8597 (mt) cc_final: 0.8355 (tt) REVERT: I2 169 LYS cc_start: 0.8812 (OUTLIER) cc_final: 0.8513 (mptm) REVERT: J2 163 MET cc_start: 0.8757 (mtt) cc_final: 0.8418 (mtt) REVERT: K2 42 ARG cc_start: 0.8706 (ttt90) cc_final: 0.8506 (ttm-80) REVERT: K2 145 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7696 (ptpp) REVERT: L2 78 GLU cc_start: 0.8318 (mt-10) cc_final: 0.8108 (mt-10) REVERT: L2 132 ARG cc_start: 0.7121 (OUTLIER) cc_final: 0.5482 (ttp-110) REVERT: N2 31 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7069 (ttm170) REVERT: N2 49 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8093 (ptm-80) REVERT: N2 159 LYS cc_start: 0.8378 (ttpp) cc_final: 0.7867 (ttmt) REVERT: N2 169 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7764 (mtp180) REVERT: N2 173 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.7848 (tm-30) REVERT: N2 177 LEU cc_start: 0.9004 (mt) cc_final: 0.8677 (mp) REVERT: N2 180 GLN cc_start: 0.8241 (tp-100) cc_final: 0.7932 (tp40) REVERT: O2 13 LYS cc_start: 0.8282 (mtpt) cc_final: 0.8041 (mtmt) REVERT: O2 128 ARG cc_start: 0.8539 (OUTLIER) cc_final: 0.7853 (ptm160) REVERT: O2 151 THR cc_start: 0.8498 (m) cc_final: 0.8267 (m) REVERT: P2 14 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7448 (ptt90) REVERT: P2 91 ARG cc_start: 0.8808 (OUTLIER) cc_final: 0.7944 (ptt-90) REVERT: P2 170 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8485 (ptmt) REVERT: Q2 3 MET cc_start: 0.8633 (OUTLIER) cc_final: 0.7506 (tmm) REVERT: Q2 16 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7810 (mtp85) REVERT: Q2 50 ILE cc_start: 0.9377 (OUTLIER) cc_final: 0.9116 (mt) REVERT: R2 74 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7743 (ptp90) REVERT: R2 143 LYS cc_start: 0.8888 (mtpp) cc_final: 0.8612 (mtpm) REVERT: S2 79 GLN cc_start: 0.9118 (OUTLIER) cc_final: 0.8126 (tm-30) REVERT: T2 47 ILE cc_start: 0.7704 (OUTLIER) cc_final: 0.7400 (mp) REVERT: T2 114 TYR cc_start: 0.8009 (OUTLIER) cc_final: 0.7546 (m-80) REVERT: U2 71 GLU cc_start: 0.8128 (pm20) cc_final: 0.7770 (pm20) REVERT: U2 72 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8601 (mt) REVERT: V2 1 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.5687 (tpp) REVERT: W2 152 LYS cc_start: 0.8215 (pptt) cc_final: 0.7901 (pptt) REVERT: X2 75 ARG cc_start: 0.8996 (OUTLIER) cc_final: 0.8360 (mtt180) REVERT: X2 84 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.7842 (mtm180) REVERT: X2 93 THR cc_start: 0.8476 (m) cc_final: 0.8257 (p) REVERT: X2 105 VAL cc_start: 0.8721 (p) cc_final: 0.8477 (t) REVERT: Y2 59 LYS cc_start: 0.7876 (pttm) cc_final: 0.7399 (pmtt) REVERT: Y2 102 ARG cc_start: 0.6911 (ptp90) cc_final: 0.6616 (mmp80) REVERT: a2 63 LYS cc_start: 0.7535 (tttm) cc_final: 0.7070 (mtpp) REVERT: c2 33 ILE cc_start: 0.8889 (mm) cc_final: 0.8684 (tp) REVERT: d2 33 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7470 (ttm170) REVERT: f2 100 GLN cc_start: 0.8306 (tp40) cc_final: 0.7979 (tp-100) REVERT: g2 99 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.8179 (mt-10) REVERT: h2 59 GLU cc_start: 0.8258 (mm-30) cc_final: 0.8044 (tp30) REVERT: k2 8 ARG cc_start: 0.7561 (ptp90) cc_final: 0.7293 (ptp90) REVERT: l2 72 LYS cc_start: 0.8222 (tttt) cc_final: 0.7686 (mttt) REVERT: l2 100 LYS cc_start: 0.7876 (OUTLIER) cc_final: 0.7568 (mmtp) REVERT: n2 92 GLU cc_start: 0.7541 (OUTLIER) cc_final: 0.7225 (tp30) REVERT: p2 111 ILE cc_start: 0.9497 (OUTLIER) cc_final: 0.9030 (mp) REVERT: q2 55 MET cc_start: 0.5135 (ttt) cc_final: 0.4908 (ttm) REVERT: r2 115 GLN cc_start: 0.1251 (OUTLIER) cc_final: -0.0580 (mt0) REVERT: s2 1064 LEU cc_start: 0.5138 (mt) cc_final: 0.4934 (mp) REVERT: t2 72 MET cc_start: 0.3354 (ptm) cc_final: 0.2766 (ptt) REVERT: t2 174 MET cc_start: 0.4588 (mtp) cc_final: 0.3977 (mpt) outliers start: 278 outliers final: 123 residues processed: 1260 average time/residue: 2.3110 time to fit residues: 4102.1855 Evaluate side-chains 1183 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1023 time to evaluate : 7.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 3 ARG Chi-restraints excluded: chain A2 residue 15 VAL Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 154 SER Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 56 ILE Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain B2 residue 162 VAL Chi-restraints excluded: chain B2 residue 203 GLN Chi-restraints excluded: chain C2 residue 14 LYS Chi-restraints excluded: chain C2 residue 16 GLU Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 287 THR Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 75 VAL Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 272 SER Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 49 ILE Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 138 TYR Chi-restraints excluded: chain F2 residue 219 MET Chi-restraints excluded: chain G2 residue 96 GLN Chi-restraints excluded: chain G2 residue 143 GLN Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 125 THR Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 169 LYS Chi-restraints excluded: chain J2 residue 23 ASN Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain J2 residue 73 THR Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 145 LYS Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain L2 residue 132 ARG Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 151 ILE Chi-restraints excluded: chain M2 residue 155 VAL Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 31 ARG Chi-restraints excluded: chain N2 residue 49 ARG Chi-restraints excluded: chain N2 residue 169 ARG Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain O2 residue 24 VAL Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 43 LYS Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 95 LEU Chi-restraints excluded: chain O2 residue 128 ARG Chi-restraints excluded: chain O2 residue 142 SER Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 170 LYS Chi-restraints excluded: chain P2 residue 175 GLU Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 16 ARG Chi-restraints excluded: chain Q2 residue 50 ILE Chi-restraints excluded: chain R2 residue 54 MET Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 82 LEU Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain R2 residue 135 SER Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 41 ASP Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 110 LYS Chi-restraints excluded: chain T2 residue 47 ILE Chi-restraints excluded: chain T2 residue 114 TYR Chi-restraints excluded: chain U2 residue 64 THR Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 87 SER Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 1 MET Chi-restraints excluded: chain V2 residue 3 VAL Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 63 LYS Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain W2 residue 115 LYS Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 84 ARG Chi-restraints excluded: chain Y2 residue 21 ARG Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 61 LYS Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 140 VAL Chi-restraints excluded: chain a2 residue 36 ASP Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain d2 residue 91 CYS Chi-restraints excluded: chain e2 residue 67 THR Chi-restraints excluded: chain e2 residue 73 LYS Chi-restraints excluded: chain f2 residue 15 THR Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain g2 residue 16 GLU Chi-restraints excluded: chain g2 residue 82 ASP Chi-restraints excluded: chain g2 residue 99 GLU Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain g2 residue 109 ARG Chi-restraints excluded: chain h2 residue 12 ASN Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 45 ARG Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain l2 residue 100 LYS Chi-restraints excluded: chain n2 residue 33 LEU Chi-restraints excluded: chain n2 residue 79 SER Chi-restraints excluded: chain n2 residue 92 GLU Chi-restraints excluded: chain o2 residue 10 ILE Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 59 SER Chi-restraints excluded: chain o2 residue 81 SER Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 78 VAL Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain r2 residue 115 GLN Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1025 LEU Chi-restraints excluded: chain s2 residue 1026 THR Chi-restraints excluded: chain s2 residue 1113 ASP Chi-restraints excluded: chain s2 residue 1171 LEU Chi-restraints excluded: chain s2 residue 1215 VAL Chi-restraints excluded: chain s2 residue 1268 HIS Chi-restraints excluded: chain s2 residue 1286 VAL Chi-restraints excluded: chain t2 residue 170 LEU Chi-restraints excluded: chain t2 residue 237 GLU Chi-restraints excluded: chain t2 residue 347 THR Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 565 optimal weight: 3.9990 chunk 315 optimal weight: 3.9990 chunk 846 optimal weight: 1.9990 chunk 692 optimal weight: 1.9990 chunk 280 optimal weight: 6.9990 chunk 1018 optimal weight: 2.9990 chunk 1100 optimal weight: 9.9990 chunk 907 optimal weight: 3.9990 chunk 1010 optimal weight: 9.9990 chunk 347 optimal weight: 8.9990 chunk 817 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2 140 ASN B2 138 GLN C2 50 GLN E2 185 ASN G2 194 ASN H2 108 ASN H2 140 GLN I2 177 ASN K2 159 ASN L2 33 GLN L2 131 GLN M2 37 HIS M2 196 ASN O2 25 HIS Q2 30 ASN Q2 36 ASN ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 69 GLN S2 127 GLN T2 38 ASN T2 41 GLN U2 36 ASN V2 48 GLN W2 93 ASN W2 151 ASN Z2 120 GLN ** b2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c2 121 ASN d2 126 ASN g2 20 GLN g2 65 GLN g2 68 ASN k2 17 GLN k2 25 GLN l2 93 ASN q2 12 ASN q2 191 GLN ** r2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s21268 HIS Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 153880 Z= 0.227 Angle : 0.591 12.352 226179 Z= 0.308 Chirality : 0.038 0.334 28142 Planarity : 0.005 0.073 14420 Dihedral : 24.192 179.947 69034 Min Nonbonded Distance : 1.494 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.98 % Favored : 96.99 % Rotamer: Outliers : 3.75 % Allowed : 15.37 % Favored : 80.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.09), residues: 7480 helix: 0.20 (0.10), residues: 2857 sheet: -0.58 (0.16), residues: 1041 loop : -0.75 (0.10), residues: 3582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPM2 120 HIS 0.012 0.001 HISK2 67 PHE 0.015 0.001 PHEt2 247 TYR 0.029 0.002 TYRt2 189 ARG 0.009 0.000 ARGC2 350 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 245 poor density : 1113 time to evaluate : 7.630 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 68 ARG cc_start: 0.8310 (mtt90) cc_final: 0.8099 (mtt90) REVERT: A2 144 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.6997 (mmtp) REVERT: B2 39 LYS cc_start: 0.8546 (mttt) cc_final: 0.8285 (mptt) REVERT: B2 169 ARG cc_start: 0.8133 (ptt90) cc_final: 0.7904 (ppt170) REVERT: C2 14 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7362 (mtpp) REVERT: D2 212 MET cc_start: 0.7881 (ttm) cc_final: 0.7502 (mtp) REVERT: E2 117 ARG cc_start: 0.8330 (ptp90) cc_final: 0.7760 (ptt-90) REVERT: G2 143 GLN cc_start: 0.7634 (OUTLIER) cc_final: 0.6840 (pp30) REVERT: G2 206 GLN cc_start: 0.8188 (mt0) cc_final: 0.7929 (mt0) REVERT: H2 80 MET cc_start: 0.8414 (mtp) cc_final: 0.7987 (mtp) REVERT: I2 142 LEU cc_start: 0.8567 (mt) cc_final: 0.8340 (tt) REVERT: I2 169 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8427 (mptm) REVERT: J2 28 GLU cc_start: 0.7493 (OUTLIER) cc_final: 0.7243 (mp0) REVERT: K2 42 ARG cc_start: 0.8557 (ttt90) cc_final: 0.8199 (ttp80) REVERT: K2 118 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.7988 (mtpt) REVERT: K2 164 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7202 (mt-10) REVERT: L2 78 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7984 (mt-10) REVERT: L2 98 ARG cc_start: 0.8449 (ttm-80) cc_final: 0.8201 (ttp-110) REVERT: N2 49 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7583 (ptm-80) REVERT: N2 159 LYS cc_start: 0.8339 (ttpp) cc_final: 0.7826 (ttmt) REVERT: N2 173 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7870 (tm-30) REVERT: N2 175 MET cc_start: 0.8632 (tpp) cc_final: 0.8426 (tpt) REVERT: N2 180 GLN cc_start: 0.8207 (tp-100) cc_final: 0.7951 (tp40) REVERT: O2 13 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7917 (mtmt) REVERT: O2 128 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7138 (ptm160) REVERT: O2 151 THR cc_start: 0.8558 (m) cc_final: 0.8324 (m) REVERT: P2 14 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7310 (ptt90) REVERT: Q2 3 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.7448 (tmm) REVERT: Q2 16 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7844 (mtp85) REVERT: Q2 71 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7399 (tpp80) REVERT: R2 143 LYS cc_start: 0.8831 (mtpp) cc_final: 0.8577 (mtpm) REVERT: S2 79 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: T2 40 GLU cc_start: 0.7373 (tm-30) cc_final: 0.7127 (tm-30) REVERT: T2 47 ILE cc_start: 0.7723 (OUTLIER) cc_final: 0.7466 (mp) REVERT: U2 71 GLU cc_start: 0.8046 (pm20) cc_final: 0.7773 (pm20) REVERT: U2 72 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8560 (mt) REVERT: U2 74 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (mtmt) REVERT: V2 1 MET cc_start: 0.7417 (pmm) cc_final: 0.5846 (tpp) REVERT: W2 152 LYS cc_start: 0.8201 (pptt) cc_final: 0.7913 (pptt) REVERT: X2 75 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8456 (mtm180) REVERT: X2 84 ARG cc_start: 0.8358 (OUTLIER) cc_final: 0.7788 (mtm180) REVERT: X2 105 VAL cc_start: 0.8751 (p) cc_final: 0.8422 (t) REVERT: Y2 46 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8135 (mt) REVERT: a2 63 LYS cc_start: 0.7617 (tttm) cc_final: 0.7122 (mtpp) REVERT: d2 33 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7416 (ttm170) REVERT: g2 105 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8332 (mppt) REVERT: l2 72 LYS cc_start: 0.8171 (tttt) cc_final: 0.7639 (mttt) REVERT: l2 100 LYS cc_start: 0.7900 (OUTLIER) cc_final: 0.7606 (mmtp) REVERT: m2 1 MET cc_start: 0.4994 (OUTLIER) cc_final: 0.3455 (ptt) REVERT: n2 92 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7208 (tp30) REVERT: o2 88 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6629 (mt-10) REVERT: p2 111 ILE cc_start: 0.9466 (OUTLIER) cc_final: 0.9038 (mp) REVERT: s2 926 ASN cc_start: 0.4694 (m-40) cc_final: 0.4479 (t0) REVERT: t2 174 MET cc_start: 0.4692 (mtp) cc_final: 0.4214 (mpt) REVERT: t2 368 MET cc_start: 0.6737 (OUTLIER) cc_final: 0.5928 (mtt) outliers start: 245 outliers final: 107 residues processed: 1233 average time/residue: 2.1912 time to fit residues: 3831.8672 Evaluate side-chains 1177 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1042 time to evaluate : 7.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 154 SER Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain B2 residue 215 GLU Chi-restraints excluded: chain B2 residue 289 GLN Chi-restraints excluded: chain C2 residue 14 LYS Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 72 ASP Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 272 SER Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain F2 residue 128 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain G2 residue 143 GLN Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain I2 residue 125 THR Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain I2 residue 169 LYS Chi-restraints excluded: chain J2 residue 23 ASN Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain K2 residue 148 THR Chi-restraints excluded: chain L2 residue 105 THR Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 104 GLU Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 49 ARG Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain O2 residue 14 SER Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 43 LYS Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 128 ARG Chi-restraints excluded: chain O2 residue 142 SER Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 19 LYS Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 158 THR Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 16 ARG Chi-restraints excluded: chain Q2 residue 71 ARG Chi-restraints excluded: chain Q2 residue 111 GLU Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 54 MET Chi-restraints excluded: chain R2 residue 82 LEU Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain R2 residue 135 SER Chi-restraints excluded: chain R2 residue 158 VAL Chi-restraints excluded: chain R2 residue 161 ARG Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 47 ILE Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 74 LYS Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 101 ASP Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 84 ARG Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 61 LYS Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain c2 residue 101 LYS Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain d2 residue 91 CYS Chi-restraints excluded: chain e2 residue 10 ILE Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain g2 residue 36 VAL Chi-restraints excluded: chain g2 residue 82 ASP Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain g2 residue 105 LYS Chi-restraints excluded: chain h2 residue 12 ASN Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 77 VAL Chi-restraints excluded: chain i2 residue 6 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 45 ARG Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain j2 residue 60 LEU Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain l2 residue 100 LYS Chi-restraints excluded: chain m2 residue 1 MET Chi-restraints excluded: chain n2 residue 79 SER Chi-restraints excluded: chain n2 residue 92 GLU Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 59 SER Chi-restraints excluded: chain o2 residue 81 SER Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 75 THR Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain r2 residue 98 ILE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1283 ASP Chi-restraints excluded: chain s2 residue 1286 VAL Chi-restraints excluded: chain t2 residue 145 VAL Chi-restraints excluded: chain t2 residue 237 GLU Chi-restraints excluded: chain t2 residue 268 LEU Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 1006 optimal weight: 5.9990 chunk 766 optimal weight: 2.9990 chunk 528 optimal weight: 7.9990 chunk 112 optimal weight: 10.0000 chunk 486 optimal weight: 1.9990 chunk 684 optimal weight: 0.9980 chunk 1022 optimal weight: 6.9990 chunk 1082 optimal weight: 7.9990 chunk 534 optimal weight: 1.9990 chunk 969 optimal weight: 4.9990 chunk 291 optimal weight: 8.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D2 291 GLN E2 185 ASN H2 140 GLN I2 177 ASN ** J2 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2 33 GLN L2 131 GLN M2 37 HIS ** O2 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q2 30 ASN ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 127 GLN T2 41 GLN T2 94 ASN U2 27 ASN U2 36 ASN W2 151 ASN Z2 120 GLN a2 61 ASN ** b2 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b2 40 GLN c2 121 ASN d2 34 ASN d2 92 ASN d2 126 ASN f2 100 GLN g2 20 GLN g2 65 GLN g2 68 ASN k2 25 GLN l2 64 ASN n2 45 GLN q2 12 ASN s21268 HIS t2 266 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 153880 Z= 0.249 Angle : 0.596 10.052 226179 Z= 0.310 Chirality : 0.038 0.350 28142 Planarity : 0.005 0.064 14420 Dihedral : 24.130 179.975 69034 Min Nonbonded Distance : 1.325 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 4.61 % Allowed : 16.26 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.09), residues: 7480 helix: 0.48 (0.10), residues: 2858 sheet: -0.47 (0.16), residues: 1015 loop : -0.65 (0.10), residues: 3607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRPM2 120 HIS 0.012 0.001 HISK2 67 PHE 0.014 0.001 PHEt2 247 TYR 0.027 0.002 TYRt2 309 ARG 0.009 0.000 ARGJ2 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1080 time to evaluate : 7.666 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: A2 144 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6959 (mmtp) REVERT: A2 245 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7685 (tmt170) REVERT: C2 14 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7383 (mtpp) REVERT: C2 20 LYS cc_start: 0.7801 (mmmt) cc_final: 0.7247 (mttp) REVERT: D2 212 MET cc_start: 0.7910 (ttm) cc_final: 0.7573 (mtp) REVERT: E2 117 ARG cc_start: 0.8358 (ptp90) cc_final: 0.7749 (ptt-90) REVERT: G2 143 GLN cc_start: 0.7642 (OUTLIER) cc_final: 0.6850 (pp30) REVERT: H2 80 MET cc_start: 0.8408 (mtp) cc_final: 0.8151 (mtm) REVERT: I2 128 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8663 (mtm180) REVERT: I2 142 LEU cc_start: 0.8584 (mt) cc_final: 0.8360 (tt) REVERT: I2 169 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8456 (mptm) REVERT: J2 28 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: J2 163 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8410 (mtt) REVERT: K2 42 ARG cc_start: 0.8566 (ttt90) cc_final: 0.8203 (ttp80) REVERT: K2 118 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.7990 (mtpt) REVERT: K2 164 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: L2 70 GLN cc_start: 0.8464 (tt0) cc_final: 0.8183 (mt0) REVERT: L2 98 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8259 (ttp-110) REVERT: L2 132 ARG cc_start: 0.7023 (ttt90) cc_final: 0.6812 (ttt-90) REVERT: N2 49 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.7596 (ptm-80) REVERT: N2 159 LYS cc_start: 0.8317 (ttpp) cc_final: 0.7794 (ttmt) REVERT: N2 173 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: N2 180 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7946 (tp40) REVERT: O2 13 LYS cc_start: 0.8231 (mtpt) cc_final: 0.7986 (mtpt) REVERT: O2 128 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.7181 (ptm160) REVERT: P2 14 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7338 (ptt90) REVERT: P2 91 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.7828 (ptt-90) REVERT: Q2 3 MET cc_start: 0.8627 (OUTLIER) cc_final: 0.7510 (tmm) REVERT: Q2 16 ARG cc_start: 0.8051 (OUTLIER) cc_final: 0.7849 (mtp85) REVERT: Q2 31 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.6973 (mm-30) REVERT: Q2 71 ARG cc_start: 0.7732 (OUTLIER) cc_final: 0.7451 (tpp80) REVERT: Q2 152 LYS cc_start: 0.7918 (tptm) cc_final: 0.7254 (pttt) REVERT: R2 29 ARG cc_start: 0.8487 (OUTLIER) cc_final: 0.7612 (ttp-170) REVERT: R2 143 LYS cc_start: 0.8840 (mtpp) cc_final: 0.8583 (mtpm) REVERT: S2 79 GLN cc_start: 0.9062 (OUTLIER) cc_final: 0.8082 (tm-30) REVERT: S2 137 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7489 (pt0) REVERT: T2 47 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7622 (mp) REVERT: T2 94 ASN cc_start: 0.6679 (OUTLIER) cc_final: 0.5733 (t0) REVERT: U2 71 GLU cc_start: 0.8056 (pm20) cc_final: 0.7781 (pm20) REVERT: U2 72 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8574 (mt) REVERT: U2 74 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.8119 (mtmt) REVERT: V2 1 MET cc_start: 0.7533 (pmm) cc_final: 0.5949 (tpp) REVERT: W2 57 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7598 (mp10) REVERT: W2 152 LYS cc_start: 0.8123 (pptt) cc_final: 0.7861 (pptt) REVERT: X2 67 ILE cc_start: 0.8943 (OUTLIER) cc_final: 0.8694 (mt) REVERT: X2 75 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8462 (mtm180) REVERT: X2 84 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.7790 (mtm180) REVERT: X2 105 VAL cc_start: 0.8762 (p) cc_final: 0.8383 (t) REVERT: Y2 46 ILE cc_start: 0.8655 (OUTLIER) cc_final: 0.8069 (mt) REVERT: Y2 85 TYR cc_start: 0.8811 (m-80) cc_final: 0.8538 (m-80) REVERT: Y2 109 LYS cc_start: 0.8279 (mmpt) cc_final: 0.7809 (mptp) REVERT: a2 63 LYS cc_start: 0.7541 (tttm) cc_final: 0.7036 (mtpp) REVERT: b2 17 ARG cc_start: 0.7497 (ttm-80) cc_final: 0.7246 (ttm-80) REVERT: d2 33 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7474 (ttm170) REVERT: g2 105 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8340 (mppt) REVERT: j2 8 ILE cc_start: 0.7713 (mp) cc_final: 0.7460 (mt) REVERT: l2 72 LYS cc_start: 0.8244 (tttt) cc_final: 0.7697 (mttt) REVERT: l2 100 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7608 (mmtp) REVERT: m2 1 MET cc_start: 0.5067 (OUTLIER) cc_final: 0.3539 (ptt) REVERT: n2 82 MET cc_start: 0.9336 (OUTLIER) cc_final: 0.7892 (mmp) REVERT: n2 92 GLU cc_start: 0.7526 (OUTLIER) cc_final: 0.7210 (tp30) REVERT: o2 88 GLU cc_start: 0.7232 (OUTLIER) cc_final: 0.6698 (mt-10) REVERT: p2 82 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8600 (mm) REVERT: p2 111 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9007 (mp) REVERT: t2 148 GLN cc_start: 0.5033 (OUTLIER) cc_final: 0.4343 (mp10) REVERT: t2 174 MET cc_start: 0.4706 (mtp) cc_final: 0.4133 (mpt) REVERT: t2 368 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.5967 (mtt) outliers start: 301 outliers final: 141 residues processed: 1241 average time/residue: 2.2638 time to fit residues: 3981.4167 Evaluate side-chains 1223 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1040 time to evaluate : 7.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 154 SER Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain B2 residue 289 GLN Chi-restraints excluded: chain B2 residue 298 LEU Chi-restraints excluded: chain C2 residue 14 LYS Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 72 ASP Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 272 SER Chi-restraints excluded: chain D2 residue 289 ARG Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain F2 residue 128 SER Chi-restraints excluded: chain F2 residue 177 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain G2 residue 142 ARG Chi-restraints excluded: chain G2 residue 143 GLN Chi-restraints excluded: chain G2 residue 299 SER Chi-restraints excluded: chain H2 residue 8 GLN Chi-restraints excluded: chain H2 residue 66 GLU Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 125 THR Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain I2 residue 169 LYS Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain J2 residue 163 MET Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain K2 residue 148 THR Chi-restraints excluded: chain K2 residue 164 GLU Chi-restraints excluded: chain K2 residue 207 VAL Chi-restraints excluded: chain L2 residue 105 THR Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 49 ARG Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain O2 residue 14 SER Chi-restraints excluded: chain O2 residue 24 VAL Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 43 LYS Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 103 GLU Chi-restraints excluded: chain O2 residue 128 ARG Chi-restraints excluded: chain O2 residue 142 SER Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 19 LYS Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 76 GLU Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 138 LEU Chi-restraints excluded: chain P2 residue 158 THR Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 16 ARG Chi-restraints excluded: chain Q2 residue 31 GLU Chi-restraints excluded: chain Q2 residue 71 ARG Chi-restraints excluded: chain Q2 residue 111 GLU Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 54 MET Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 82 LEU Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain R2 residue 135 SER Chi-restraints excluded: chain R2 residue 161 ARG Chi-restraints excluded: chain S2 residue 29 THR Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 47 ILE Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain T2 residue 94 ASN Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 74 LYS Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 57 GLN Chi-restraints excluded: chain W2 residue 95 THR Chi-restraints excluded: chain W2 residue 101 ASP Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 67 ILE Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 84 ARG Chi-restraints excluded: chain X2 residue 104 VAL Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 61 LYS Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 134 GLU Chi-restraints excluded: chain Z2 residue 140 VAL Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain c2 residue 86 VAL Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain d2 residue 91 CYS Chi-restraints excluded: chain e2 residue 67 THR Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain g2 residue 36 VAL Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain g2 residue 105 LYS Chi-restraints excluded: chain g2 residue 116 LEU Chi-restraints excluded: chain h2 residue 12 ASN Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 25 ARG Chi-restraints excluded: chain h2 residue 64 SER Chi-restraints excluded: chain h2 residue 77 VAL Chi-restraints excluded: chain h2 residue 92 SER Chi-restraints excluded: chain i2 residue 6 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 45 ARG Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain l2 residue 100 LYS Chi-restraints excluded: chain m2 residue 1 MET Chi-restraints excluded: chain n2 residue 79 SER Chi-restraints excluded: chain n2 residue 82 MET Chi-restraints excluded: chain n2 residue 92 GLU Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 59 SER Chi-restraints excluded: chain o2 residue 81 SER Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 75 THR Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain r2 residue 98 ILE Chi-restraints excluded: chain r2 residue 129 ILE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1026 THR Chi-restraints excluded: chain s2 residue 1171 LEU Chi-restraints excluded: chain s2 residue 1283 ASP Chi-restraints excluded: chain s2 residue 1286 VAL Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 222 SER Chi-restraints excluded: chain t2 residue 237 GLU Chi-restraints excluded: chain t2 residue 268 LEU Chi-restraints excluded: chain t2 residue 347 THR Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 901 optimal weight: 0.1980 chunk 614 optimal weight: 0.9980 chunk 15 optimal weight: 10.0000 chunk 806 optimal weight: 5.9990 chunk 446 optimal weight: 4.9990 chunk 923 optimal weight: 0.9990 chunk 748 optimal weight: 0.9980 chunk 1 optimal weight: 8.9990 chunk 552 optimal weight: 0.0070 chunk 971 optimal weight: 3.9990 chunk 273 optimal weight: 10.0000 overall best weight: 0.6400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 138 GLN C2 50 GLN G2 206 GLN H2 140 GLN I2 177 ASN ** J2 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K2 115 GLN L2 33 GLN M2 37 HIS ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 112 ASN S2 127 GLN T2 94 ASN U2 36 ASN W2 151 ASN X2 86 GLN Z2 120 GLN a2 61 ASN b2 40 GLN c2 121 ASN d2 126 ASN g2 20 GLN g2 65 GLN h2 36 HIS l2 64 ASN n2 45 GLN s21268 HIS ** t2 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.086 153880 Z= 0.133 Angle : 0.546 9.861 226179 Z= 0.285 Chirality : 0.035 0.314 28142 Planarity : 0.004 0.068 14420 Dihedral : 24.135 179.673 69034 Min Nonbonded Distance : 1.311 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.01 % Rotamer: Outliers : 3.66 % Allowed : 18.14 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.10), residues: 7480 helix: 0.71 (0.10), residues: 2869 sheet: -0.37 (0.16), residues: 1004 loop : -0.57 (0.10), residues: 3607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRPq2 9 HIS 0.007 0.001 HISs21268 PHE 0.015 0.001 PHEs21135 TYR 0.021 0.001 TYRt2 189 ARG 0.009 0.000 ARGC2 350 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1095 time to evaluate : 7.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 144 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.6949 (mmtp) REVERT: A2 245 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7658 (tmt170) REVERT: B2 17 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6819 (tp) REVERT: C2 20 LYS cc_start: 0.7738 (mmmt) cc_final: 0.7222 (mttp) REVERT: D2 212 MET cc_start: 0.7884 (ttm) cc_final: 0.7513 (mtp) REVERT: E2 117 ARG cc_start: 0.8341 (ptp90) cc_final: 0.7788 (ptt-90) REVERT: E2 252 ASP cc_start: 0.8195 (m-30) cc_final: 0.7736 (m-30) REVERT: H2 80 MET cc_start: 0.8401 (mtp) cc_final: 0.8150 (mtm) REVERT: I2 142 LEU cc_start: 0.8584 (mt) cc_final: 0.8356 (tt) REVERT: J2 28 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: J2 163 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8393 (mtt) REVERT: J2 175 LEU cc_start: 0.7421 (OUTLIER) cc_final: 0.6826 (pp) REVERT: K2 42 ARG cc_start: 0.8551 (ttt90) cc_final: 0.8168 (ttp80) REVERT: K2 118 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7994 (mtpt) REVERT: K2 164 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7206 (mt-10) REVERT: L2 70 GLN cc_start: 0.8355 (tt0) cc_final: 0.8135 (mt0) REVERT: L2 98 ARG cc_start: 0.8470 (ttm-80) cc_final: 0.8242 (ttp-110) REVERT: L2 132 ARG cc_start: 0.6951 (ttt90) cc_final: 0.6220 (ttm-80) REVERT: N2 159 LYS cc_start: 0.8320 (ttpp) cc_final: 0.7793 (ttmt) REVERT: N2 173 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.7904 (tm-30) REVERT: N2 180 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7958 (tp40) REVERT: O2 13 LYS cc_start: 0.8159 (mtpt) cc_final: 0.7957 (mtpt) REVERT: O2 128 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.6882 (ptm160) REVERT: P2 14 ARG cc_start: 0.8179 (OUTLIER) cc_final: 0.7299 (ptt90) REVERT: P2 91 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7724 (ptt-90) REVERT: P2 147 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.8133 (tp30) REVERT: P2 158 THR cc_start: 0.8606 (m) cc_final: 0.8086 (p) REVERT: Q2 3 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7514 (tmm) REVERT: Q2 16 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7747 (mtp85) REVERT: Q2 71 ARG cc_start: 0.7673 (mpt180) cc_final: 0.7412 (tpp80) REVERT: Q2 152 LYS cc_start: 0.7832 (tptm) cc_final: 0.7139 (pttt) REVERT: R2 29 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.7633 (ttp-170) REVERT: R2 74 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7592 (ptp90) REVERT: R2 143 LYS cc_start: 0.8819 (mtpp) cc_final: 0.8578 (mtpm) REVERT: S2 79 GLN cc_start: 0.9000 (OUTLIER) cc_final: 0.8044 (tm-30) REVERT: S2 137 GLU cc_start: 0.7792 (OUTLIER) cc_final: 0.7519 (pt0) REVERT: U2 18 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8600 (mt) REVERT: U2 71 GLU cc_start: 0.7976 (pm20) cc_final: 0.7726 (pm20) REVERT: U2 72 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8572 (mt) REVERT: V2 1 MET cc_start: 0.7467 (pmm) cc_final: 0.5924 (tpp) REVERT: W2 57 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7566 (mp10) REVERT: W2 152 LYS cc_start: 0.8128 (pptt) cc_final: 0.7847 (pptt) REVERT: X2 75 ARG cc_start: 0.8832 (OUTLIER) cc_final: 0.8367 (mtm-85) REVERT: X2 84 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.7806 (mtm180) REVERT: X2 105 VAL cc_start: 0.8742 (p) cc_final: 0.8413 (t) REVERT: Y2 46 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8141 (mt) REVERT: Y2 85 TYR cc_start: 0.8790 (m-80) cc_final: 0.8537 (m-80) REVERT: d2 33 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7418 (ttm170) REVERT: g2 105 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8319 (mppt) REVERT: h2 59 GLU cc_start: 0.8353 (tp30) cc_final: 0.7993 (tp30) REVERT: h2 65 LYS cc_start: 0.8534 (mttp) cc_final: 0.8167 (mmmt) REVERT: j2 8 ILE cc_start: 0.7641 (mp) cc_final: 0.7390 (mt) REVERT: l2 72 LYS cc_start: 0.8137 (tttt) cc_final: 0.7612 (mttt) REVERT: l2 100 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7563 (mmtp) REVERT: m2 1 MET cc_start: 0.4952 (OUTLIER) cc_final: 0.3358 (ptt) REVERT: n2 82 MET cc_start: 0.9333 (OUTLIER) cc_final: 0.7886 (mmp) REVERT: o2 87 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7893 (tttm) REVERT: o2 88 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6711 (mt-10) REVERT: o2 89 LEU cc_start: 0.7320 (OUTLIER) cc_final: 0.6267 (mt) REVERT: p2 82 ILE cc_start: 0.8921 (OUTLIER) cc_final: 0.8572 (mm) REVERT: p2 111 ILE cc_start: 0.9438 (OUTLIER) cc_final: 0.9026 (mp) REVERT: q2 88 PHE cc_start: 0.2908 (OUTLIER) cc_final: 0.1132 (m-10) REVERT: t2 148 GLN cc_start: 0.4984 (OUTLIER) cc_final: 0.4427 (mp10) REVERT: t2 174 MET cc_start: 0.4447 (mtp) cc_final: 0.4177 (mpt) REVERT: t2 423 GLN cc_start: 0.6001 (OUTLIER) cc_final: 0.4752 (mp-120) outliers start: 239 outliers final: 109 residues processed: 1227 average time/residue: 2.2588 time to fit residues: 3940.8580 Evaluate side-chains 1185 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1038 time to evaluate : 7.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 160 SER Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 17 LEU Chi-restraints excluded: chain B2 residue 180 LEU Chi-restraints excluded: chain B2 residue 181 MET Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 72 ASP Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 289 ARG Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 200 THR Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 177 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain G2 residue 142 ARG Chi-restraints excluded: chain H2 residue 8 GLN Chi-restraints excluded: chain H2 residue 46 SER Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 125 THR Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain J2 residue 163 MET Chi-restraints excluded: chain J2 residue 175 LEU Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 148 THR Chi-restraints excluded: chain K2 residue 162 LYS Chi-restraints excluded: chain K2 residue 164 GLU Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 38 ARG Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 43 LYS Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 128 ARG Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 19 LYS Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 76 GLU Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 138 LEU Chi-restraints excluded: chain P2 residue 147 GLU Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 16 ARG Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 82 LEU Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain R2 residue 158 VAL Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 52 MET Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 109 VAL Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain U2 residue 18 LEU Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 87 SER Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 57 GLN Chi-restraints excluded: chain W2 residue 95 THR Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 84 ARG Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Y2 residue 100 VAL Chi-restraints excluded: chain Z2 residue 38 MET Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 134 GLU Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain c2 residue 86 VAL Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain g2 residue 105 LYS Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 22 SER Chi-restraints excluded: chain h2 residue 25 ARG Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain l2 residue 100 LYS Chi-restraints excluded: chain m2 residue 1 MET Chi-restraints excluded: chain n2 residue 82 MET Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 87 LYS Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain q2 residue 47 LEU Chi-restraints excluded: chain q2 residue 88 PHE Chi-restraints excluded: chain r2 residue 98 ILE Chi-restraints excluded: chain r2 residue 129 ILE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1020 LEU Chi-restraints excluded: chain s2 residue 1026 THR Chi-restraints excluded: chain s2 residue 1268 HIS Chi-restraints excluded: chain t2 residue 52 LYS Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 233 LEU Chi-restraints excluded: chain t2 residue 268 LEU Chi-restraints excluded: chain t2 residue 347 THR Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 423 GLN Chi-restraints excluded: chain t2 residue 430 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 364 optimal weight: 10.0000 chunk 974 optimal weight: 10.0000 chunk 213 optimal weight: 8.9990 chunk 635 optimal weight: 6.9990 chunk 267 optimal weight: 10.0000 chunk 1083 optimal weight: 20.0000 chunk 899 optimal weight: 10.0000 chunk 501 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 358 optimal weight: 10.0000 chunk 568 optimal weight: 0.2980 overall best weight: 5.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2 50 GLN C2 299 GLN E2 185 ASN I2 177 ASN J2 23 ASN L2 33 GLN L2 131 GLN M2 37 HIS N2 72 HIS O2 25 HIS P2 44 ASN ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 69 GLN S2 112 ASN S2 127 GLN T2 41 GLN U2 77 HIS X2 86 GLN Z2 120 GLN b2 40 GLN c2 121 ASN d2 34 ASN d2 92 ASN d2 126 ASN f2 100 GLN g2 20 GLN g2 65 GLN k2 19 GLN k2 25 GLN k2 38 ASN l2 64 ASN n2 45 GLN s21023 HIS t2 374 GLN ** u2 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 153880 Z= 0.452 Angle : 0.733 12.243 226179 Z= 0.375 Chirality : 0.046 0.501 28142 Planarity : 0.006 0.091 14420 Dihedral : 24.205 179.902 69034 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 4.86 % Allowed : 18.11 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.09), residues: 7480 helix: 0.38 (0.10), residues: 2883 sheet: -0.43 (0.16), residues: 1008 loop : -0.69 (0.10), residues: 3589 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRPM2 120 HIS 0.019 0.002 HISs21268 PHE 0.019 0.002 PHEI2 34 TYR 0.036 0.002 TYRe2 106 ARG 0.008 0.001 ARGC2 350 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1366 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 1049 time to evaluate : 7.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 144 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7016 (mmtp) REVERT: A2 245 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7759 (tmt170) REVERT: D2 212 MET cc_start: 0.7827 (ttm) cc_final: 0.7472 (mtp) REVERT: E2 117 ARG cc_start: 0.8395 (ptp90) cc_final: 0.7813 (ptt-90) REVERT: E2 252 ASP cc_start: 0.8197 (m-30) cc_final: 0.7688 (m-30) REVERT: F2 40 MET cc_start: 0.7342 (OUTLIER) cc_final: 0.7007 (mmm) REVERT: G2 143 GLN cc_start: 0.7706 (OUTLIER) cc_final: 0.6849 (pp30) REVERT: I2 128 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8502 (mtm180) REVERT: I2 162 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.8031 (ttt180) REVERT: I2 169 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8487 (mptm) REVERT: I2 213 HIS cc_start: 0.8287 (OUTLIER) cc_final: 0.7244 (m-70) REVERT: J2 28 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7250 (mp0) REVERT: J2 163 MET cc_start: 0.8954 (OUTLIER) cc_final: 0.8501 (mtt) REVERT: K2 118 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8011 (mtpt) REVERT: K2 145 LYS cc_start: 0.8127 (OUTLIER) cc_final: 0.7830 (ptpp) REVERT: K2 164 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7251 (mt-10) REVERT: L2 70 GLN cc_start: 0.8584 (tt0) cc_final: 0.8344 (mt0) REVERT: L2 98 ARG cc_start: 0.8453 (ttm-80) cc_final: 0.8244 (ttp-110) REVERT: L2 132 ARG cc_start: 0.6999 (ttt90) cc_final: 0.6750 (ttt-90) REVERT: N2 49 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.7581 (ptm-80) REVERT: N2 159 LYS cc_start: 0.8335 (ttpp) cc_final: 0.7848 (ttmt) REVERT: N2 173 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: N2 180 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7992 (tp40) REVERT: O2 13 LYS cc_start: 0.8180 (mtpt) cc_final: 0.7934 (mtpt) REVERT: O2 99 GLU cc_start: 0.8289 (tp30) cc_final: 0.7783 (tp30) REVERT: O2 128 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.7838 (ptm160) REVERT: P2 14 ARG cc_start: 0.8306 (OUTLIER) cc_final: 0.7513 (ptt90) REVERT: P2 91 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.7918 (ptt-90) REVERT: P2 147 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8268 (tp30) REVERT: Q2 3 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.7546 (tmm) REVERT: Q2 16 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7825 (mtp85) REVERT: Q2 31 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7444 (tp30) REVERT: Q2 71 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.7647 (mtt-85) REVERT: Q2 152 LYS cc_start: 0.7968 (tptm) cc_final: 0.7161 (ptpt) REVERT: R2 23 ARG cc_start: 0.6863 (ttm-80) cc_final: 0.6613 (ttt180) REVERT: R2 29 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.7638 (ttp-170) REVERT: R2 74 ARG cc_start: 0.8125 (OUTLIER) cc_final: 0.7722 (ptp90) REVERT: R2 143 LYS cc_start: 0.8830 (mtpp) cc_final: 0.8562 (mtpm) REVERT: S2 79 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8113 (tm-30) REVERT: S2 137 GLU cc_start: 0.7826 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: U2 71 GLU cc_start: 0.8107 (pm20) cc_final: 0.7792 (pm20) REVERT: U2 72 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8643 (mt) REVERT: U2 74 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.8161 (mtmt) REVERT: V2 1 MET cc_start: 0.7669 (pmm) cc_final: 0.5938 (tpp) REVERT: W2 41 ARG cc_start: 0.8632 (OUTLIER) cc_final: 0.8110 (mtt90) REVERT: W2 57 GLN cc_start: 0.8441 (OUTLIER) cc_final: 0.7600 (mp10) REVERT: W2 84 GLU cc_start: 0.7619 (pt0) cc_final: 0.7323 (pm20) REVERT: W2 152 LYS cc_start: 0.8101 (pptt) cc_final: 0.7894 (pptt) REVERT: X2 56 GLN cc_start: 0.8852 (OUTLIER) cc_final: 0.8606 (tt0) REVERT: X2 67 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8696 (mt) REVERT: X2 75 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8511 (mtm180) REVERT: X2 84 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7806 (mtm180) REVERT: X2 105 VAL cc_start: 0.8820 (p) cc_final: 0.8419 (t) REVERT: Y2 46 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8084 (mt) REVERT: Y2 85 TYR cc_start: 0.8879 (m-80) cc_final: 0.8577 (m-80) REVERT: a2 111 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6173 (mtt-85) REVERT: b2 17 ARG cc_start: 0.7541 (ttm-80) cc_final: 0.7332 (ttm-80) REVERT: d2 33 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7479 (ttm170) REVERT: e2 101 ILE cc_start: 0.8542 (OUTLIER) cc_final: 0.8330 (pt) REVERT: f2 29 ARG cc_start: 0.8327 (OUTLIER) cc_final: 0.8097 (ptt90) REVERT: l2 72 LYS cc_start: 0.8257 (tttt) cc_final: 0.7690 (mttt) REVERT: l2 100 LYS cc_start: 0.7991 (OUTLIER) cc_final: 0.7625 (mmtp) REVERT: m2 1 MET cc_start: 0.5217 (OUTLIER) cc_final: 0.3741 (ptt) REVERT: o2 87 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.8069 (tptm) REVERT: o2 88 GLU cc_start: 0.7253 (OUTLIER) cc_final: 0.6728 (mt-10) REVERT: p2 82 ILE cc_start: 0.8957 (OUTLIER) cc_final: 0.8648 (mm) REVERT: p2 111 ILE cc_start: 0.9505 (OUTLIER) cc_final: 0.9020 (mp) REVERT: q2 88 PHE cc_start: 0.3053 (OUTLIER) cc_final: 0.1018 (m-10) REVERT: t2 57 MET cc_start: 0.1330 (tpt) cc_final: 0.1052 (tpt) REVERT: t2 148 GLN cc_start: 0.5198 (OUTLIER) cc_final: 0.4514 (mp10) REVERT: t2 174 MET cc_start: 0.4778 (mtp) cc_final: 0.4098 (mpm) REVERT: t2 357 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.6219 (mm) REVERT: t2 368 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6105 (mtt) REVERT: t2 423 GLN cc_start: 0.6052 (OUTLIER) cc_final: 0.4826 (mp-120) outliers start: 317 outliers final: 170 residues processed: 1237 average time/residue: 2.2786 time to fit residues: 4002.9142 Evaluate side-chains 1235 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1014 time to evaluate : 6.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 15 VAL Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 154 SER Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 5 LYS Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain B2 residue 289 GLN Chi-restraints excluded: chain B2 residue 298 LEU Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 36 LEU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 72 ASP Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 267 ASN Chi-restraints excluded: chain D2 residue 289 ARG Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 40 MET Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain F2 residue 177 SER Chi-restraints excluded: chain F2 residue 219 MET Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain G2 residue 142 ARG Chi-restraints excluded: chain G2 residue 143 GLN Chi-restraints excluded: chain G2 residue 229 LYS Chi-restraints excluded: chain G2 residue 245 ARG Chi-restraints excluded: chain G2 residue 254 THR Chi-restraints excluded: chain G2 residue 300 VAL Chi-restraints excluded: chain H2 residue 66 GLU Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 162 ARG Chi-restraints excluded: chain I2 residue 169 LYS Chi-restraints excluded: chain I2 residue 213 HIS Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain J2 residue 57 VAL Chi-restraints excluded: chain J2 residue 115 LEU Chi-restraints excluded: chain J2 residue 163 MET Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain K2 residue 145 LYS Chi-restraints excluded: chain K2 residue 148 THR Chi-restraints excluded: chain K2 residue 163 LYS Chi-restraints excluded: chain K2 residue 164 GLU Chi-restraints excluded: chain K2 residue 207 VAL Chi-restraints excluded: chain L2 residue 57 LEU Chi-restraints excluded: chain L2 residue 59 ASP Chi-restraints excluded: chain L2 residue 104 MET Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 155 VAL Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 49 ARG Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 195 VAL Chi-restraints excluded: chain O2 residue 14 SER Chi-restraints excluded: chain O2 residue 24 VAL Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 43 LYS Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 128 ARG Chi-restraints excluded: chain O2 residue 142 SER Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 76 GLU Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 138 LEU Chi-restraints excluded: chain P2 residue 147 GLU Chi-restraints excluded: chain P2 residue 158 THR Chi-restraints excluded: chain P2 residue 175 GLU Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 16 ARG Chi-restraints excluded: chain Q2 residue 31 GLU Chi-restraints excluded: chain Q2 residue 40 GLN Chi-restraints excluded: chain Q2 residue 71 ARG Chi-restraints excluded: chain Q2 residue 93 VAL Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 54 MET Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 82 LEU Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain R2 residue 135 SER Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 106 LEU Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain T2 residue 103 VAL Chi-restraints excluded: chain T2 residue 108 GLU Chi-restraints excluded: chain U2 residue 64 THR Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 74 LYS Chi-restraints excluded: chain U2 residue 87 SER Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 3 VAL Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 41 ARG Chi-restraints excluded: chain W2 residue 57 GLN Chi-restraints excluded: chain W2 residue 95 THR Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 56 GLN Chi-restraints excluded: chain X2 residue 67 ILE Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 84 ARG Chi-restraints excluded: chain X2 residue 104 VAL Chi-restraints excluded: chain Y2 residue 26 VAL Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 61 LYS Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Y2 residue 100 VAL Chi-restraints excluded: chain Z2 residue 38 MET Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 140 VAL Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 111 ARG Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain b2 residue 91 VAL Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain d2 residue 91 CYS Chi-restraints excluded: chain e2 residue 67 THR Chi-restraints excluded: chain e2 residue 101 ILE Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 29 ARG Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain f2 residue 87 VAL Chi-restraints excluded: chain g2 residue 7 ARG Chi-restraints excluded: chain g2 residue 16 GLU Chi-restraints excluded: chain g2 residue 36 VAL Chi-restraints excluded: chain g2 residue 82 ASP Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain g2 residue 103 LYS Chi-restraints excluded: chain h2 residue 12 ASN Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 22 SER Chi-restraints excluded: chain h2 residue 25 ARG Chi-restraints excluded: chain h2 residue 64 SER Chi-restraints excluded: chain h2 residue 77 VAL Chi-restraints excluded: chain h2 residue 92 SER Chi-restraints excluded: chain i2 residue 6 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain l2 residue 100 LYS Chi-restraints excluded: chain m2 residue 1 MET Chi-restraints excluded: chain n2 residue 79 SER Chi-restraints excluded: chain o2 residue 16 THR Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 59 SER Chi-restraints excluded: chain o2 residue 81 SER Chi-restraints excluded: chain o2 residue 87 LYS Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain q2 residue 47 LEU Chi-restraints excluded: chain q2 residue 88 PHE Chi-restraints excluded: chain q2 residue 167 VAL Chi-restraints excluded: chain r2 residue 98 ILE Chi-restraints excluded: chain r2 residue 129 ILE Chi-restraints excluded: chain s2 residue 939 ILE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1020 LEU Chi-restraints excluded: chain s2 residue 1026 THR Chi-restraints excluded: chain s2 residue 1113 ASP Chi-restraints excluded: chain s2 residue 1171 LEU Chi-restraints excluded: chain s2 residue 1215 VAL Chi-restraints excluded: chain s2 residue 1286 VAL Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 145 VAL Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 222 SER Chi-restraints excluded: chain t2 residue 233 LEU Chi-restraints excluded: chain t2 residue 237 GLU Chi-restraints excluded: chain t2 residue 268 LEU Chi-restraints excluded: chain t2 residue 354 THR Chi-restraints excluded: chain t2 residue 357 LEU Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 423 GLN Chi-restraints excluded: chain t2 residue 430 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 1044 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 617 optimal weight: 0.8980 chunk 791 optimal weight: 0.9980 chunk 613 optimal weight: 4.9990 chunk 912 optimal weight: 2.9990 chunk 605 optimal weight: 3.9990 chunk 1079 optimal weight: 0.0980 chunk 675 optimal weight: 6.9990 chunk 658 optimal weight: 5.9990 chunk 498 optimal weight: 0.0370 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 138 GLN C2 50 GLN D2 291 GLN I2 177 ASN J2 23 ASN L2 33 GLN M2 37 HIS O2 25 HIS ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 69 GLN S2 112 ASN T2 41 GLN ** T2 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z2 120 GLN a2 61 ASN c2 121 ASN d2 117 GLN d2 126 ASN g2 20 GLN g2 65 GLN g2 108 GLN h2 36 HIS k2 25 GLN k2 38 ASN n2 45 GLN s21023 HIS s21268 HIS t2 107 ASN ** t2 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u2 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 153880 Z= 0.143 Angle : 0.547 13.053 226179 Z= 0.282 Chirality : 0.035 0.297 28142 Planarity : 0.004 0.056 14420 Dihedral : 24.074 179.425 69034 Min Nonbonded Distance : 1.220 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.11 % Rotamer: Outliers : 3.31 % Allowed : 19.92 % Favored : 76.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.10), residues: 7480 helix: 0.85 (0.10), residues: 2874 sheet: -0.31 (0.16), residues: 1005 loop : -0.52 (0.10), residues: 3601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPq2 9 HIS 0.007 0.001 HISK2 67 PHE 0.022 0.001 PHEs21016 TYR 0.024 0.001 TYRT2 90 ARG 0.012 0.000 ARGC2 350 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1301 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1085 time to evaluate : 7.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 144 LYS cc_start: 0.7922 (OUTLIER) cc_final: 0.6925 (mmtp) REVERT: A2 245 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7700 (tmt170) REVERT: B2 17 LEU cc_start: 0.7179 (OUTLIER) cc_final: 0.6973 (tp) REVERT: B2 55 HIS cc_start: 0.7405 (m170) cc_final: 0.6641 (m170) REVERT: C2 20 LYS cc_start: 0.7902 (mmmt) cc_final: 0.7314 (mttp) REVERT: D2 212 MET cc_start: 0.7812 (ttm) cc_final: 0.7494 (mtp) REVERT: D2 291 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.6858 (tt0) REVERT: E2 117 ARG cc_start: 0.8292 (ptp90) cc_final: 0.7768 (ptt-90) REVERT: E2 252 ASP cc_start: 0.8130 (m-30) cc_final: 0.7677 (m-30) REVERT: F2 40 MET cc_start: 0.7337 (OUTLIER) cc_final: 0.6974 (mmm) REVERT: G2 86 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5603 (tm-30) REVERT: I2 128 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8281 (mtm180) REVERT: I2 142 LEU cc_start: 0.8450 (tt) cc_final: 0.7800 (mt) REVERT: I2 213 HIS cc_start: 0.8252 (OUTLIER) cc_final: 0.7195 (m-70) REVERT: J2 28 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: J2 163 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: K2 118 LYS cc_start: 0.8398 (OUTLIER) cc_final: 0.7962 (mtpt) REVERT: K2 136 LYS cc_start: 0.6825 (mptt) cc_final: 0.6546 (ttpt) REVERT: K2 164 GLU cc_start: 0.7818 (mt-10) cc_final: 0.7281 (mt-10) REVERT: K2 165 LYS cc_start: 0.7618 (tttt) cc_final: 0.7204 (tttt) REVERT: L2 98 ARG cc_start: 0.8434 (ttm-80) cc_final: 0.8216 (ttp-110) REVERT: N2 159 LYS cc_start: 0.8368 (ttpp) cc_final: 0.7855 (ttmt) REVERT: N2 173 GLN cc_start: 0.8778 (OUTLIER) cc_final: 0.7864 (tm-30) REVERT: N2 180 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7930 (tp40) REVERT: O2 13 LYS cc_start: 0.8168 (mtpt) cc_final: 0.7947 (mtpt) REVERT: P2 14 ARG cc_start: 0.8142 (OUTLIER) cc_final: 0.7261 (ptt90) REVERT: P2 147 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8161 (tp30) REVERT: P2 158 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8250 (p) REVERT: Q2 3 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: Q2 31 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6951 (mm-30) REVERT: Q2 71 ARG cc_start: 0.7682 (mpt180) cc_final: 0.7450 (mpt180) REVERT: R2 29 ARG cc_start: 0.8473 (OUTLIER) cc_final: 0.7630 (ttp-170) REVERT: R2 74 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7638 (ptp90) REVERT: R2 143 LYS cc_start: 0.8776 (mtpp) cc_final: 0.8541 (mtpm) REVERT: S2 79 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: S2 137 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.7473 (pt0) REVERT: T2 47 ILE cc_start: 0.7805 (mp) cc_final: 0.7580 (mp) REVERT: T2 94 ASN cc_start: 0.6537 (m110) cc_final: 0.6006 (t0) REVERT: U2 18 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8379 (mp) REVERT: U2 71 GLU cc_start: 0.8011 (pm20) cc_final: 0.7772 (pm20) REVERT: U2 72 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8632 (mt) REVERT: V2 1 MET cc_start: 0.7528 (pmm) cc_final: 0.5829 (mmt) REVERT: W2 57 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: W2 84 GLU cc_start: 0.7586 (pt0) cc_final: 0.7244 (pm20) REVERT: W2 85 SER cc_start: 0.8920 (t) cc_final: 0.8696 (m) REVERT: W2 111 GLN cc_start: 0.8072 (mm-40) cc_final: 0.7760 (mm110) REVERT: W2 152 LYS cc_start: 0.8108 (pptt) cc_final: 0.7883 (pptt) REVERT: X2 105 VAL cc_start: 0.8746 (p) cc_final: 0.8399 (t) REVERT: Y2 46 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8167 (mt) REVERT: Y2 85 TYR cc_start: 0.8892 (m-80) cc_final: 0.8628 (m-80) REVERT: Y2 109 LYS cc_start: 0.8222 (mmpt) cc_final: 0.7816 (mptp) REVERT: a2 111 ARG cc_start: 0.6657 (OUTLIER) cc_final: 0.6147 (mtt-85) REVERT: b2 17 ARG cc_start: 0.7488 (ttm-80) cc_final: 0.7015 (ttm-80) REVERT: c2 55 LYS cc_start: 0.8377 (ttmm) cc_final: 0.7970 (tppt) REVERT: d2 33 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7350 (ttm170) REVERT: e2 101 ILE cc_start: 0.8213 (OUTLIER) cc_final: 0.7875 (pt) REVERT: f2 29 ARG cc_start: 0.8273 (OUTLIER) cc_final: 0.8063 (ptt90) REVERT: g2 105 LYS cc_start: 0.8809 (OUTLIER) cc_final: 0.8310 (mppt) REVERT: h2 59 GLU cc_start: 0.8342 (tp30) cc_final: 0.8005 (tp30) REVERT: l2 72 LYS cc_start: 0.8150 (tttt) cc_final: 0.7624 (mttt) REVERT: l2 80 ARG cc_start: 0.7748 (mtp85) cc_final: 0.7430 (mtp85) REVERT: m2 17 ARG cc_start: 0.8285 (mtt180) cc_final: 0.8046 (mtm-85) REVERT: o2 88 GLU cc_start: 0.7258 (OUTLIER) cc_final: 0.6688 (mt-10) REVERT: o2 89 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6240 (mt) REVERT: p2 82 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8544 (mm) REVERT: q2 61 MET cc_start: 0.5034 (OUTLIER) cc_final: 0.3903 (mtt) REVERT: q2 88 PHE cc_start: 0.2938 (OUTLIER) cc_final: 0.1245 (m-10) REVERT: t2 52 LYS cc_start: 0.3910 (OUTLIER) cc_final: 0.3641 (tmtp) REVERT: t2 174 MET cc_start: 0.4675 (mtp) cc_final: 0.4166 (mpt) REVERT: t2 224 PRO cc_start: 0.4620 (Cg_endo) cc_final: 0.4403 (Cg_exo) REVERT: t2 368 MET cc_start: 0.6688 (OUTLIER) cc_final: 0.6058 (mtt) REVERT: t2 423 GLN cc_start: 0.5960 (OUTLIER) cc_final: 0.4710 (mp-120) outliers start: 216 outliers final: 99 residues processed: 1207 average time/residue: 2.2411 time to fit residues: 3861.5139 Evaluate side-chains 1186 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1050 time to evaluate : 7.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 17 LEU Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 289 ARG Chi-restraints excluded: chain D2 residue 291 GLN Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 260 ILE Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 40 MET Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain H2 residue 8 GLN Chi-restraints excluded: chain H2 residue 66 GLU Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain I2 residue 213 HIS Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain J2 residue 163 MET Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 64 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 43 THR Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain N2 residue 195 VAL Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 103 GLU Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 147 GLU Chi-restraints excluded: chain P2 residue 158 THR Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 31 GLU Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 127 GLN Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain T2 residue 73 THR Chi-restraints excluded: chain U2 residue 18 LEU Chi-restraints excluded: chain U2 residue 64 THR Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 57 GLN Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 104 VAL Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 100 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 111 ARG Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain e2 residue 101 ILE Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 29 ARG Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain f2 residue 87 VAL Chi-restraints excluded: chain g2 residue 7 ARG Chi-restraints excluded: chain g2 residue 29 SER Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain g2 residue 105 LYS Chi-restraints excluded: chain g2 residue 116 LEU Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 22 SER Chi-restraints excluded: chain h2 residue 77 VAL Chi-restraints excluded: chain h2 residue 92 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain j2 residue 45 LEU Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain o2 residue 16 THR Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain q2 residue 47 LEU Chi-restraints excluded: chain q2 residue 61 MET Chi-restraints excluded: chain q2 residue 88 PHE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1020 LEU Chi-restraints excluded: chain s2 residue 1286 VAL Chi-restraints excluded: chain t2 residue 52 LYS Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 96 VAL Chi-restraints excluded: chain t2 residue 145 VAL Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 354 THR Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Chi-restraints excluded: chain t2 residue 423 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 667 optimal weight: 3.9990 chunk 431 optimal weight: 0.0670 chunk 644 optimal weight: 5.9990 chunk 325 optimal weight: 8.9990 chunk 212 optimal weight: 8.9990 chunk 209 optimal weight: 10.0000 chunk 686 optimal weight: 7.9990 chunk 735 optimal weight: 4.9990 chunk 533 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 848 optimal weight: 0.9980 overall best weight: 2.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 138 GLN C2 50 GLN ** E2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I2 177 ASN J2 23 ASN K2 115 GLN L2 33 GLN M2 37 HIS P2 21 GLN ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 69 GLN S2 112 ASN T2 41 GLN ** T2 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 86 GLN Z2 120 GLN a2 61 ASN c2 121 ASN d2 34 ASN d2 117 GLN d2 126 ASN e2 20 ASN g2 20 GLN g2 65 GLN g2 108 GLN h2 36 HIS k2 25 GLN k2 38 ASN l2 58 GLN s21023 HIS t2 107 ASN ** u2 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 153880 Z= 0.247 Angle : 0.589 20.124 226179 Z= 0.305 Chirality : 0.038 0.358 28142 Planarity : 0.005 0.057 14420 Dihedral : 24.040 179.943 69034 Min Nonbonded Distance : 1.114 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.52 % Favored : 96.44 % Rotamer: Outliers : 3.55 % Allowed : 20.18 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7480 helix: 0.84 (0.10), residues: 2873 sheet: -0.35 (0.16), residues: 1011 loop : -0.50 (0.10), residues: 3596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRPM2 120 HIS 0.010 0.001 HISK2 67 PHE 0.017 0.001 PHEs21308 TYR 0.027 0.002 TYRT2 90 ARG 0.012 0.000 ARGC2 350 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1052 time to evaluate : 7.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 144 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.6964 (mmtp) REVERT: A2 245 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7767 (tmt170) REVERT: B2 17 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6896 (tp) REVERT: B2 55 HIS cc_start: 0.7484 (m170) cc_final: 0.6718 (m170) REVERT: C2 14 LYS cc_start: 0.8247 (OUTLIER) cc_final: 0.7924 (mttm) REVERT: D2 212 MET cc_start: 0.7793 (ttm) cc_final: 0.7413 (mtp) REVERT: E2 117 ARG cc_start: 0.8348 (ptp90) cc_final: 0.7779 (ptt-90) REVERT: E2 252 ASP cc_start: 0.8142 (m-30) cc_final: 0.7701 (m-30) REVERT: G2 86 GLU cc_start: 0.6158 (tm-30) cc_final: 0.5810 (tm-30) REVERT: H2 80 MET cc_start: 0.8409 (mtp) cc_final: 0.8168 (mtm) REVERT: I2 128 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8399 (mtm180) REVERT: I2 142 LEU cc_start: 0.8458 (tt) cc_final: 0.7790 (mt) REVERT: I2 213 HIS cc_start: 0.8259 (OUTLIER) cc_final: 0.7174 (m-70) REVERT: J2 163 MET cc_start: 0.8940 (OUTLIER) cc_final: 0.8444 (mtt) REVERT: J2 175 LEU cc_start: 0.7444 (OUTLIER) cc_final: 0.6871 (pp) REVERT: K2 118 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7997 (mtpt) REVERT: K2 164 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7267 (mt-10) REVERT: K2 165 LYS cc_start: 0.7655 (tttt) cc_final: 0.7320 (tttt) REVERT: N2 159 LYS cc_start: 0.8359 (ttpp) cc_final: 0.7842 (ttmt) REVERT: N2 173 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8013 (tm-30) REVERT: N2 180 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7964 (tp40) REVERT: O2 13 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7971 (mtpt) REVERT: P2 14 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7432 (ptt90) REVERT: P2 91 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7725 (ptt-90) REVERT: P2 147 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8242 (tp30) REVERT: Q2 3 MET cc_start: 0.8632 (OUTLIER) cc_final: 0.7538 (tmm) REVERT: Q2 71 ARG cc_start: 0.7849 (mpt180) cc_final: 0.7445 (mpt180) REVERT: R2 29 ARG cc_start: 0.8500 (OUTLIER) cc_final: 0.7676 (ttp-170) REVERT: R2 74 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7668 (ptp90) REVERT: R2 143 LYS cc_start: 0.8797 (mtpp) cc_final: 0.8553 (mtpm) REVERT: S2 79 GLN cc_start: 0.9070 (OUTLIER) cc_final: 0.8107 (tm-30) REVERT: S2 137 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7453 (pt0) REVERT: T2 94 ASN cc_start: 0.6736 (m110) cc_final: 0.6122 (t0) REVERT: U2 71 GLU cc_start: 0.8039 (pm20) cc_final: 0.7798 (pm20) REVERT: U2 72 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8635 (mt) REVERT: U2 74 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8150 (mtmt) REVERT: V2 1 MET cc_start: 0.7599 (pmm) cc_final: 0.5860 (mmt) REVERT: W2 57 GLN cc_start: 0.8401 (OUTLIER) cc_final: 0.7579 (mp10) REVERT: W2 84 GLU cc_start: 0.7635 (pt0) cc_final: 0.7321 (pm20) REVERT: W2 111 GLN cc_start: 0.8134 (mm-40) cc_final: 0.7815 (mm110) REVERT: W2 152 LYS cc_start: 0.8071 (pptt) cc_final: 0.7838 (pptt) REVERT: X2 75 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8462 (mtm180) REVERT: X2 105 VAL cc_start: 0.8784 (p) cc_final: 0.8402 (t) REVERT: Y2 46 ILE cc_start: 0.8649 (OUTLIER) cc_final: 0.8058 (mt) REVERT: Y2 85 TYR cc_start: 0.8882 (m-80) cc_final: 0.8614 (m-80) REVERT: Y2 109 LYS cc_start: 0.8321 (mmpt) cc_final: 0.7874 (mptp) REVERT: a2 111 ARG cc_start: 0.6671 (OUTLIER) cc_final: 0.6173 (mtt-85) REVERT: d2 33 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7493 (ttm170) REVERT: f2 29 ARG cc_start: 0.8317 (OUTLIER) cc_final: 0.8089 (ptt90) REVERT: h2 59 GLU cc_start: 0.8394 (tp30) cc_final: 0.8038 (tp30) REVERT: l2 72 LYS cc_start: 0.8220 (tttt) cc_final: 0.7651 (mttt) REVERT: o2 87 LYS cc_start: 0.8242 (OUTLIER) cc_final: 0.8000 (tptm) REVERT: o2 88 GLU cc_start: 0.7303 (OUTLIER) cc_final: 0.6754 (mt-10) REVERT: o2 89 LEU cc_start: 0.7371 (OUTLIER) cc_final: 0.6314 (mt) REVERT: p2 82 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8595 (mm) REVERT: p2 111 ILE cc_start: 0.9462 (OUTLIER) cc_final: 0.8999 (mp) REVERT: q2 61 MET cc_start: 0.5018 (OUTLIER) cc_final: 0.4043 (mtt) REVERT: q2 88 PHE cc_start: 0.2915 (OUTLIER) cc_final: 0.1186 (m-10) REVERT: s2 1184 LEU cc_start: 0.2944 (OUTLIER) cc_final: 0.2703 (tt) REVERT: t2 92 LEU cc_start: 0.2377 (OUTLIER) cc_final: 0.1585 (mt) REVERT: t2 135 ASN cc_start: 0.5858 (p0) cc_final: 0.5552 (p0) REVERT: t2 174 MET cc_start: 0.4779 (mtp) cc_final: 0.4191 (mpt) REVERT: t2 368 MET cc_start: 0.6720 (OUTLIER) cc_final: 0.6081 (mtt) outliers start: 232 outliers final: 127 residues processed: 1191 average time/residue: 2.2361 time to fit residues: 3805.7224 Evaluate side-chains 1193 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1030 time to evaluate : 7.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 17 LEU Chi-restraints excluded: chain B2 residue 56 ILE Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain C2 residue 14 LYS Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 36 LEU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 72 ASP Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 260 ILE Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain G2 residue 142 ARG Chi-restraints excluded: chain G2 residue 143 GLN Chi-restraints excluded: chain H2 residue 8 GLN Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain I2 residue 213 HIS Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain J2 residue 163 MET Chi-restraints excluded: chain J2 residue 175 LEU Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain L2 residue 57 LEU Chi-restraints excluded: chain L2 residue 59 ASP Chi-restraints excluded: chain L2 residue 105 THR Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 43 THR Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain N2 residue 195 VAL Chi-restraints excluded: chain O2 residue 14 SER Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 147 GLU Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 54 MET Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain S2 residue 29 THR Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 127 GLN Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain T2 residue 73 THR Chi-restraints excluded: chain U2 residue 64 THR Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 74 LYS Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 57 GLN Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 104 VAL Chi-restraints excluded: chain X2 residue 112 ASP Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Y2 residue 100 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 140 VAL Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 111 ARG Chi-restraints excluded: chain a2 residue 112 ILE Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain b2 residue 34 SER Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain c2 residue 86 VAL Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain e2 residue 105 LEU Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 29 ARG Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain f2 residue 87 VAL Chi-restraints excluded: chain g2 residue 7 ARG Chi-restraints excluded: chain g2 residue 36 VAL Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain h2 residue 12 ASN Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 22 SER Chi-restraints excluded: chain h2 residue 54 GLU Chi-restraints excluded: chain h2 residue 77 VAL Chi-restraints excluded: chain h2 residue 92 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain j2 residue 60 LEU Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain o2 residue 16 THR Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 59 SER Chi-restraints excluded: chain o2 residue 87 LYS Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain q2 residue 47 LEU Chi-restraints excluded: chain q2 residue 61 MET Chi-restraints excluded: chain q2 residue 88 PHE Chi-restraints excluded: chain q2 residue 167 VAL Chi-restraints excluded: chain r2 residue 129 ILE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1020 LEU Chi-restraints excluded: chain s2 residue 1184 LEU Chi-restraints excluded: chain s2 residue 1286 VAL Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 92 LEU Chi-restraints excluded: chain t2 residue 96 VAL Chi-restraints excluded: chain t2 residue 145 VAL Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 268 LEU Chi-restraints excluded: chain t2 residue 275 THR Chi-restraints excluded: chain t2 residue 347 THR Chi-restraints excluded: chain t2 residue 354 THR Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 981 optimal weight: 10.0000 chunk 1034 optimal weight: 0.6980 chunk 943 optimal weight: 0.9990 chunk 1005 optimal weight: 10.0000 chunk 1033 optimal weight: 0.9990 chunk 605 optimal weight: 6.9990 chunk 438 optimal weight: 7.9990 chunk 789 optimal weight: 9.9990 chunk 308 optimal weight: 8.9990 chunk 909 optimal weight: 5.9990 chunk 951 optimal weight: 0.4980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B2 138 GLN D2 291 GLN G2 96 GLN I2 177 ASN J2 23 ASN L2 33 GLN M2 37 HIS ** P2 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 112 ASN ** T2 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 86 GLN Z2 120 GLN c2 121 ASN d2 92 ASN d2 117 GLN d2 126 ASN g2 20 GLN g2 65 GLN h2 36 HIS k2 25 GLN k2 38 ASN l2 58 GLN s2 965 HIS s21023 HIS t2 107 ASN t2 229 ASN ** u2 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 153880 Z= 0.199 Angle : 0.573 18.632 226179 Z= 0.297 Chirality : 0.036 0.325 28142 Planarity : 0.005 0.082 14420 Dihedral : 24.051 179.856 69034 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 3.19 % Allowed : 20.81 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.10), residues: 7480 helix: 0.86 (0.10), residues: 2873 sheet: -0.36 (0.16), residues: 1023 loop : -0.46 (0.10), residues: 3584 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPM2 120 HIS 0.008 0.001 HISK2 67 PHE 0.017 0.001 PHEs21016 TYR 0.029 0.002 TYRe2 106 ARG 0.013 0.000 ARGC2 350 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1258 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1050 time to evaluate : 7.616 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 144 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.6972 (mmtp) REVERT: A2 245 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7749 (tmt170) REVERT: B2 55 HIS cc_start: 0.7433 (m170) cc_final: 0.6666 (m170) REVERT: C2 20 LYS cc_start: 0.7835 (mmmt) cc_final: 0.7229 (mttp) REVERT: D2 212 MET cc_start: 0.7767 (ttm) cc_final: 0.7391 (mtp) REVERT: D2 291 GLN cc_start: 0.7177 (OUTLIER) cc_final: 0.6925 (tt0) REVERT: E2 117 ARG cc_start: 0.8315 (ptp90) cc_final: 0.7754 (ptt-90) REVERT: E2 252 ASP cc_start: 0.8136 (m-30) cc_final: 0.7662 (m-30) REVERT: G2 86 GLU cc_start: 0.6150 (tm-30) cc_final: 0.5797 (tm-30) REVERT: H2 80 MET cc_start: 0.8410 (mtp) cc_final: 0.8165 (mtm) REVERT: I2 128 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8350 (mtm180) REVERT: I2 142 LEU cc_start: 0.8461 (tt) cc_final: 0.7751 (mt) REVERT: I2 213 HIS cc_start: 0.8258 (OUTLIER) cc_final: 0.7176 (m-70) REVERT: J2 28 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: K2 118 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.7980 (mtpt) REVERT: K2 164 GLU cc_start: 0.7813 (mt-10) cc_final: 0.7253 (mt-10) REVERT: K2 165 LYS cc_start: 0.7672 (tttt) cc_final: 0.7358 (tttt) REVERT: M2 24 ARG cc_start: 0.8452 (mtp180) cc_final: 0.7945 (mtp180) REVERT: N2 159 LYS cc_start: 0.8372 (ttpp) cc_final: 0.7865 (ttmt) REVERT: N2 173 GLN cc_start: 0.8859 (OUTLIER) cc_final: 0.8009 (tm-30) REVERT: N2 180 GLN cc_start: 0.8189 (tp-100) cc_final: 0.7971 (tp40) REVERT: O2 13 LYS cc_start: 0.8223 (mtpt) cc_final: 0.7991 (mtpt) REVERT: P2 14 ARG cc_start: 0.8248 (OUTLIER) cc_final: 0.7396 (ptt90) REVERT: P2 91 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7725 (ptt-90) REVERT: P2 147 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8228 (tp30) REVERT: Q2 3 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.7535 (tmm) REVERT: Q2 71 ARG cc_start: 0.7818 (mpt180) cc_final: 0.7406 (mpt180) REVERT: Q2 151 ARG cc_start: 0.6787 (tmm160) cc_final: 0.6413 (ppt90) REVERT: R2 29 ARG cc_start: 0.8492 (OUTLIER) cc_final: 0.7666 (ttp-170) REVERT: R2 74 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7653 (ptp90) REVERT: R2 143 LYS cc_start: 0.8778 (mtpp) cc_final: 0.8539 (mtpm) REVERT: S2 79 GLN cc_start: 0.9050 (OUTLIER) cc_final: 0.8084 (tm-30) REVERT: S2 137 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7495 (pt0) REVERT: T2 34 MET cc_start: 0.6975 (tmt) cc_final: 0.6756 (tmm) REVERT: T2 94 ASN cc_start: 0.6622 (m110) cc_final: 0.6062 (t0) REVERT: U2 18 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8379 (mp) REVERT: U2 71 GLU cc_start: 0.8019 (pm20) cc_final: 0.7776 (pm20) REVERT: U2 72 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8631 (mt) REVERT: V2 1 MET cc_start: 0.7595 (pmm) cc_final: 0.5856 (mmt) REVERT: W2 67 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7514 (ptp-110) REVERT: W2 84 GLU cc_start: 0.7615 (pt0) cc_final: 0.7302 (pm20) REVERT: W2 111 GLN cc_start: 0.8128 (mm-40) cc_final: 0.7803 (mm110) REVERT: W2 152 LYS cc_start: 0.8063 (pptt) cc_final: 0.7836 (pptt) REVERT: X2 75 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8444 (mtm180) REVERT: X2 105 VAL cc_start: 0.8779 (p) cc_final: 0.8409 (t) REVERT: Y2 46 ILE cc_start: 0.8694 (OUTLIER) cc_final: 0.8095 (mt) REVERT: Y2 85 TYR cc_start: 0.8876 (m-80) cc_final: 0.8625 (m-80) REVERT: Y2 109 LYS cc_start: 0.8322 (mmpt) cc_final: 0.7874 (mptp) REVERT: a2 63 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7179 (ttmm) REVERT: a2 111 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6171 (mtt-85) REVERT: b2 17 ARG cc_start: 0.7707 (ttm-80) cc_final: 0.6992 (ttm-80) REVERT: d2 33 ARG cc_start: 0.7889 (OUTLIER) cc_final: 0.7482 (ttm170) REVERT: f2 29 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.8072 (ptt90) REVERT: h2 59 GLU cc_start: 0.8388 (tp30) cc_final: 0.8033 (tp30) REVERT: j2 67 LYS cc_start: 0.7763 (tmtm) cc_final: 0.7218 (tptm) REVERT: l2 72 LYS cc_start: 0.8197 (tttt) cc_final: 0.7640 (mttt) REVERT: o2 87 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7990 (tptm) REVERT: o2 88 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.6748 (mt-10) REVERT: o2 89 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6266 (mt) REVERT: p2 82 ILE cc_start: 0.8938 (OUTLIER) cc_final: 0.8600 (mm) REVERT: p2 111 ILE cc_start: 0.9454 (OUTLIER) cc_final: 0.8996 (mp) REVERT: q2 61 MET cc_start: 0.4997 (OUTLIER) cc_final: 0.4038 (mtt) REVERT: q2 88 PHE cc_start: 0.2899 (OUTLIER) cc_final: 0.1174 (m-10) REVERT: s2 1184 LEU cc_start: 0.2919 (OUTLIER) cc_final: 0.2667 (tt) REVERT: t2 92 LEU cc_start: 0.2315 (OUTLIER) cc_final: 0.1534 (mt) REVERT: t2 135 ASN cc_start: 0.5852 (p0) cc_final: 0.5529 (p0) REVERT: t2 174 MET cc_start: 0.4757 (mtp) cc_final: 0.4191 (mpt) REVERT: t2 368 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.6061 (mtt) outliers start: 208 outliers final: 133 residues processed: 1176 average time/residue: 2.2012 time to fit residues: 3703.5173 Evaluate side-chains 1207 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 168 poor density : 1039 time to evaluate : 7.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 56 ILE Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 36 LEU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 72 ASP Chi-restraints excluded: chain D2 residue 75 VAL Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain D2 residue 291 GLN Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 260 ILE Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain G2 residue 142 ARG Chi-restraints excluded: chain H2 residue 8 GLN Chi-restraints excluded: chain H2 residue 66 GLU Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain I2 residue 213 HIS Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 64 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain K2 residue 207 VAL Chi-restraints excluded: chain L2 residue 59 ASP Chi-restraints excluded: chain L2 residue 105 THR Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain N2 residue 195 VAL Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 103 GLU Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 147 GLU Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain S2 residue 29 THR Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 127 GLN Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain T2 residue 73 THR Chi-restraints excluded: chain T2 residue 103 VAL Chi-restraints excluded: chain U2 residue 18 LEU Chi-restraints excluded: chain U2 residue 64 THR Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 67 ARG Chi-restraints excluded: chain W2 residue 85 SER Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain W2 residue 118 ASP Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 104 VAL Chi-restraints excluded: chain X2 residue 112 ASP Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 86 SER Chi-restraints excluded: chain Y2 residue 100 VAL Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 140 VAL Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 63 LYS Chi-restraints excluded: chain a2 residue 111 ARG Chi-restraints excluded: chain a2 residue 112 ILE Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain b2 residue 34 SER Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain c2 residue 86 VAL Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain e2 residue 105 LEU Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 29 ARG Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain f2 residue 87 VAL Chi-restraints excluded: chain g2 residue 36 VAL Chi-restraints excluded: chain g2 residue 82 ASP Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 22 SER Chi-restraints excluded: chain h2 residue 54 GLU Chi-restraints excluded: chain h2 residue 92 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain i2 residue 82 THR Chi-restraints excluded: chain j2 residue 60 LEU Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain o2 residue 16 THR Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 81 SER Chi-restraints excluded: chain o2 residue 87 LYS Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain q2 residue 47 LEU Chi-restraints excluded: chain q2 residue 60 MET Chi-restraints excluded: chain q2 residue 61 MET Chi-restraints excluded: chain q2 residue 88 PHE Chi-restraints excluded: chain q2 residue 167 VAL Chi-restraints excluded: chain r2 residue 80 LEU Chi-restraints excluded: chain r2 residue 98 ILE Chi-restraints excluded: chain s2 residue 993 VAL Chi-restraints excluded: chain s2 residue 1020 LEU Chi-restraints excluded: chain s2 residue 1184 LEU Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 92 LEU Chi-restraints excluded: chain t2 residue 96 VAL Chi-restraints excluded: chain t2 residue 145 VAL Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 222 SER Chi-restraints excluded: chain t2 residue 268 LEU Chi-restraints excluded: chain t2 residue 275 THR Chi-restraints excluded: chain t2 residue 347 THR Chi-restraints excluded: chain t2 residue 354 THR Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 1002 optimal weight: 1.9990 chunk 660 optimal weight: 3.9990 chunk 1063 optimal weight: 0.9980 chunk 649 optimal weight: 5.9990 chunk 504 optimal weight: 2.9990 chunk 739 optimal weight: 0.7980 chunk 1115 optimal weight: 7.9990 chunk 1026 optimal weight: 0.9990 chunk 888 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 686 optimal weight: 6.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I2 177 ASN J2 23 ASN K2 67 HIS L2 33 GLN M2 37 HIS ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S2 112 ASN ** T2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 86 GLN Z2 120 GLN c2 121 ASN d2 117 GLN d2 126 ASN ** f2 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g2 20 GLN g2 65 GLN h2 36 HIS ** j2 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k2 25 GLN k2 38 ASN l2 58 GLN ** r2 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s2 965 HIS s21023 HIS t2 107 ASN t2 229 ASN ** u2 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 153880 Z= 0.166 Angle : 0.558 17.519 226179 Z= 0.290 Chirality : 0.036 0.496 28142 Planarity : 0.004 0.060 14420 Dihedral : 24.045 179.792 69034 Min Nonbonded Distance : 1.138 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.32 % Favored : 96.64 % Rotamer: Outliers : 2.90 % Allowed : 21.25 % Favored : 75.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.10), residues: 7480 helix: 0.90 (0.10), residues: 2872 sheet: -0.34 (0.16), residues: 1018 loop : -0.44 (0.10), residues: 3590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRPM2 120 HIS 0.008 0.001 HISI2 147 PHE 0.019 0.001 PHEs21135 TYR 0.027 0.001 TYRT2 90 ARG 0.014 0.000 ARGC2 350 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14960 Ramachandran restraints generated. 7480 Oldfield, 0 Emsley, 7480 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1238 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1049 time to evaluate : 7.747 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A2 144 LYS cc_start: 0.7961 (OUTLIER) cc_final: 0.6942 (mmtp) REVERT: A2 245 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7734 (tmt170) REVERT: B2 17 LEU cc_start: 0.7146 (OUTLIER) cc_final: 0.6911 (tp) REVERT: B2 55 HIS cc_start: 0.7410 (m170) cc_final: 0.6644 (m170) REVERT: C2 20 LYS cc_start: 0.7808 (mmmt) cc_final: 0.7221 (mttp) REVERT: D2 212 MET cc_start: 0.7765 (ttm) cc_final: 0.7407 (mtp) REVERT: E2 117 ARG cc_start: 0.8303 (ptp90) cc_final: 0.7791 (ptt-90) REVERT: E2 252 ASP cc_start: 0.8085 (m-30) cc_final: 0.7646 (m-30) REVERT: G2 86 GLU cc_start: 0.6147 (tm-30) cc_final: 0.5675 (tm-30) REVERT: H2 80 MET cc_start: 0.8408 (mtp) cc_final: 0.8144 (mtm) REVERT: I2 128 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8340 (mtm180) REVERT: I2 142 LEU cc_start: 0.8423 (tt) cc_final: 0.7736 (mt) REVERT: J2 28 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7223 (mp0) REVERT: J2 163 MET cc_start: 0.8913 (mtp) cc_final: 0.8486 (mtt) REVERT: K2 118 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.7979 (mtpt) REVERT: K2 164 GLU cc_start: 0.7817 (mt-10) cc_final: 0.7254 (mt-10) REVERT: K2 165 LYS cc_start: 0.7714 (tttt) cc_final: 0.7396 (tttt) REVERT: M2 24 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7935 (mtp180) REVERT: N2 159 LYS cc_start: 0.8365 (ttpp) cc_final: 0.7863 (ttmt) REVERT: N2 173 GLN cc_start: 0.8843 (OUTLIER) cc_final: 0.7997 (tm-30) REVERT: N2 180 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7975 (tp40) REVERT: O2 13 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7998 (mtpt) REVERT: P2 14 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7370 (ptt90) REVERT: P2 91 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7731 (ptt-90) REVERT: P2 147 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8215 (tp30) REVERT: Q2 3 MET cc_start: 0.8640 (OUTLIER) cc_final: 0.7552 (tmm) REVERT: Q2 71 ARG cc_start: 0.7800 (mpt180) cc_final: 0.7402 (mpt180) REVERT: Q2 151 ARG cc_start: 0.6749 (tmm160) cc_final: 0.6205 (tmm160) REVERT: Q2 152 LYS cc_start: 0.7836 (tttp) cc_final: 0.7286 (mptm) REVERT: R2 29 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.7659 (ttp-170) REVERT: R2 74 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7636 (ptp90) REVERT: R2 143 LYS cc_start: 0.8775 (mtpp) cc_final: 0.8538 (mtpm) REVERT: S2 79 GLN cc_start: 0.9032 (OUTLIER) cc_final: 0.8054 (tm-30) REVERT: S2 137 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7485 (pt0) REVERT: T2 94 ASN cc_start: 0.6595 (m110) cc_final: 0.6081 (t0) REVERT: U2 71 GLU cc_start: 0.8010 (pm20) cc_final: 0.7767 (pm20) REVERT: U2 72 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8648 (mt) REVERT: V2 1 MET cc_start: 0.7583 (pmm) cc_final: 0.5850 (mmt) REVERT: W2 67 ARG cc_start: 0.7791 (OUTLIER) cc_final: 0.7507 (ptp-110) REVERT: W2 84 GLU cc_start: 0.7608 (pt0) cc_final: 0.7290 (pm20) REVERT: W2 85 SER cc_start: 0.8966 (OUTLIER) cc_final: 0.8711 (m) REVERT: W2 111 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7798 (mm110) REVERT: W2 152 LYS cc_start: 0.8084 (pptt) cc_final: 0.7879 (pptt) REVERT: X2 75 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8431 (mtm180) REVERT: X2 105 VAL cc_start: 0.8766 (p) cc_final: 0.8406 (t) REVERT: Y2 46 ILE cc_start: 0.8671 (OUTLIER) cc_final: 0.8073 (mt) REVERT: Y2 85 TYR cc_start: 0.8884 (m-80) cc_final: 0.8630 (m-80) REVERT: Y2 109 LYS cc_start: 0.8296 (mmpt) cc_final: 0.7858 (mptp) REVERT: a2 63 LYS cc_start: 0.7528 (OUTLIER) cc_final: 0.7184 (ttmm) REVERT: a2 111 ARG cc_start: 0.6666 (OUTLIER) cc_final: 0.6170 (mtt-85) REVERT: b2 17 ARG cc_start: 0.7668 (ttm-80) cc_final: 0.6968 (ttm-80) REVERT: b2 103 ASP cc_start: 0.6237 (OUTLIER) cc_final: 0.5745 (p0) REVERT: d2 33 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7463 (ttm170) REVERT: e2 101 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8011 (pt) REVERT: f2 29 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8073 (ptt90) REVERT: h2 59 GLU cc_start: 0.8374 (tp30) cc_final: 0.8018 (tp30) REVERT: j2 67 LYS cc_start: 0.7730 (tmtm) cc_final: 0.7188 (tptm) REVERT: l2 72 LYS cc_start: 0.8170 (tttt) cc_final: 0.7619 (mttt) REVERT: n2 82 MET cc_start: 0.9326 (OUTLIER) cc_final: 0.7866 (mmp) REVERT: o2 87 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7977 (tptm) REVERT: o2 88 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6759 (mt-10) REVERT: o2 89 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6232 (mt) REVERT: p2 82 ILE cc_start: 0.8927 (OUTLIER) cc_final: 0.8591 (mm) REVERT: p2 111 ILE cc_start: 0.9445 (OUTLIER) cc_final: 0.8995 (mp) REVERT: q2 61 MET cc_start: 0.4981 (OUTLIER) cc_final: 0.4043 (mtt) REVERT: q2 88 PHE cc_start: 0.2968 (OUTLIER) cc_final: 0.1255 (m-10) REVERT: q2 101 MET cc_start: 0.3561 (pmm) cc_final: 0.2649 (pmm) REVERT: s2 1184 LEU cc_start: 0.2903 (OUTLIER) cc_final: 0.2654 (tt) REVERT: s2 1331 ASN cc_start: 0.1964 (m-40) cc_final: 0.1311 (t0) REVERT: t2 92 LEU cc_start: 0.2403 (OUTLIER) cc_final: 0.1610 (mt) REVERT: t2 135 ASN cc_start: 0.5863 (p0) cc_final: 0.5533 (p0) REVERT: t2 174 MET cc_start: 0.4739 (mtp) cc_final: 0.4193 (mpt) REVERT: t2 368 MET cc_start: 0.6701 (OUTLIER) cc_final: 0.6060 (mtt) REVERT: t2 388 GLU cc_start: 0.5362 (mm-30) cc_final: 0.5043 (tp30) outliers start: 189 outliers final: 128 residues processed: 1153 average time/residue: 2.2443 time to fit residues: 3704.3336 Evaluate side-chains 1210 residues out of total 6528 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1045 time to evaluate : 7.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A2 residue 101 VAL Chi-restraints excluded: chain A2 residue 144 LYS Chi-restraints excluded: chain A2 residue 165 VAL Chi-restraints excluded: chain A2 residue 245 ARG Chi-restraints excluded: chain B2 residue 17 LEU Chi-restraints excluded: chain B2 residue 56 ILE Chi-restraints excluded: chain B2 residue 152 SER Chi-restraints excluded: chain B2 residue 181 MET Chi-restraints excluded: chain C2 residue 232 VAL Chi-restraints excluded: chain C2 residue 262 ASP Chi-restraints excluded: chain C2 residue 297 GLU Chi-restraints excluded: chain D2 residue 36 LEU Chi-restraints excluded: chain D2 residue 37 VAL Chi-restraints excluded: chain D2 residue 118 ILE Chi-restraints excluded: chain D2 residue 133 GLU Chi-restraints excluded: chain D2 residue 261 VAL Chi-restraints excluded: chain E2 residue 130 SER Chi-restraints excluded: chain E2 residue 197 VAL Chi-restraints excluded: chain E2 residue 260 ILE Chi-restraints excluded: chain E2 residue 290 VAL Chi-restraints excluded: chain F2 residue 82 VAL Chi-restraints excluded: chain F2 residue 101 SER Chi-restraints excluded: chain G2 residue 139 VAL Chi-restraints excluded: chain H2 residue 8 GLN Chi-restraints excluded: chain H2 residue 66 GLU Chi-restraints excluded: chain H2 residue 84 VAL Chi-restraints excluded: chain H2 residue 104 VAL Chi-restraints excluded: chain H2 residue 128 MET Chi-restraints excluded: chain I2 residue 43 VAL Chi-restraints excluded: chain I2 residue 44 ASP Chi-restraints excluded: chain I2 residue 128 ARG Chi-restraints excluded: chain I2 residue 129 VAL Chi-restraints excluded: chain J2 residue 28 GLU Chi-restraints excluded: chain J2 residue 47 THR Chi-restraints excluded: chain K2 residue 59 VAL Chi-restraints excluded: chain K2 residue 64 VAL Chi-restraints excluded: chain K2 residue 118 LYS Chi-restraints excluded: chain K2 residue 122 SER Chi-restraints excluded: chain K2 residue 148 THR Chi-restraints excluded: chain K2 residue 207 VAL Chi-restraints excluded: chain L2 residue 59 ASP Chi-restraints excluded: chain L2 residue 105 THR Chi-restraints excluded: chain L2 residue 112 VAL Chi-restraints excluded: chain L2 residue 113 MET Chi-restraints excluded: chain M2 residue 38 ARG Chi-restraints excluded: chain M2 residue 64 ILE Chi-restraints excluded: chain M2 residue 89 VAL Chi-restraints excluded: chain M2 residue 126 THR Chi-restraints excluded: chain M2 residue 182 HIS Chi-restraints excluded: chain N2 residue 27 VAL Chi-restraints excluded: chain N2 residue 173 GLN Chi-restraints excluded: chain N2 residue 174 LEU Chi-restraints excluded: chain N2 residue 195 VAL Chi-restraints excluded: chain O2 residue 36 ILE Chi-restraints excluded: chain O2 residue 91 LEU Chi-restraints excluded: chain O2 residue 103 GLU Chi-restraints excluded: chain P2 residue 14 ARG Chi-restraints excluded: chain P2 residue 20 SER Chi-restraints excluded: chain P2 residue 91 ARG Chi-restraints excluded: chain P2 residue 147 GLU Chi-restraints excluded: chain P2 residue 158 THR Chi-restraints excluded: chain Q2 residue 3 MET Chi-restraints excluded: chain Q2 residue 122 SER Chi-restraints excluded: chain R2 residue 29 ARG Chi-restraints excluded: chain R2 residue 54 MET Chi-restraints excluded: chain R2 residue 67 VAL Chi-restraints excluded: chain R2 residue 74 ARG Chi-restraints excluded: chain R2 residue 90 THR Chi-restraints excluded: chain R2 residue 107 THR Chi-restraints excluded: chain S2 residue 29 THR Chi-restraints excluded: chain S2 residue 32 ARG Chi-restraints excluded: chain S2 residue 79 GLN Chi-restraints excluded: chain S2 residue 127 GLN Chi-restraints excluded: chain S2 residue 137 GLU Chi-restraints excluded: chain S2 residue 144 ASN Chi-restraints excluded: chain T2 residue 72 VAL Chi-restraints excluded: chain T2 residue 73 THR Chi-restraints excluded: chain T2 residue 103 VAL Chi-restraints excluded: chain U2 residue 64 THR Chi-restraints excluded: chain U2 residue 72 LEU Chi-restraints excluded: chain U2 residue 138 SER Chi-restraints excluded: chain V2 residue 53 VAL Chi-restraints excluded: chain W2 residue 67 ARG Chi-restraints excluded: chain W2 residue 85 SER Chi-restraints excluded: chain W2 residue 102 VAL Chi-restraints excluded: chain W2 residue 118 ASP Chi-restraints excluded: chain X2 residue 55 VAL Chi-restraints excluded: chain X2 residue 75 ARG Chi-restraints excluded: chain X2 residue 79 VAL Chi-restraints excluded: chain X2 residue 104 VAL Chi-restraints excluded: chain X2 residue 112 ASP Chi-restraints excluded: chain Y2 residue 35 ASP Chi-restraints excluded: chain Y2 residue 46 ILE Chi-restraints excluded: chain Y2 residue 100 VAL Chi-restraints excluded: chain Z2 residue 88 VAL Chi-restraints excluded: chain Z2 residue 122 VAL Chi-restraints excluded: chain Z2 residue 140 VAL Chi-restraints excluded: chain a2 residue 4 SER Chi-restraints excluded: chain a2 residue 63 LYS Chi-restraints excluded: chain a2 residue 111 ARG Chi-restraints excluded: chain a2 residue 112 ILE Chi-restraints excluded: chain a2 residue 114 ARG Chi-restraints excluded: chain b2 residue 14 ILE Chi-restraints excluded: chain b2 residue 19 GLN Chi-restraints excluded: chain b2 residue 28 VAL Chi-restraints excluded: chain b2 residue 34 SER Chi-restraints excluded: chain b2 residue 65 MET Chi-restraints excluded: chain b2 residue 103 ASP Chi-restraints excluded: chain c2 residue 26 THR Chi-restraints excluded: chain c2 residue 86 VAL Chi-restraints excluded: chain d2 residue 33 ARG Chi-restraints excluded: chain d2 residue 57 ASN Chi-restraints excluded: chain d2 residue 87 VAL Chi-restraints excluded: chain d2 residue 89 LEU Chi-restraints excluded: chain d2 residue 91 CYS Chi-restraints excluded: chain e2 residue 101 ILE Chi-restraints excluded: chain e2 residue 105 LEU Chi-restraints excluded: chain f2 residue 25 THR Chi-restraints excluded: chain f2 residue 29 ARG Chi-restraints excluded: chain f2 residue 85 LYS Chi-restraints excluded: chain g2 residue 14 LYS Chi-restraints excluded: chain g2 residue 82 ASP Chi-restraints excluded: chain g2 residue 102 LEU Chi-restraints excluded: chain h2 residue 21 VAL Chi-restraints excluded: chain h2 residue 22 SER Chi-restraints excluded: chain h2 residue 92 SER Chi-restraints excluded: chain i2 residue 13 ASN Chi-restraints excluded: chain i2 residue 33 THR Chi-restraints excluded: chain i2 residue 58 THR Chi-restraints excluded: chain i2 residue 61 THR Chi-restraints excluded: chain j2 residue 60 LEU Chi-restraints excluded: chain l2 residue 82 VAL Chi-restraints excluded: chain n2 residue 82 MET Chi-restraints excluded: chain o2 residue 16 THR Chi-restraints excluded: chain o2 residue 26 VAL Chi-restraints excluded: chain o2 residue 52 VAL Chi-restraints excluded: chain o2 residue 87 LYS Chi-restraints excluded: chain o2 residue 88 GLU Chi-restraints excluded: chain o2 residue 89 LEU Chi-restraints excluded: chain p2 residue 68 SER Chi-restraints excluded: chain p2 residue 82 ILE Chi-restraints excluded: chain p2 residue 103 HIS Chi-restraints excluded: chain p2 residue 111 ILE Chi-restraints excluded: chain q2 residue 14 PHE Chi-restraints excluded: chain q2 residue 47 LEU Chi-restraints excluded: chain q2 residue 60 MET Chi-restraints excluded: chain q2 residue 61 MET Chi-restraints excluded: chain q2 residue 88 PHE Chi-restraints excluded: chain q2 residue 167 VAL Chi-restraints excluded: chain r2 residue 80 LEU Chi-restraints excluded: chain s2 residue 1020 LEU Chi-restraints excluded: chain s2 residue 1184 LEU Chi-restraints excluded: chain t2 residue 72 MET Chi-restraints excluded: chain t2 residue 92 LEU Chi-restraints excluded: chain t2 residue 96 VAL Chi-restraints excluded: chain t2 residue 145 VAL Chi-restraints excluded: chain t2 residue 148 GLN Chi-restraints excluded: chain t2 residue 222 SER Chi-restraints excluded: chain t2 residue 275 THR Chi-restraints excluded: chain t2 residue 347 THR Chi-restraints excluded: chain t2 residue 354 THR Chi-restraints excluded: chain t2 residue 368 MET Chi-restraints excluded: chain t2 residue 393 LEU Chi-restraints excluded: chain t2 residue 410 VAL Chi-restraints excluded: chain t2 residue 416 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1120 random chunks: chunk 544 optimal weight: 7.9990 chunk 705 optimal weight: 4.9990 chunk 946 optimal weight: 1.9990 chunk 272 optimal weight: 10.0000 chunk 819 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 chunk 246 optimal weight: 10.0000 chunk 889 optimal weight: 1.9990 chunk 372 optimal weight: 10.0000 chunk 913 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C2 299 GLN D2 291 GLN I2 177 ASN J2 23 ASN K2 67 HIS L2 33 GLN L2 131 GLN M2 37 HIS O2 25 HIS P2 21 GLN ** R2 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R2 156 HIS S2 69 GLN S2 112 ASN ** T2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T2 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X2 14 ASN X2 86 GLN Z2 120 GLN b2 40 GLN c2 121 ASN d2 92 ASN d2 117 GLN d2 126 ASN g2 20 GLN g2 65 GLN h2 36 HIS j2 28 ASN k2 25 GLN k2 38 ASN l2 58 GLN s21023 HIS s21185 HIS s21268 HIS ** s21328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t2 107 ASN t2 229 ASN ** u2 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u2 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.132065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.095203 restraints weight = 191625.886| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 0.84 r_work: 0.2886 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.095 153880 Z= 0.464 Angle : 0.752 15.147 226179 Z= 0.384 Chirality : 0.046 0.505 28142 Planarity : 0.006 0.084 14420 Dihedral : 24.164 179.927 69034 Min Nonbonded Distance : 1.059 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.13 % Favored : 95.84 % Rotamer: Outliers : 3.46 % Allowed : 20.71 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.09), residues: 7480 helix: 0.42 (0.10), residues: 2888 sheet: -0.49 (0.16), residues: 1029 loop : -0.62 (0.10), residues: 3563 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRPM2 120 HIS 0.013 0.002 HISf2 73 PHE 0.023 0.002 PHEs21135 TYR 0.039 0.003 TYRT2 90 ARG 0.012 0.001 ARGC2 350 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53751.08 seconds wall clock time: 930 minutes 28.29 seconds (55828.29 seconds total)