Starting phenix.real_space_refine on Mon Mar 18 23:38:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdw_4531/03_2024/6qdw_4531.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdw_4531/03_2024/6qdw_4531.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdw_4531/03_2024/6qdw_4531.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdw_4531/03_2024/6qdw_4531.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdw_4531/03_2024/6qdw_4531.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6qdw_4531/03_2024/6qdw_4531.pdb" } resolution = 2.83 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3080 5.49 5 S 76 5.16 5 C 44911 2.51 5 N 16888 2.21 5 O 25735 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ARG 3": "NH1" <-> "NH2" Residue "0 ARG 11": "NH1" <-> "NH2" Residue "0 ARG 18": "NH1" <-> "NH2" Residue "0 ARG 37": "NH1" <-> "NH2" Residue "0 PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 50": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ASP 65": "OD1" <-> "OD2" Residue "0 ARG 74": "NH1" <-> "NH2" Residue "0 GLU 76": "OE1" <-> "OE2" Residue "1 ARG 29": "NH1" <-> "NH2" Residue "1 ARG 47": "NH1" <-> "NH2" Residue "1 ARG 52": "NH1" <-> "NH2" Residue "2 ARG 11": "NH1" <-> "NH2" Residue "2 ARG 30": "NH1" <-> "NH2" Residue "2 ASP 40": "OD1" <-> "OD2" Residue "2 ARG 45": "NH1" <-> "NH2" Residue "3 ARG 10": "NH1" <-> "NH2" Residue "3 ARG 16": "NH1" <-> "NH2" Residue "3 ARG 52": "NH1" <-> "NH2" Residue "4 ARG 44": "NH1" <-> "NH2" Residue "6 ARG 3": "NH1" <-> "NH2" Residue "6 ARG 12": "NH1" <-> "NH2" Residue "6 ARG 14": "NH1" <-> "NH2" Residue "6 ARG 19": "NH1" <-> "NH2" Residue "6 ARG 21": "NH1" <-> "NH2" Residue "6 ARG 33": "NH1" <-> "NH2" Residue "6 ARG 41": "NH1" <-> "NH2" Residue "7 ARG 13": "NH1" <-> "NH2" Residue "7 ARG 30": "NH1" <-> "NH2" Residue "7 ARG 40": "NH1" <-> "NH2" Residue "7 ARG 42": "NH1" <-> "NH2" Residue "8 ARG 24": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c ARG 63": "NH1" <-> "NH2" Residue "c ASP 66": "OD1" <-> "OD2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c ARG 80": "NH1" <-> "NH2" Residue "c TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 114": "OD1" <-> "OD2" Residue "c ARG 133": "NH1" <-> "NH2" Residue "c GLU 145": "OE1" <-> "OE2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 177": "NH1" <-> "NH2" Residue "c GLU 180": "OE1" <-> "OE2" Residue "c ARG 182": "NH1" <-> "NH2" Residue "c ARG 189": "NH1" <-> "NH2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "c ARG 212": "NH1" <-> "NH2" Residue "c ASP 264": "OD1" <-> "OD2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ASP 39": "OD1" <-> "OD2" Residue "d ARG 59": "NH1" <-> "NH2" Residue "d ARG 77": "NH1" <-> "NH2" Residue "d ARG 83": "NH1" <-> "NH2" Residue "d ASP 131": "OD1" <-> "OD2" Residue "d GLU 168": "OE1" <-> "OE2" Residue "d ARG 169": "NH1" <-> "NH2" Residue "d ARG 184": "NH1" <-> "NH2" Residue "e PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ASP 22": "OD1" <-> "OD2" Residue "e ARG 44": "NH1" <-> "NH2" Residue "e ARG 49": "NH1" <-> "NH2" Residue "e ARG 61": "NH1" <-> "NH2" Residue "e ARG 88": "NH1" <-> "NH2" Residue "e ARG 102": "NH1" <-> "NH2" Residue "e PHE 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 127": "OE1" <-> "OE2" Residue "e ARG 162": "NH1" <-> "NH2" Residue "e ASP 168": "OD1" <-> "OD2" Residue "e ARG 170": "NH1" <-> "NH2" Residue "f ASP 51": "OD1" <-> "OD2" Residue "f ARG 71": "NH1" <-> "NH2" Residue "f ARG 80": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f ARG 102": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "f ARG 112": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 133": "NH1" <-> "NH2" Residue "f GLU 165": "OE1" <-> "OE2" Residue "f ASP 174": "OD1" <-> "OD2" Residue "f PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 3": "NH1" <-> "NH2" Residue "g ASP 16": "OD1" <-> "OD2" Residue "g GLU 32": "OE1" <-> "OE2" Residue "g ASP 60": "OD1" <-> "OD2" Residue "g GLU 124": "OE1" <-> "OE2" Residue "g ARG 153": "NH1" <-> "NH2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g ARG 163": "NH1" <-> "NH2" Residue "g ARG 170": "NH1" <-> "NH2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h ARG 27": "NH1" <-> "NH2" Residue "j GLU 9": "OE1" <-> "OE2" Residue "j ARG 13": "NH1" <-> "NH2" Residue "j ASP 19": "OD1" <-> "OD2" Residue "j ARG 37": "NH1" <-> "NH2" Residue "j GLU 91": "OE1" <-> "OE2" Residue "j ARG 96": "NH1" <-> "NH2" Residue "j ARG 120": "NH1" <-> "NH2" Residue "j ASP 141": "OD1" <-> "OD2" Residue "k ASP 37": "OD1" <-> "OD2" Residue "k GLU 45": "OE1" <-> "OE2" Residue "k GLU 92": "OE1" <-> "OE2" Residue "k GLU 110": "OE1" <-> "OE2" Residue "l ARG 21": "NH1" <-> "NH2" Residue "l ARG 33": "NH1" <-> "NH2" Residue "l ARG 41": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 60": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l GLU 106": "OE1" <-> "OE2" Residue "l ARG 126": "NH1" <-> "NH2" Residue "m ARG 10": "NH1" <-> "NH2" Residue "m ARG 18": "NH1" <-> "NH2" Residue "m ASP 25": "OD1" <-> "OD2" Residue "m PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 40": "NH1" <-> "NH2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m ARG 50": "NH1" <-> "NH2" Residue "m ARG 55": "NH1" <-> "NH2" Residue "m ARG 59": "NH1" <-> "NH2" Residue "m ASP 70": "OD1" <-> "OD2" Residue "m TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m GLU 104": "OE1" <-> "OE2" Residue "m ARG 114": "NH1" <-> "NH2" Residue "n ARG 8": "NH1" <-> "NH2" Residue "n ARG 12": "NH1" <-> "NH2" Residue "n ARG 17": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "n GLU 43": "OE1" <-> "OE2" Residue "n ARG 46": "NH1" <-> "NH2" Residue "n ARG 63": "NH1" <-> "NH2" Residue "n ARG 64": "NH1" <-> "NH2" Residue "n ARG 69": "NH1" <-> "NH2" Residue "n ARG 71": "NH1" <-> "NH2" Residue "n ARG 96": "NH1" <-> "NH2" Residue "n ARG 118": "NH1" <-> "NH2" Residue "o ARG 10": "NH1" <-> "NH2" Residue "o ARG 16": "NH1" <-> "NH2" Residue "o ARG 25": "NH1" <-> "NH2" Residue "o ARG 81": "NH1" <-> "NH2" Residue "o ARG 94": "NH1" <-> "NH2" Residue "o ARG 102": "NH1" <-> "NH2" Residue "o ASP 108": "OD1" <-> "OD2" Residue "o ARG 111": "NH1" <-> "NH2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "o PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 39": "NH1" <-> "NH2" Residue "p GLU 44": "OE1" <-> "OE2" Residue "p ARG 51": "NH1" <-> "NH2" Residue "p ARG 62": "NH1" <-> "NH2" Residue "p ARG 89": "NH1" <-> "NH2" Residue "p ARG 101": "NH1" <-> "NH2" Residue "p ARG 109": "NH1" <-> "NH2" Residue "q ARG 3": "NH1" <-> "NH2" Residue "q ARG 6": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 48": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ASP 97": "OD1" <-> "OD2" Residue "r ARG 21": "NH1" <-> "NH2" Residue "r GLU 23": "OE1" <-> "OE2" Residue "r ARG 68": "NH1" <-> "NH2" Residue "r GLU 70": "OE1" <-> "OE2" Residue "r ARG 78": "NH1" <-> "NH2" Residue "r ARG 79": "NH1" <-> "NH2" Residue "r ARG 84": "NH1" <-> "NH2" Residue "r PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s GLU 2": "OE1" <-> "OE2" Residue "s ASP 65": "OD1" <-> "OD2" Residue "s ASP 77": "OD1" <-> "OD2" Residue "s ARG 84": "NH1" <-> "NH2" Residue "s ARG 88": "NH1" <-> "NH2" Residue "s ARG 95": "NH1" <-> "NH2" Residue "t ARG 12": "NH1" <-> "NH2" Residue "t ARG 73": "NH1" <-> "NH2" Residue "t TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 6": "NH1" <-> "NH2" Residue "u ARG 7": "NH1" <-> "NH2" Residue "u ASP 8": "OD1" <-> "OD2" Residue "u ASP 9": "OD1" <-> "OD2" Residue "u ASP 18": "OD1" <-> "OD2" Residue "u ARG 82": "NH1" <-> "NH2" Residue "u ARG 86": "NH1" <-> "NH2" Residue "u ASP 89": "OD1" <-> "OD2" Residue "u ARG 94": "NH1" <-> "NH2" Residue "u GLU 101": "OE1" <-> "OE2" Residue "w ASP 43": "OD1" <-> "OD2" Residue "w ASP 45": "OD1" <-> "OD2" Residue "w GLU 55": "OE1" <-> "OE2" Residue "w ASP 66": "OD1" <-> "OD2" Residue "w GLU 69": "OE1" <-> "OE2" Residue "w ASP 76": "OD1" <-> "OD2" Residue "z PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "z ARG 26": "NH1" <-> "NH2" Residue "z ARG 26": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 90690 Number of models: 1 Model: "" Number of chains: 32 Chain: "0" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "1" Number of atoms: 495 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 495 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "2" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 439 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "3" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 434 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 1, 'TRANS': 53} Chain: "4" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "6" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "7" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "8" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "a" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2528 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 15, 'rna3p': 102} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "b" Number of atoms: 62008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2888, 62008 Classifications: {'RNA': 2888} Modifications used: {'p5*END': 1, 'rna2p_pur': 272, 'rna2p_pyr': 147, 'rna3p_pur': 1396, 'rna3p_pyr': 1073} Link IDs: {'rna2p': 419, 'rna3p': 2468} Chain breaks: 5 Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 287 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "j" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "k" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "l" Number of atoms: 1042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1042 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "m" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "n" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "o" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "p" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 908 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 3, 'TRANS': 109} Chain: "q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "r" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 791 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 1, 'TRANS': 97} Chain breaks: 1 Chain: "s" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 845 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 2, 'TRANS': 106} Chain: "t" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "u" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "v" Number of atoms: 1583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1583 Classifications: {'RNA': 75} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 5, 'rna3p_pur': 25, 'rna3p_pyr': 38} Link IDs: {'rna2p': 11, 'rna3p': 63} Chain: "w" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "y" Number of atoms: 559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 559 Classifications: {'peptide': 74} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "z" Number of atoms: 412 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Conformer: "B" Number of residues, atoms: 26, 206 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 2, 'TRANS': 23} Residues with excluded nonbonded symmetry interactions: 26 residue: pdb=" N APRO z 3 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO z 3 " occ=0.50 residue: pdb=" N AASN z 4 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN z 4 " occ=0.50 residue: pdb=" N ALEU z 5 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU z 5 " occ=0.50 residue: pdb=" N AGLN z 6 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN z 6 " occ=0.50 residue: pdb=" N APRO z 7 " occ=0.50 ... (12 atoms not shown) pdb=" CD BPRO z 7 " occ=0.50 residue: pdb=" N ATYR z 8 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR z 8 " occ=0.50 residue: pdb=" N APHE z 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE z 9 " occ=0.50 residue: pdb=" N ASER z 10 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER z 10 " occ=0.50 residue: pdb=" N AARG z 11 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG z 11 " occ=0.50 residue: pdb=" N ACYS z 12 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS z 12 " occ=0.50 residue: pdb=" N APHE z 13 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE z 13 " occ=0.50 residue: pdb=" N ASER z 14 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER z 14 " occ=0.50 ... (remaining 14 not shown) Time building chain proxies: 35.54, per 1000 atoms: 0.39 Number of scatterers: 90690 At special positions: 0 Unit cell: (207.9, 203.7, 224.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 3080 15.00 O 25735 8.00 N 16888 7.00 C 44911 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 8 14 " - pdb=" SG CYS 8 27 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.65 Conformation dependent library (CDL) restraints added in 3.8 seconds 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5746 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 48 sheets defined 25.3% alpha, 21.1% beta 925 base pairs and 1638 stacking pairs defined. Time for finding SS restraints: 36.73 Creating SS restraints... Processing helix chain '0' and resid 53 through 63 removed outlier: 3.637A pdb=" N ARG 0 57 " --> pdb=" O ALA 0 53 " (cutoff:3.500A) Processing helix chain '0' and resid 63 through 73 Processing helix chain '1' and resid 5 through 9 removed outlier: 3.676A pdb=" N GLU 1 8 " --> pdb=" O GLU 1 5 " (cutoff:3.500A) Processing helix chain '1' and resid 10 through 34 removed outlier: 3.565A pdb=" N GLU 1 17 " --> pdb=" O GLU 1 13 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALA 1 33 " --> pdb=" O ARG 1 29 " (cutoff:3.500A) Processing helix chain '1' and resid 41 through 61 removed outlier: 3.924A pdb=" N LYS 1 60 " --> pdb=" O LEU 1 56 " (cutoff:3.500A) Processing helix chain '2' and resid 17 through 28 Processing helix chain '2' and resid 41 through 51 removed outlier: 3.765A pdb=" N MET 2 47 " --> pdb=" O ALA 2 43 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL 2 51 " --> pdb=" O MET 2 47 " (cutoff:3.500A) Processing helix chain '3' and resid 9 through 17 removed outlier: 3.540A pdb=" N ARG 3 17 " --> pdb=" O ARG 3 13 " (cutoff:3.500A) Processing helix chain '6' and resid 8 through 16 Processing helix chain '6' and resid 17 through 22 Processing helix chain '6' and resid 24 through 38 removed outlier: 3.669A pdb=" N VAL 6 30 " --> pdb=" O ASN 6 26 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 44 removed outlier: 3.535A pdb=" N LEU 7 44 " --> pdb=" O ARG 7 40 " (cutoff:3.500A) Processing helix chain '7' and resid 54 through 62 removed outlier: 3.515A pdb=" N ALA 7 60 " --> pdb=" O GLY 7 56 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N CYS 7 61 " --> pdb=" O LEU 7 57 " (cutoff:3.500A) Processing helix chain '8' and resid 30 through 33 Processing helix chain 'c' and resid 30 through 32 No H-bonds generated for 'chain 'c' and resid 30 through 32' Processing helix chain 'c' and resid 199 through 203 Processing helix chain 'c' and resid 207 through 213 removed outlier: 3.826A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 225 Processing helix chain 'd' and resid 61 through 72 removed outlier: 3.729A pdb=" N HIS d 67 " --> pdb=" O PRO d 63 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA d 71 " --> pdb=" O HIS d 67 " (cutoff:3.500A) Processing helix chain 'd' and resid 97 through 104 removed outlier: 3.687A pdb=" N ALA d 102 " --> pdb=" O GLU d 99 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP d 103 " --> pdb=" O LEU d 100 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL d 104 " --> pdb=" O PHE d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 120 through 126 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 38 Processing helix chain 'e' and resid 97 through 113 removed outlier: 3.514A pdb=" N GLU e 111 " --> pdb=" O SER e 107 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL e 113 " --> pdb=" O LEU e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 130 through 137 removed outlier: 3.578A pdb=" N LEU e 134 " --> pdb=" O LYS e 130 " (cutoff:3.500A) Processing helix chain 'e' and resid 154 through 161 removed outlier: 3.535A pdb=" N ALA e 161 " --> pdb=" O LEU e 157 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 182 removed outlier: 3.615A pdb=" N LEU e 180 " --> pdb=" O ASP e 176 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 200 removed outlier: 3.575A pdb=" N GLN e 195 " --> pdb=" O ASP e 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 3 through 11 removed outlier: 3.842A pdb=" N TYR f 8 " --> pdb=" O LEU f 4 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LYS f 9 " --> pdb=" O HIS f 5 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP f 10 " --> pdb=" O ASP f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 49 through 61 removed outlier: 3.586A pdb=" N ASP f 56 " --> pdb=" O ASN f 52 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU f 57 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA f 59 " --> pdb=" O ALA f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 102 removed outlier: 3.979A pdb=" N TRP f 97 " --> pdb=" O GLY f 93 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N PHE f 99 " --> pdb=" O ARG f 95 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ARG f 102 " --> pdb=" O GLU f 98 " (cutoff:3.500A) Processing helix chain 'f' and resid 162 through 171 removed outlier: 3.636A pdb=" N LEU f 170 " --> pdb=" O GLY f 166 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA f 171 " --> pdb=" O ARG f 167 " (cutoff:3.500A) Processing helix chain 'f' and resid 172 through 174 No H-bonds generated for 'chain 'f' and resid 172 through 174' Processing helix chain 'g' and resid 61 through 77 Processing helix chain 'g' and resid 137 through 150 Processing helix chain 'j' and resid 24 through 38 removed outlier: 3.560A pdb=" N THR j 30 " --> pdb=" O GLY j 26 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLU j 31 " --> pdb=" O ARG j 27 " (cutoff:3.500A) Processing helix chain 'j' and resid 58 through 62 Processing helix chain 'j' and resid 67 through 72 Processing helix chain 'j' and resid 89 through 96 Processing helix chain 'j' and resid 97 through 109 removed outlier: 4.384A pdb=" N ILE j 101 " --> pdb=" O PRO j 97 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET j 108 " --> pdb=" O ALA j 104 " (cutoff:3.500A) Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 104 through 108 removed outlier: 3.683A pdb=" N LEU k 107 " --> pdb=" O THR k 104 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG k 108 " --> pdb=" O ARG k 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 104 through 108' Processing helix chain 'k' and resid 112 through 117 Processing helix chain 'l' and resid 56 through 61 Processing helix chain 'l' and resid 78 through 83 removed outlier: 4.111A pdb=" N ALA l 83 " --> pdb=" O SER l 80 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 98 removed outlier: 3.613A pdb=" N LYS l 96 " --> pdb=" O LEU l 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA l 98 " --> pdb=" O THR l 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 128 through 136 Processing helix chain 'm' and resid 43 through 57 removed outlier: 3.551A pdb=" N ALA m 56 " --> pdb=" O ALA m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 122 removed outlier: 3.714A pdb=" N ALA m 122 " --> pdb=" O LYS m 118 " (cutoff:3.500A) Processing helix chain 'n' and resid 13 through 31 Processing helix chain 'n' and resid 44 through 55 Proline residue: n 50 - end of helix Processing helix chain 'n' and resid 59 through 70 removed outlier: 3.888A pdb=" N LEU n 65 " --> pdb=" O ALA n 61 " (cutoff:3.500A) Processing helix chain 'n' and resid 72 through 82 Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'o' and resid 3 through 15 removed outlier: 3.756A pdb=" N ARG o 9 " --> pdb=" O SER o 5 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N ARG o 13 " --> pdb=" O ARG o 9 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 59 removed outlier: 3.701A pdb=" N ALA o 59 " --> pdb=" O LYS o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 67 through 84 removed outlier: 3.680A pdb=" N ALA o 79 " --> pdb=" O GLY o 75 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLU o 84 " --> pdb=" O GLU o 80 " (cutoff:3.500A) Processing helix chain 'o' and resid 101 through 114 removed outlier: 3.737A pdb=" N ALA o 113 " --> pdb=" O ALA o 109 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 10 Processing helix chain 'p' and resid 97 through 102 Processing helix chain 'q' and resid 6 through 20 removed outlier: 3.586A pdb=" N ILE q 17 " --> pdb=" O ARG q 13 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN q 20 " --> pdb=" O LYS q 16 " (cutoff:3.500A) Processing helix chain 'q' and resid 25 through 29 Processing helix chain 'q' and resid 31 through 72 removed outlier: 3.868A pdb=" N GLN q 37 " --> pdb=" O ARG q 33 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG q 51 " --> pdb=" O TYR q 47 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LYS q 54 " --> pdb=" O ARG q 50 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG q 55 " --> pdb=" O ARG q 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG q 58 " --> pdb=" O LYS q 54 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ASN q 72 " --> pdb=" O ALA q 68 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 86 Processing helix chain 'q' and resid 91 through 102 removed outlier: 3.618A pdb=" N VAL q 100 " --> pdb=" O ALA q 96 " (cutoff:3.500A) Processing helix chain 'q' and resid 103 through 118 removed outlier: 3.597A pdb=" N ALA q 108 " --> pdb=" O VAL q 104 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU q 109 " --> pdb=" O ALA q 105 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA q 116 " --> pdb=" O LYS q 112 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA q 118 " --> pdb=" O LYS q 114 " (cutoff:3.500A) Processing helix chain 's' and resid 13 through 22 removed outlier: 3.531A pdb=" N LEU s 19 " --> pdb=" O GLN s 15 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N VAL s 20 " --> pdb=" O LYS s 16 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 34 removed outlier: 3.737A pdb=" N ASP s 34 " --> pdb=" O SER s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 61 removed outlier: 3.754A pdb=" N VAL s 45 " --> pdb=" O LYS s 41 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LYS s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN s 61 " --> pdb=" O ASN s 57 " (cutoff:3.500A) Processing helix chain 's' and resid 65 through 69 removed outlier: 3.744A pdb=" N ASP s 68 " --> pdb=" O ASP s 65 " (cutoff:3.500A) Processing helix chain 's' and resid 89 through 91 No H-bonds generated for 'chain 's' and resid 89 through 91' Processing helix chain 't' and resid 3 through 8 Processing helix chain 't' and resid 19 through 27 Processing helix chain 't' and resid 39 through 51 Processing helix chain 'w' and resid 13 through 23 Processing helix chain 'w' and resid 44 through 48 Processing sheet with id=AA1, first strand: chain '0' and resid 13 through 18 Processing sheet with id=AA2, first strand: chain '0' and resid 33 through 40 Processing sheet with id=AA3, first strand: chain '2' and resid 35 through 38 removed outlier: 3.997A pdb=" N LYS 2 6 " --> pdb=" O GLU 2 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '3' and resid 29 through 30 Processing sheet with id=AA5, first strand: chain '3' and resid 48 through 49 Processing sheet with id=AA6, first strand: chain '4' and resid 7 through 12 Processing sheet with id=AA7, first strand: chain '4' and resid 36 through 40 removed outlier: 3.663A pdb=" N GLN 4 45 " --> pdb=" O ASP 4 40 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '7' and resid 14 through 16 Processing sheet with id=AA9, first strand: chain '8' and resid 2 through 4 removed outlier: 6.250A pdb=" N LYS 8 2 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '8' and resid 14 through 19 Processing sheet with id=AB2, first strand: chain 'c' and resid 3 through 5 Processing sheet with id=AB3, first strand: chain 'c' and resid 34 through 37 removed outlier: 3.993A pdb=" N ASN c 37 " --> pdb=" O GLN c 60 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N GLN c 60 " --> pdb=" O ASN c 37 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'c' and resid 101 through 105 removed outlier: 6.546A pdb=" N LEU c 95 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N VAL c 78 " --> pdb=" O LEU c 95 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 129 through 131 removed outlier: 6.105A pdb=" N ILE c 164 " --> pdb=" O ARG c 175 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARG c 175 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA c 166 " --> pdb=" O THR c 173 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LYS c 183 " --> pdb=" O ILE c 267 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N ILE c 267 " --> pdb=" O LYS c 183 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'c' and resid 144 through 145 Processing sheet with id=AB7, first strand: chain 'd' and resid 4 through 15 removed outlier: 6.617A pdb=" N VAL d 26 " --> pdb=" O VAL d 9 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N MET d 11 " --> pdb=" O VAL d 24 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL d 24 " --> pdb=" O MET d 11 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG d 13 " --> pdb=" O ILE d 22 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE d 22 " --> pdb=" O ARG d 13 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU d 186 " --> pdb=" O VAL d 180 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N VAL d 180 " --> pdb=" O LEU d 186 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU d 188 " --> pdb=" O VAL d 178 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ASP d 176 " --> pdb=" O LYS d 190 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N THR d 171 " --> pdb=" O GLY d 111 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY d 111 " --> pdb=" O THR d 171 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN d 173 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL d 109 " --> pdb=" O GLN d 173 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR d 112 " --> pdb=" O ASP d 200 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASP d 200 " --> pdb=" O THR d 112 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'd' and resid 80 through 83 removed outlier: 6.283A pdb=" N ALA d 47 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N VAL d 37 " --> pdb=" O ALA d 47 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'd' and resid 117 through 119 removed outlier: 3.561A pdb=" N GLY d 117 " --> pdb=" O MET d 165 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'e' and resid 2 through 3 removed outlier: 3.560A pdb=" N LEU e 3 " --> pdb=" O LEU e 12 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'e' and resid 118 through 120 removed outlier: 6.150A pdb=" N LEU e 147 " --> pdb=" O VAL e 187 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'f' and resid 66 through 68 removed outlier: 4.031A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'g' and resid 9 through 10 Processing sheet with id=AC5, first strand: chain 'g' and resid 19 through 20 removed outlier: 3.518A pdb=" N ASN g 20 " --> pdb=" O VAL g 23 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N VAL g 23 " --> pdb=" O ASN g 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'g' and resid 122 through 124 removed outlier: 3.651A pdb=" N GLY g 135 " --> pdb=" O PHE g 83 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE g 83 " --> pdb=" O GLY g 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'g' and resid 95 through 98 Processing sheet with id=AC8, first strand: chain 'h' and resid 18 through 20 Processing sheet with id=AC9, first strand: chain 'j' and resid 122 through 124 removed outlier: 6.731A pdb=" N TYR j 16 " --> pdb=" O ILE j 55 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N LEU j 57 " --> pdb=" O TYR j 16 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL j 18 " --> pdb=" O LEU j 57 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'j' and resid 73 through 77 Processing sheet with id=AD2, first strand: chain 'k' and resid 7 through 10 removed outlier: 3.579A pdb=" N VAL k 10 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ARG k 17 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLU k 45 " --> pdb=" O ARG k 17 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL k 19 " --> pdb=" O ILE k 43 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE k 43 " --> pdb=" O VAL k 19 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N CYS k 21 " --> pdb=" O ILE k 41 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE k 41 " --> pdb=" O CYS k 21 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS k 23 " --> pdb=" O ILE k 39 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N ILE k 39 " --> pdb=" O LYS k 23 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ALA k 83 " --> pdb=" O VAL k 63 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N CYS k 84 " --> pdb=" O MET k 7 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ASN k 9 " --> pdb=" O CYS k 84 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU k 86 " --> pdb=" O ASN k 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'k' and resid 69 through 70 removed outlier: 3.594A pdb=" N ILE k 77 " --> pdb=" O VAL k 69 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ALA p 49 " --> pdb=" O THR p 60 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ARG p 62 " --> pdb=" O VAL p 47 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N VAL p 47 " --> pdb=" O ARG p 62 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N ILE p 64 " --> pdb=" O GLY p 45 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N GLY p 45 " --> pdb=" O ILE p 64 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N THR p 25 " --> pdb=" O LYS p 87 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER p 83 " --> pdb=" O LYS p 29 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N TRP p 31 " --> pdb=" O VAL p 81 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL p 81 " --> pdb=" O TRP p 31 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'l' and resid 74 through 77 Processing sheet with id=AD5, first strand: chain 'l' and resid 89 through 90 removed outlier: 6.690A pdb=" N VAL l 122 " --> pdb=" O GLU l 143 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'm' and resid 62 through 65 removed outlier: 5.859A pdb=" N VAL m 101 " --> pdb=" O ALA m 35 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA m 35 " --> pdb=" O VAL m 101 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TYR m 103 " --> pdb=" O LEU m 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'm' and resid 39 through 42 removed outlier: 3.958A pdb=" N ASN m 88 " --> pdb=" O GLU m 75 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N ILE m 73 " --> pdb=" O GLU m 90 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N TRP m 92 " --> pdb=" O LYS m 71 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LYS m 71 " --> pdb=" O TRP m 92 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'n' and resid 33 through 37 removed outlier: 6.381A pdb=" N MET n 110 " --> pdb=" O CYS n 100 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'o' and resid 47 through 52 removed outlier: 6.726A pdb=" N VAL o 39 " --> pdb=" O LEU o 48 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ALA o 50 " --> pdb=" O ALA o 37 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N ALA o 37 " --> pdb=" O ALA o 50 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N SER o 52 " --> pdb=" O ILE o 35 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N ILE o 35 " --> pdb=" O SER o 52 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N HIS o 34 " --> pdb=" O THR o 31 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N THR o 31 " --> pdb=" O HIS o 34 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N LEU o 26 " --> pdb=" O ASP o 93 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'r' and resid 11 through 15 removed outlier: 7.585A pdb=" N GLN r 6 " --> pdb=" O VAL r 38 " (cutoff:3.500A) removed outlier: 7.138A pdb=" N VAL r 38 " --> pdb=" O GLN r 6 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'r' and resid 19 through 23 removed outlier: 6.526A pdb=" N ASP r 95 " --> pdb=" O VAL r 64 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N LYS r 60 " --> pdb=" O THR r 99 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'r' and resid 72 through 78 removed outlier: 4.029A pdb=" N TYR r 83 " --> pdb=" O ARG r 78 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 's' and resid 3 through 10 removed outlier: 5.287A pdb=" N SER s 101 " --> pdb=" O HIS s 9 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N THR s 100 " --> pdb=" O PRO s 80 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N HIS s 102 " --> pdb=" O GLU s 78 " (cutoff:3.500A) removed outlier: 5.558A pdb=" N GLU s 78 " --> pdb=" O HIS s 102 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N THR s 104 " --> pdb=" O VAL s 76 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N VAL s 76 " --> pdb=" O THR s 104 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N VAL s 106 " --> pdb=" O ILE s 74 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ILE s 74 " --> pdb=" O VAL s 106 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER s 108 " --> pdb=" O THR s 72 " (cutoff:3.500A) removed outlier: 5.869A pdb=" N THR s 72 " --> pdb=" O SER s 108 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 't' and resid 11 through 14 removed outlier: 4.012A pdb=" N LYS t 81 " --> pdb=" O VAL t 34 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL t 57 " --> pdb=" O THR t 86 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 't' and resid 67 through 68 Processing sheet with id=AE7, first strand: chain 'u' and resid 65 through 66 removed outlier: 7.240A pdb=" N LYS u 33 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N VAL u 28 " --> pdb=" O LYS u 33 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ILE u 35 " --> pdb=" O LYS u 26 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N GLU u 10 " --> pdb=" O PHE u 73 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ILE u 72 " --> pdb=" O ASP u 81 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'u' and resid 41 through 45 Processing sheet with id=AE9, first strand: chain 'u' and resid 83 through 88 Processing sheet with id=AF1, first strand: chain 'w' and resid 3 through 8 removed outlier: 7.756A pdb=" N ASN w 5 " --> pdb=" O ASP w 43 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N ASP w 43 " --> pdb=" O ASN w 5 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N LYS w 25 " --> pdb=" O GLN w 87 " (cutoff:3.500A) removed outlier: 9.908A pdb=" N ILE w 89 " --> pdb=" O LYS w 25 " (cutoff:3.500A) removed outlier: 8.646A pdb=" N PHE w 91 " --> pdb=" O PRO w 27 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ILE w 29 " --> pdb=" O PHE w 91 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ARG w 93 " --> pdb=" O ILE w 29 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N TYR w 31 " --> pdb=" O ARG w 93 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N LEU w 86 " --> pdb=" O ARG w 79 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N ARG w 79 " --> pdb=" O LEU w 86 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N HIS w 88 " --> pdb=" O VAL w 77 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL w 77 " --> pdb=" O HIS w 88 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ASP w 90 " --> pdb=" O GLN w 75 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'y' and resid 22 through 23 removed outlier: 6.985A pdb=" N LEU y 59 " --> pdb=" O ILE y 37 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'y' and resid 30 through 31 780 hydrogen bonds defined for protein. 2130 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2303 hydrogen bonds 3574 hydrogen bond angles 0 basepair planarities 925 basepair parallelities 1638 stacking parallelities Total time for adding SS restraints: 159.89 Time building geometry restraints manager: 42.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.44: 53244 1.44 - 1.68: 45564 1.68 - 1.93: 137 1.93 - 2.17: 0 2.17 - 2.42: 2 Bond restraints: 98947 Sorted by residual: bond pdb=" O3' U b 511 " pdb=" P G b 512 " ideal model delta sigma weight residual 1.607 2.419 -0.812 1.50e-02 4.44e+03 2.93e+03 bond pdb=" O3' G b 512 " pdb=" P A b 513 " ideal model delta sigma weight residual 1.607 2.261 -0.654 1.50e-02 4.44e+03 1.90e+03 bond pdb=" C ASER z 14 " pdb=" N ATHR z 15 " ideal model delta sigma weight residual 1.327 1.396 -0.069 2.31e-02 1.87e+03 8.81e+00 bond pdb=" CB ARG c 221 " pdb=" CG ARG c 221 " ideal model delta sigma weight residual 1.520 1.433 0.087 3.00e-02 1.11e+03 8.46e+00 bond pdb=" N ARG f 30 " pdb=" CA ARG f 30 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.21e-02 6.83e+03 8.09e+00 ... (remaining 98942 not shown) Histogram of bond angle deviations from ideal: 76.28 - 90.68: 3 90.68 - 105.07: 14865 105.07 - 119.46: 89708 119.46 - 133.86: 44251 133.86 - 148.25: 31 Bond angle restraints: 148858 Sorted by residual: angle pdb=" O3' U b 511 " pdb=" P G b 512 " pdb=" O5' G b 512 " ideal model delta sigma weight residual 104.00 76.28 27.72 1.50e+00 4.44e-01 3.41e+02 angle pdb=" O3' U b 511 " pdb=" P G b 512 " pdb=" OP2 G b 512 " ideal model delta sigma weight residual 108.00 148.25 -40.25 3.00e+00 1.11e-01 1.80e+02 angle pdb=" C3' U b 511 " pdb=" O3' U b 511 " pdb=" P G b 512 " ideal model delta sigma weight residual 120.20 100.68 19.52 1.50e+00 4.44e-01 1.69e+02 angle pdb=" O3' G b 512 " pdb=" P A b 513 " pdb=" O5' A b 513 " ideal model delta sigma weight residual 104.00 90.64 13.36 1.50e+00 4.44e-01 7.93e+01 angle pdb=" N ILE 4 5 " pdb=" CA ILE 4 5 " pdb=" C ILE 4 5 " ideal model delta sigma weight residual 112.17 105.08 7.09 9.50e-01 1.11e+00 5.57e+01 ... (remaining 148853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 54803 35.89 - 71.78: 7761 71.78 - 107.68: 831 107.68 - 143.57: 23 143.57 - 179.46: 29 Dihedral angle restraints: 63447 sinusoidal: 54520 harmonic: 8927 Sorted by residual: dihedral pdb=" O4' U b2888 " pdb=" C1' U b2888 " pdb=" N1 U b2888 " pdb=" C2 U b2888 " ideal model delta sinusoidal sigma weight residual 200.00 25.27 174.73 1 1.50e+01 4.44e-03 8.52e+01 dihedral pdb=" O4' U b 99 " pdb=" C1' U b 99 " pdb=" N1 U b 99 " pdb=" C2 U b 99 " ideal model delta sinusoidal sigma weight residual 200.00 28.06 171.94 1 1.50e+01 4.44e-03 8.49e+01 dihedral pdb=" O4' C b1732 " pdb=" C1' C b1732 " pdb=" N1 C b1732 " pdb=" C2 C b1732 " ideal model delta sinusoidal sigma weight residual 200.00 39.94 160.06 1 1.50e+01 4.44e-03 8.28e+01 ... (remaining 63444 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 16624 0.094 - 0.187: 2308 0.187 - 0.281: 172 0.281 - 0.374: 26 0.374 - 0.468: 9 Chirality restraints: 19139 Sorted by residual: chirality pdb=" CB ILE j 84 " pdb=" CA ILE j 84 " pdb=" CG1 ILE j 84 " pdb=" CG2 ILE j 84 " both_signs ideal model delta sigma weight residual False 2.64 2.18 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" C1' G b2736 " pdb=" O4' G b2736 " pdb=" C2' G b2736 " pdb=" N9 G b2736 " both_signs ideal model delta sigma weight residual False 2.46 2.01 0.45 2.00e-01 2.50e+01 5.06e+00 chirality pdb=" C3' C b2059 " pdb=" C4' C b2059 " pdb=" O3' C b2059 " pdb=" C2' C b2059 " both_signs ideal model delta sigma weight residual False -2.48 -2.04 -0.44 2.00e-01 2.50e+01 4.83e+00 ... (remaining 19136 not shown) Planarity restraints: 7375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G b2462 " 0.061 2.00e-02 2.50e+03 2.53e-02 1.93e+01 pdb=" N9 G b2462 " -0.055 2.00e-02 2.50e+03 pdb=" C8 G b2462 " -0.011 2.00e-02 2.50e+03 pdb=" N7 G b2462 " -0.000 2.00e-02 2.50e+03 pdb=" C5 G b2462 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G b2462 " 0.018 2.00e-02 2.50e+03 pdb=" O6 G b2462 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G b2462 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G b2462 " -0.009 2.00e-02 2.50e+03 pdb=" N2 G b2462 " 0.002 2.00e-02 2.50e+03 pdb=" N3 G b2462 " -0.011 2.00e-02 2.50e+03 pdb=" C4 G b2462 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A b 912 " 0.057 2.00e-02 2.50e+03 2.62e-02 1.88e+01 pdb=" N9 A b 912 " -0.059 2.00e-02 2.50e+03 pdb=" C8 A b 912 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A b 912 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A b 912 " 0.008 2.00e-02 2.50e+03 pdb=" C6 A b 912 " 0.014 2.00e-02 2.50e+03 pdb=" N6 A b 912 " 0.009 2.00e-02 2.50e+03 pdb=" N1 A b 912 " 0.000 2.00e-02 2.50e+03 pdb=" C2 A b 912 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A b 912 " -0.015 2.00e-02 2.50e+03 pdb=" C4 A b 912 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP c 213 " 0.049 2.00e-02 2.50e+03 2.68e-02 1.80e+01 pdb=" CG TRP c 213 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP c 213 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP c 213 " -0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP c 213 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP c 213 " 0.010 2.00e-02 2.50e+03 pdb=" CE3 TRP c 213 " -0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP c 213 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP c 213 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP c 213 " 0.015 2.00e-02 2.50e+03 ... (remaining 7372 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 551 2.50 - 3.10: 57435 3.10 - 3.70: 177009 3.70 - 4.30: 272095 4.30 - 4.90: 356463 Nonbonded interactions: 863553 Sorted by model distance: nonbonded pdb=" O LYS e 137 " pdb=" CG LEU e 138 " model vdw 1.901 3.470 nonbonded pdb=" O2' A b2664 " pdb=" O4' G b2665 " model vdw 1.907 2.440 nonbonded pdb=" N1 A b 588 " pdb=" O2' G b 811 " model vdw 1.967 2.520 nonbonded pdb=" N2 G b 463 " pdb=" OP2 A b 466 " model vdw 2.031 2.520 nonbonded pdb=" N7 A b 52 " pdb=" N6 A b 119 " model vdw 2.034 2.600 ... (remaining 863548 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 6.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 26.060 Check model and map are aligned: 1.030 Set scattering table: 0.620 Process input model: 336.790 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.220 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: 0.010 Load rotamer database and sin/cos tables:9.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 382.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.013 0.812 98947 Z= 0.737 Angle : 1.097 40.250 148858 Z= 0.556 Chirality : 0.064 0.468 19139 Planarity : 0.007 0.086 7375 Dihedral : 24.580 179.459 57698 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.11 % Favored : 92.73 % Rotamer: Outliers : 1.25 % Allowed : 8.91 % Favored : 89.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.12), residues: 3091 helix: -4.24 (0.09), residues: 764 sheet: -2.05 (0.18), residues: 632 loop : -2.35 (0.12), residues: 1695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP c 213 HIS 0.025 0.003 HIS s 7 PHE 0.024 0.003 PHE q 57 TYR 0.021 0.004 TYR 0 78 ARG 0.017 0.001 ARG q 6 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 756 time to evaluate : 3.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 31 ARG cc_start: 0.8495 (ptp90) cc_final: 0.8220 (ptp-170) REVERT: 2 40 ASP cc_start: 0.8305 (t0) cc_final: 0.7967 (t0) REVERT: 2 56 LYS cc_start: 0.8570 (tmmt) cc_final: 0.7513 (tttm) REVERT: c 111 LYS cc_start: 0.8176 (ptpp) cc_final: 0.7957 (ptpt) REVERT: c 140 THR cc_start: 0.8287 (t) cc_final: 0.7946 (m) REVERT: c 157 SER cc_start: 0.8661 (t) cc_final: 0.8453 (t) REVERT: d 28 GLU cc_start: 0.7056 (tt0) cc_final: 0.6665 (tt0) REVERT: d 174 SER cc_start: 0.8335 (m) cc_final: 0.7954 (t) REVERT: d 179 ARG cc_start: 0.8110 (ptp-170) cc_final: 0.7900 (ptp-110) REVERT: d 181 ASP cc_start: 0.6585 (t0) cc_final: 0.6372 (t70) REVERT: e 141 MET cc_start: 0.7932 (mmm) cc_final: 0.7654 (tpp) REVERT: e 145 ASP cc_start: 0.6821 (t0) cc_final: 0.6290 (t70) REVERT: f 56 ASP cc_start: 0.7361 (p0) cc_final: 0.6957 (p0) REVERT: f 101 GLU cc_start: 0.6851 (tt0) cc_final: 0.6297 (mt-10) REVERT: g 88 GLN cc_start: 0.7249 (tm-30) cc_final: 0.6982 (mt0) REVERT: j 125 TYR cc_start: 0.8287 (m-80) cc_final: 0.7904 (m-80) REVERT: k 32 TYR cc_start: 0.8606 (m-80) cc_final: 0.8396 (m-80) REVERT: k 93 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7584 (mm-40) REVERT: n 1 MET cc_start: 0.8382 (ptp) cc_final: 0.8158 (ptp) REVERT: q 87 SER cc_start: 0.8823 (m) cc_final: 0.8353 (p) REVERT: r 1 MET cc_start: 0.8393 (tpt) cc_final: 0.8158 (tpp) REVERT: s 77 ASP cc_start: 0.7579 (m-30) cc_final: 0.7378 (m-30) REVERT: s 95 ARG cc_start: 0.8052 (tpp-160) cc_final: 0.7751 (tpm170) REVERT: t 5 GLU cc_start: 0.6672 (pm20) cc_final: 0.6445 (mp0) REVERT: w 49 ASN cc_start: 0.8150 (m-40) cc_final: 0.7926 (m110) outliers start: 23 outliers final: 10 residues processed: 773 average time/residue: 1.9392 time to fit residues: 1983.8756 Evaluate side-chains 546 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 536 time to evaluate : 3.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain e residue 108 ILE Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 29 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 510 optimal weight: 6.9990 chunk 458 optimal weight: 1.9990 chunk 254 optimal weight: 0.7980 chunk 156 optimal weight: 20.0000 chunk 309 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 474 optimal weight: 9.9990 chunk 183 optimal weight: 1.9990 chunk 288 optimal weight: 6.9990 chunk 352 optimal weight: 0.9980 chunk 549 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 6 GLN 0 16 ASN 1 20 ASN 1 36 GLN 1 38 GLN 3 6 ASN c 200 HIS c 260 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 136 ASN d 150 GLN f 5 HIS f 27 GLN f 127 ASN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN g 22 GLN g 45 HIS h 2 GLN h 28 ASN k 90 ASN m 3 GLN n 13 ASN o 38 GLN q 52 GLN q 56 GLN q 72 ASN q 81 ASN r 86 GLN s 7 HIS s 15 GLN s 31 GLN s 40 ASN t 59 ASN u 66 GLN u 69 ASN w 51 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 98947 Z= 0.170 Angle : 0.631 16.113 148858 Z= 0.325 Chirality : 0.037 0.306 19139 Planarity : 0.005 0.068 7375 Dihedral : 24.826 179.945 51537 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.63 % Favored : 95.34 % Rotamer: Outliers : 3.56 % Allowed : 19.89 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.13), residues: 3091 helix: -2.42 (0.14), residues: 816 sheet: -1.56 (0.19), residues: 634 loop : -1.86 (0.14), residues: 1641 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP c 213 HIS 0.007 0.001 HIS s 7 PHE 0.014 0.001 PHE u 95 TYR 0.012 0.001 TYR f 143 ARG 0.010 0.001 ARG o 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 689 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 607 time to evaluate : 3.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 39 GLN cc_start: 0.8253 (mt0) cc_final: 0.8022 (mt0) REVERT: 2 31 ARG cc_start: 0.8384 (ptp90) cc_final: 0.8131 (ptp-170) REVERT: 2 44 ILE cc_start: 0.9253 (mm) cc_final: 0.9044 (mt) REVERT: 6 22 MET cc_start: 0.8861 (mmm) cc_final: 0.8652 (mmm) REVERT: 7 15 LYS cc_start: 0.8302 (mmtm) cc_final: 0.8072 (mmtm) REVERT: 7 28 ASN cc_start: 0.8992 (m110) cc_final: 0.8693 (m110) REVERT: c 18 LYS cc_start: 0.8437 (mtpt) cc_final: 0.8232 (mtpt) REVERT: c 98 ASP cc_start: 0.8432 (p0) cc_final: 0.8201 (p0) REVERT: c 111 LYS cc_start: 0.8121 (ptpp) cc_final: 0.7561 (ptpt) REVERT: c 140 THR cc_start: 0.8488 (t) cc_final: 0.8185 (m) REVERT: c 175 ARG cc_start: 0.8047 (ttm110) cc_final: 0.7831 (ttm110) REVERT: d 28 GLU cc_start: 0.7177 (tt0) cc_final: 0.6970 (tt0) REVERT: d 91 THR cc_start: 0.8669 (m) cc_final: 0.8184 (p) REVERT: d 128 ARG cc_start: 0.8261 (mtm-85) cc_final: 0.7953 (mmt180) REVERT: d 165 MET cc_start: 0.8694 (ttt) cc_final: 0.8304 (ttt) REVERT: d 176 ASP cc_start: 0.7969 (m-30) cc_final: 0.7734 (m-30) REVERT: e 137 LYS cc_start: 0.6089 (OUTLIER) cc_final: 0.5674 (tptt) REVERT: e 145 ASP cc_start: 0.7355 (t0) cc_final: 0.6504 (t70) REVERT: f 78 LYS cc_start: 0.6911 (mmtt) cc_final: 0.6653 (tmtt) REVERT: f 101 GLU cc_start: 0.6382 (tt0) cc_final: 0.6114 (mt-10) REVERT: j 125 TYR cc_start: 0.8232 (m-80) cc_final: 0.7742 (m-80) REVERT: k 32 TYR cc_start: 0.8920 (m-80) cc_final: 0.8718 (m-80) REVERT: o 67 ASN cc_start: 0.8061 (p0) cc_final: 0.7731 (p0) REVERT: o 69 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5964 (p0) REVERT: q 18 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8724 (mm) REVERT: q 87 SER cc_start: 0.8738 (m) cc_final: 0.8249 (p) REVERT: r 1 MET cc_start: 0.8616 (tpt) cc_final: 0.8406 (tpp) REVERT: s 1 MET cc_start: 0.5727 (OUTLIER) cc_final: 0.5414 (pmt) REVERT: s 101 SER cc_start: 0.8071 (p) cc_final: 0.7857 (p) REVERT: t 26 LYS cc_start: 0.7704 (mtpm) cc_final: 0.7455 (mmtp) REVERT: u 9 ASP cc_start: 0.6328 (m-30) cc_final: 0.6093 (m-30) REVERT: w 68 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7326 (ttpm) REVERT: y 66 LYS cc_start: 0.8680 (mmtp) cc_final: 0.8349 (mmtm) outliers start: 82 outliers final: 28 residues processed: 652 average time/residue: 1.8434 time to fit residues: 1616.6846 Evaluate side-chains 569 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 536 time to evaluate : 3.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 35 SER Chi-restraints excluded: chain 0 residue 48 THR Chi-restraints excluded: chain 1 residue 31 GLN Chi-restraints excluded: chain 1 residue 55 THR Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 4 residue 7 GLU Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 121 VAL Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain f residue 12 VAL Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain t residue 10 VAL Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain w residue 68 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 305 optimal weight: 6.9990 chunk 170 optimal weight: 6.9990 chunk 457 optimal weight: 9.9990 chunk 374 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 chunk 550 optimal weight: 5.9990 chunk 594 optimal weight: 7.9990 chunk 490 optimal weight: 6.9990 chunk 545 optimal weight: 10.0000 chunk 187 optimal weight: 6.9990 chunk 441 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 38 GLN 4 26 ASN c 200 HIS c 226 ASN ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 136 GLN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 76 HIS j 80 HIS k 93 GLN m 13 HIS n 13 ASN o 38 GLN p 10 GLN q 56 GLN r 18 GLN r 86 GLN s 31 GLN u 69 ASN w 51 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.079 98947 Z= 0.629 Angle : 0.873 12.801 148858 Z= 0.438 Chirality : 0.052 0.393 19139 Planarity : 0.007 0.087 7375 Dihedral : 24.840 179.701 51532 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.68 % Favored : 93.28 % Rotamer: Outliers : 5.90 % Allowed : 20.44 % Favored : 73.66 % 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: -2.32 (0.14), residues: 3091 helix: -1.40 (0.17), residues: 803 sheet: -1.34 (0.19), residues: 667 loop : -1.65 (0.14), residues: 1621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP c 213 HIS 0.012 0.002 HIS m 13 PHE 0.029 0.003 PHE q 57 TYR 0.017 0.003 TYR t 84 ARG 0.012 0.001 ARG n 2 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 586 time to evaluate : 3.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8140 (p0) cc_final: 0.7856 (p0) REVERT: 0 64 ILE cc_start: 0.9060 (tp) cc_final: 0.8843 (tp) REVERT: 1 31 GLN cc_start: 0.7954 (OUTLIER) cc_final: 0.7735 (mt0) REVERT: 2 40 ASP cc_start: 0.8379 (t0) cc_final: 0.8151 (t0) REVERT: 2 44 ILE cc_start: 0.9313 (mm) cc_final: 0.9068 (mt) REVERT: 2 56 LYS cc_start: 0.8666 (tmmt) cc_final: 0.8078 (tttm) REVERT: 3 52 ARG cc_start: 0.7640 (mtm110) cc_final: 0.7336 (ttp-170) REVERT: 6 29 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8272 (mt0) REVERT: 7 15 LYS cc_start: 0.8737 (mmtm) cc_final: 0.8514 (mmtm) REVERT: c 111 LYS cc_start: 0.8171 (ptpp) cc_final: 0.7938 (ptpt) REVERT: c 140 THR cc_start: 0.8980 (OUTLIER) cc_final: 0.8709 (m) REVERT: c 194 GLU cc_start: 0.7940 (pt0) cc_final: 0.7730 (pt0) REVERT: c 251 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.8200 (tp40) REVERT: d 89 GLU cc_start: 0.7059 (mm-30) cc_final: 0.6856 (tp30) REVERT: d 128 ARG cc_start: 0.8320 (mtm-85) cc_final: 0.7920 (mmt180) REVERT: d 165 MET cc_start: 0.9216 (ttt) cc_final: 0.8915 (ttt) REVERT: d 179 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7553 (ptp-110) REVERT: e 137 LYS cc_start: 0.7581 (OUTLIER) cc_final: 0.7380 (tptt) REVERT: e 145 ASP cc_start: 0.7558 (t0) cc_final: 0.7007 (t70) REVERT: e 184 ASP cc_start: 0.7916 (m-30) cc_final: 0.7352 (m-30) REVERT: f 96 MET cc_start: 0.7435 (ptm) cc_final: 0.7145 (ptp) REVERT: f 101 GLU cc_start: 0.6920 (tt0) cc_final: 0.6373 (mt-10) REVERT: f 148 ARG cc_start: 0.6175 (mmt90) cc_final: 0.5741 (mmm160) REVERT: g 69 ARG cc_start: 0.8042 (tmt170) cc_final: 0.7743 (tmt170) REVERT: h 1 MET cc_start: 0.7255 (OUTLIER) cc_final: 0.6908 (ttt) REVERT: h 2 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7347 (mt0) REVERT: j 11 VAL cc_start: 0.8060 (p) cc_final: 0.7691 (m) REVERT: k 17 ARG cc_start: 0.8297 (mmp-170) cc_final: 0.8096 (mmm160) REVERT: k 32 TYR cc_start: 0.9268 (m-80) cc_final: 0.8944 (m-80) REVERT: k 51 LYS cc_start: 0.8403 (mttp) cc_final: 0.8168 (mmtm) REVERT: k 113 MET cc_start: 0.7601 (mmm) cc_final: 0.7399 (tpt) REVERT: l 51 GLU cc_start: 0.8240 (OUTLIER) cc_final: 0.7717 (mm-30) REVERT: l 93 ASN cc_start: 0.7647 (t160) cc_final: 0.7358 (m110) REVERT: n 106 ASP cc_start: 0.9107 (p0) cc_final: 0.8887 (p0) REVERT: n 114 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: o 68 LYS cc_start: 0.7729 (mtmt) cc_final: 0.7458 (mtmt) REVERT: p 37 LYS cc_start: 0.6994 (mppt) cc_final: 0.6768 (mmmm) REVERT: p 89 ARG cc_start: 0.7883 (mtm180) cc_final: 0.7434 (mmm-85) REVERT: p 106 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.4430 (mtmm) REVERT: q 104 VAL cc_start: 0.9113 (t) cc_final: 0.8895 (m) REVERT: t 18 GLU cc_start: 0.7647 (tm-30) cc_final: 0.7246 (tp30) REVERT: u 22 ARG cc_start: 0.8451 (OUTLIER) cc_final: 0.6739 (ttp-170) REVERT: w 48 MET cc_start: 0.8246 (tpp) cc_final: 0.8035 (tpt) outliers start: 141 outliers final: 68 residues processed: 663 average time/residue: 1.7931 time to fit residues: 1603.9097 Evaluate side-chains 635 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 555 time to evaluate : 3.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 1 residue 31 GLN Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 3 residue 44 THR Chi-restraints excluded: chain 4 residue 7 GLU Chi-restraints excluded: chain 6 residue 29 GLN Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain c residue 88 SER Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 251 GLN Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 18 THR Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 31 VAL Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 146 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 2 GLN Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 94 THR Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 114 GLU Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain q residue 31 VAL Chi-restraints excluded: chain r residue 19 THR Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 46 LEU Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 22 ARG Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 71 LYS Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 543 optimal weight: 0.9990 chunk 413 optimal weight: 0.9990 chunk 285 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 262 optimal weight: 40.0000 chunk 369 optimal weight: 1.9990 chunk 552 optimal weight: 0.8980 chunk 584 optimal weight: 40.0000 chunk 288 optimal weight: 7.9990 chunk 523 optimal weight: 6.9990 chunk 157 optimal weight: 30.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 23 ASN 1 38 GLN 1 39 GLN 4 26 ASN c 200 HIS ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS n 13 ASN n 62 ASN q 56 GLN r 86 GLN s 31 GLN ** w 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 98947 Z= 0.210 Angle : 0.593 8.818 148858 Z= 0.310 Chirality : 0.037 0.328 19139 Planarity : 0.005 0.055 7375 Dihedral : 24.630 179.171 51532 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 5.04 % Allowed : 23.13 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.14), residues: 3091 helix: -0.75 (0.18), residues: 829 sheet: -1.03 (0.19), residues: 660 loop : -1.39 (0.14), residues: 1602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 213 HIS 0.006 0.001 HIS c 200 PHE 0.015 0.002 PHE m 68 TYR 0.015 0.002 TYR 3 48 ARG 0.008 0.001 ARG t 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 712 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 593 time to evaluate : 3.816 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8158 (p0) cc_final: 0.7844 (p0) REVERT: 0 64 ILE cc_start: 0.9057 (tp) cc_final: 0.8805 (tp) REVERT: 2 40 ASP cc_start: 0.8346 (t0) cc_final: 0.8141 (t0) REVERT: 2 44 ILE cc_start: 0.9307 (mm) cc_final: 0.9053 (mt) REVERT: 2 56 LYS cc_start: 0.8633 (tmmt) cc_final: 0.8080 (tttm) REVERT: 3 52 ARG cc_start: 0.7607 (mtm110) cc_final: 0.7349 (ttp-170) REVERT: 8 24 ARG cc_start: 0.8508 (OUTLIER) cc_final: 0.7741 (mtt-85) REVERT: c 140 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8718 (m) REVERT: c 177 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8333 (mmm160) REVERT: c 194 GLU cc_start: 0.7899 (pt0) cc_final: 0.7678 (pt0) REVERT: d 40 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7944 (tm) REVERT: d 128 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7975 (mmt180) REVERT: e 1 MET cc_start: 0.6087 (OUTLIER) cc_final: 0.5591 (ttp) REVERT: e 90 GLN cc_start: 0.8456 (pt0) cc_final: 0.8176 (pt0) REVERT: e 94 GLN cc_start: 0.9008 (mt0) cc_final: 0.8717 (mt0) REVERT: e 137 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7513 (tmtm) REVERT: e 145 ASP cc_start: 0.7550 (t0) cc_final: 0.7289 (t70) REVERT: e 184 ASP cc_start: 0.7787 (m-30) cc_final: 0.7418 (m-30) REVERT: f 42 GLU cc_start: 0.5696 (mp0) cc_final: 0.5214 (pm20) REVERT: f 83 TYR cc_start: 0.6726 (m-10) cc_final: 0.6443 (m-10) REVERT: f 94 GLU cc_start: 0.5674 (pm20) cc_final: 0.5113 (pm20) REVERT: f 101 GLU cc_start: 0.6860 (tt0) cc_final: 0.6302 (mt-10) REVERT: f 148 ARG cc_start: 0.6097 (mmt90) cc_final: 0.5761 (mmm160) REVERT: g 69 ARG cc_start: 0.8019 (tmt170) cc_final: 0.7599 (tmt170) REVERT: g 111 HIS cc_start: 0.7682 (p-80) cc_final: 0.7448 (p90) REVERT: h 1 MET cc_start: 0.7103 (tpp) cc_final: 0.6827 (ttt) REVERT: h 12 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.7103 (pp) REVERT: j 125 TYR cc_start: 0.8544 (m-80) cc_final: 0.7972 (m-80) REVERT: k 32 TYR cc_start: 0.9177 (m-80) cc_final: 0.8925 (m-80) REVERT: k 51 LYS cc_start: 0.8435 (mttp) cc_final: 0.8181 (mmtm) REVERT: l 51 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7615 (mt-10) REVERT: l 141 LYS cc_start: 0.7975 (OUTLIER) cc_final: 0.7589 (ptmm) REVERT: m 12 MET cc_start: 0.8350 (mtt) cc_final: 0.8138 (mtp) REVERT: n 106 ASP cc_start: 0.9066 (p0) cc_final: 0.8840 (p0) REVERT: p 89 ARG cc_start: 0.7855 (mtm180) cc_final: 0.7515 (mmm-85) REVERT: q 104 VAL cc_start: 0.9155 (t) cc_final: 0.8954 (m) REVERT: r 95 ASP cc_start: 0.8438 (m-30) cc_final: 0.8132 (m-30) REVERT: w 24 ASN cc_start: 0.7808 (m-40) cc_final: 0.7489 (t0) REVERT: w 46 LYS cc_start: 0.8836 (ttmm) cc_final: 0.8477 (mttm) REVERT: w 51 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7996 (pp30) REVERT: w 53 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.7174 (mtmm) REVERT: w 85 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8129 (mtpt) REVERT: y 30 SER cc_start: 0.8780 (OUTLIER) cc_final: 0.8526 (m) REVERT: y 66 LYS cc_start: 0.9047 (mmtp) cc_final: 0.8694 (mmtm) outliers start: 119 outliers final: 44 residues processed: 654 average time/residue: 1.8063 time to fit residues: 1592.2529 Evaluate side-chains 606 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 551 time to evaluate : 3.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 4 residue 7 GLU Chi-restraints excluded: chain 4 residue 13 SER Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 140 THR Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 91 THR Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 116 ILE Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 141 LYS Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 36 VAL Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 53 LYS Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 487 optimal weight: 7.9990 chunk 331 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 435 optimal weight: 10.0000 chunk 241 optimal weight: 10.0000 chunk 499 optimal weight: 5.9990 chunk 404 optimal weight: 7.9990 chunk 0 optimal weight: 6.9990 chunk 298 optimal weight: 10.0000 chunk 524 optimal weight: 7.9990 chunk 147 optimal weight: 6.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 38 GLN 4 26 ASN 7 28 ASN c 200 HIS ** d 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 73 ASN g 115 HIS j 128 ASN n 13 ASN p 10 GLN q 56 GLN q 72 ASN r 86 GLN s 31 GLN u 69 ASN w 51 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.077 98947 Z= 0.642 Angle : 0.862 11.504 148858 Z= 0.433 Chirality : 0.053 0.416 19139 Planarity : 0.007 0.103 7375 Dihedral : 24.754 179.715 51531 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.68 % Favored : 93.32 % Rotamer: Outliers : 6.02 % Allowed : 22.63 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.14), residues: 3091 helix: -0.87 (0.18), residues: 820 sheet: -1.01 (0.19), residues: 678 loop : -1.42 (0.14), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP c 213 HIS 0.010 0.002 HIS q 14 PHE 0.026 0.003 PHE q 57 TYR 0.017 0.003 TYR f 128 ARG 0.009 0.001 ARG 0 11 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 699 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 556 time to evaluate : 4.045 Fit side-chains revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8337 (p0) cc_final: 0.7988 (p0) REVERT: 0 64 ILE cc_start: 0.9038 (tp) cc_final: 0.8789 (tp) REVERT: 1 36 GLN cc_start: 0.7996 (mp10) cc_final: 0.7738 (mp10) REVERT: 1 44 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8288 (ttpp) REVERT: 2 44 ILE cc_start: 0.9326 (mm) cc_final: 0.9103 (mt) REVERT: 2 56 LYS cc_start: 0.8604 (tmmt) cc_final: 0.8081 (tttm) REVERT: 3 52 ARG cc_start: 0.7576 (mtm110) cc_final: 0.7286 (ttp-170) REVERT: 8 17 VAL cc_start: 0.8566 (t) cc_final: 0.8356 (m) REVERT: c 132 MET cc_start: 0.8531 (OUTLIER) cc_final: 0.6741 (mmt) REVERT: c 140 THR cc_start: 0.8964 (t) cc_final: 0.8706 (m) REVERT: d 1 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.6308 (ttm) REVERT: d 40 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8031 (tm) REVERT: d 89 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7077 (tp30) REVERT: e 1 MET cc_start: 0.6367 (OUTLIER) cc_final: 0.5831 (ttp) REVERT: e 137 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.8005 (tmtm) REVERT: e 141 MET cc_start: 0.7842 (OUTLIER) cc_final: 0.7639 (mpp) REVERT: e 144 GLU cc_start: 0.7053 (OUTLIER) cc_final: 0.6684 (pt0) REVERT: e 197 GLU cc_start: 0.7545 (tp30) cc_final: 0.7274 (tp30) REVERT: f 16 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7170 (mt) REVERT: f 78 LYS cc_start: 0.7219 (mmtt) cc_final: 0.6900 (tmtt) REVERT: f 96 MET cc_start: 0.7186 (ptm) cc_final: 0.6922 (ptp) REVERT: f 101 GLU cc_start: 0.6980 (tt0) cc_final: 0.6346 (mt-10) REVERT: f 148 ARG cc_start: 0.6060 (mmt90) cc_final: 0.5639 (mmm160) REVERT: g 69 ARG cc_start: 0.8042 (tmt170) cc_final: 0.7706 (tmt170) REVERT: h 1 MET cc_start: 0.7109 (OUTLIER) cc_final: 0.6772 (ttt) REVERT: j 11 VAL cc_start: 0.8098 (p) cc_final: 0.7786 (m) REVERT: j 34 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7553 (ttp-110) REVERT: k 32 TYR cc_start: 0.9239 (m-80) cc_final: 0.8645 (m-80) REVERT: l 92 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8481 (tm) REVERT: l 141 LYS cc_start: 0.7996 (ptmm) cc_final: 0.7697 (ttpp) REVERT: m 78 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8476 (mp) REVERT: o 32 PRO cc_start: 0.8741 (Cg_exo) cc_final: 0.8517 (Cg_exo) REVERT: o 34 HIS cc_start: 0.7951 (m90) cc_final: 0.6986 (m90) REVERT: p 6 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.8111 (tppp) REVERT: p 89 ARG cc_start: 0.7928 (mtm180) cc_final: 0.7509 (mmm-85) REVERT: p 106 LYS cc_start: 0.6403 (OUTLIER) cc_final: 0.4314 (mptt) REVERT: q 104 VAL cc_start: 0.9215 (t) cc_final: 0.9014 (m) REVERT: q 112 LYS cc_start: 0.8653 (OUTLIER) cc_final: 0.8380 (ttmt) REVERT: r 62 GLU cc_start: 0.7527 (tm-30) cc_final: 0.7178 (mm-30) REVERT: r 95 ASP cc_start: 0.8526 (m-30) cc_final: 0.8213 (m-30) REVERT: s 22 ASP cc_start: 0.8129 (m-30) cc_final: 0.7730 (m-30) REVERT: t 18 GLU cc_start: 0.7578 (tm-30) cc_final: 0.7289 (tp30) REVERT: t 26 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8271 (mmtt) REVERT: u 27 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8266 (p0) REVERT: w 24 ASN cc_start: 0.7907 (m-40) cc_final: 0.7515 (t0) outliers start: 143 outliers final: 76 residues processed: 629 average time/residue: 1.9163 time to fit residues: 1605.9892 Evaluate side-chains 615 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 522 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 0 residue 66 THR Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 4 residue 23 THR Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 132 MET Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 252 THR Chi-restraints excluded: chain c residue 268 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 36 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 44 LYS Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 34 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 92 LEU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain m residue 78 LEU Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 112 LYS Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 26 LYS Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 27 ASN Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 70 ILE Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 64 ASP Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 196 optimal weight: 7.9990 chunk 526 optimal weight: 7.9990 chunk 115 optimal weight: 5.9990 chunk 343 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 585 optimal weight: 30.0000 chunk 485 optimal weight: 2.9990 chunk 271 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 chunk 307 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 38 GLN 7 43 HIS d 32 ASN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 20 ASN g 115 HIS j 128 ASN o 98 GLN q 56 GLN r 86 GLN s 31 GLN s 61 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 98947 Z= 0.343 Angle : 0.650 8.913 148858 Z= 0.337 Chirality : 0.041 0.333 19139 Planarity : 0.005 0.060 7375 Dihedral : 24.616 179.036 51531 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 5.35 % Allowed : 24.03 % Favored : 70.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.53 (0.15), residues: 3091 helix: -0.53 (0.18), residues: 824 sheet: -0.85 (0.20), residues: 671 loop : -1.30 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 213 HIS 0.008 0.001 HIS c 200 PHE 0.018 0.002 PHE q 57 TYR 0.012 0.002 TYR q 32 ARG 0.006 0.001 ARG f 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 664 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 538 time to evaluate : 3.852 Fit side-chains REVERT: 0 60 ASP cc_start: 0.8269 (p0) cc_final: 0.7912 (p0) REVERT: 0 64 ILE cc_start: 0.9043 (tp) cc_final: 0.8754 (tp) REVERT: 1 17 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7818 (tt0) REVERT: 1 36 GLN cc_start: 0.7982 (mp10) cc_final: 0.7771 (mp10) REVERT: 2 40 ASP cc_start: 0.8371 (t0) cc_final: 0.8148 (t0) REVERT: 2 44 ILE cc_start: 0.9328 (mm) cc_final: 0.9095 (mt) REVERT: 2 56 LYS cc_start: 0.8551 (tmmt) cc_final: 0.7687 (tttm) REVERT: 3 52 ARG cc_start: 0.7423 (mtm110) cc_final: 0.7207 (ttp-170) REVERT: 6 29 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8087 (mt0) REVERT: 8 24 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7806 (mtt-85) REVERT: c 140 THR cc_start: 0.8932 (t) cc_final: 0.8692 (m) REVERT: d 18 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7165 (t0) REVERT: d 40 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8088 (tm) REVERT: d 89 GLU cc_start: 0.7298 (mm-30) cc_final: 0.7078 (tp30) REVERT: d 128 ARG cc_start: 0.8220 (mtm-85) cc_final: 0.7921 (mmt180) REVERT: e 1 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.5744 (ttp) REVERT: e 90 GLN cc_start: 0.8553 (pt0) cc_final: 0.8148 (pt0) REVERT: e 137 LYS cc_start: 0.8385 (OUTLIER) cc_final: 0.8057 (tmtm) REVERT: e 144 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6613 (pt0) REVERT: f 94 GLU cc_start: 0.6213 (pm20) cc_final: 0.5641 (pm20) REVERT: f 96 MET cc_start: 0.7024 (ptm) cc_final: 0.6804 (ptp) REVERT: f 101 GLU cc_start: 0.6978 (tt0) cc_final: 0.6309 (mt-10) REVERT: f 148 ARG cc_start: 0.6019 (mmt90) cc_final: 0.5692 (mmm160) REVERT: g 69 ARG cc_start: 0.8066 (tmt170) cc_final: 0.7740 (tmt170) REVERT: h 12 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7119 (pp) REVERT: j 11 VAL cc_start: 0.8175 (p) cc_final: 0.7924 (m) REVERT: j 34 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7610 (ttp-110) REVERT: k 32 TYR cc_start: 0.9206 (m-80) cc_final: 0.8895 (m-80) REVERT: k 53 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7936 (mmtt) REVERT: k 113 MET cc_start: 0.7773 (OUTLIER) cc_final: 0.7483 (ptp) REVERT: l 51 GLU cc_start: 0.7968 (OUTLIER) cc_final: 0.7554 (mt-10) REVERT: l 129 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7474 (mtpt) REVERT: l 141 LYS cc_start: 0.7998 (ptmm) cc_final: 0.7728 (ttpp) REVERT: o 32 PRO cc_start: 0.8735 (Cg_exo) cc_final: 0.8532 (Cg_exo) REVERT: o 34 HIS cc_start: 0.7831 (m90) cc_final: 0.6885 (m90) REVERT: p 38 LYS cc_start: 0.8445 (ttpp) cc_final: 0.8190 (ttpt) REVERT: p 78 SER cc_start: 0.8781 (OUTLIER) cc_final: 0.8541 (t) REVERT: p 89 ARG cc_start: 0.7849 (mtm180) cc_final: 0.7483 (mmm-85) REVERT: p 106 LYS cc_start: 0.6391 (OUTLIER) cc_final: 0.4148 (mptt) REVERT: r 62 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7204 (mm-30) REVERT: r 95 ASP cc_start: 0.8491 (m-30) cc_final: 0.8188 (m-30) REVERT: t 18 GLU cc_start: 0.7596 (tm-30) cc_final: 0.7267 (tp30) REVERT: u 86 ARG cc_start: 0.8103 (ptp90) cc_final: 0.7844 (ptt90) REVERT: w 24 ASN cc_start: 0.7896 (m-40) cc_final: 0.7595 (t0) REVERT: y 30 SER cc_start: 0.8752 (OUTLIER) cc_final: 0.8461 (m) REVERT: y 66 LYS cc_start: 0.9027 (mmtp) cc_final: 0.8569 (mmtm) outliers start: 126 outliers final: 64 residues processed: 602 average time/residue: 1.8365 time to fit residues: 1483.8645 Evaluate side-chains 603 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 521 time to evaluate : 3.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 1 residue 17 GLU Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 6 residue 29 GLN Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 34 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 129 LYS Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 7 GLN Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 36 VAL Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 70 ILE Chi-restraints excluded: chain y residue 30 SER Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 564 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 427 optimal weight: 3.9990 chunk 331 optimal weight: 10.0000 chunk 492 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 583 optimal weight: 30.0000 chunk 364 optimal weight: 2.9990 chunk 355 optimal weight: 6.9990 chunk 269 optimal weight: 40.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 6 GLN 1 38 GLN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS n 13 ASN p 66 ASN q 56 GLN q 72 ASN r 18 GLN r 86 GLN s 31 GLN u 66 GLN w 51 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 98947 Z= 0.476 Angle : 0.737 10.807 148858 Z= 0.377 Chirality : 0.046 0.370 19139 Planarity : 0.006 0.088 7375 Dihedral : 24.650 179.586 51531 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.71 % Allowed : 24.15 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.14), residues: 3091 helix: -0.52 (0.18), residues: 816 sheet: -0.83 (0.20), residues: 672 loop : -1.30 (0.15), residues: 1603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 213 HIS 0.009 0.001 HIS c 200 PHE 0.022 0.002 PHE q 57 TYR 0.016 0.002 TYR f 128 ARG 0.007 0.001 ARG 0 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 526 time to evaluate : 3.818 Fit side-chains revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8312 (p0) cc_final: 0.7962 (p0) REVERT: 0 64 ILE cc_start: 0.9030 (tp) cc_final: 0.8758 (tp) REVERT: 1 44 LYS cc_start: 0.8600 (ttmt) cc_final: 0.8297 (ttpp) REVERT: 2 40 ASP cc_start: 0.8484 (t0) cc_final: 0.8248 (t0) REVERT: 2 44 ILE cc_start: 0.9335 (mm) cc_final: 0.9098 (mt) REVERT: 2 56 LYS cc_start: 0.8572 (ttmt) cc_final: 0.8117 (tttm) REVERT: 6 29 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: 7 28 ASN cc_start: 0.9023 (m110) cc_final: 0.8659 (m110) REVERT: c 140 THR cc_start: 0.8973 (t) cc_final: 0.8693 (m) REVERT: c 182 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.6137 (tmt90) REVERT: d 18 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7167 (t0) REVERT: d 40 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.8091 (tm) REVERT: d 89 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7038 (tp30) REVERT: d 128 ARG cc_start: 0.8225 (mtm-85) cc_final: 0.7908 (mmt180) REVERT: e 1 MET cc_start: 0.6410 (OUTLIER) cc_final: 0.5478 (ttp) REVERT: e 90 GLN cc_start: 0.8549 (pt0) cc_final: 0.8198 (pt0) REVERT: e 137 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8339 (tmtm) REVERT: e 141 MET cc_start: 0.7821 (OUTLIER) cc_final: 0.7608 (mpp) REVERT: e 144 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6818 (pt0) REVERT: e 197 GLU cc_start: 0.7433 (OUTLIER) cc_final: 0.7162 (tp30) REVERT: f 7 TYR cc_start: 0.6654 (t80) cc_final: 0.6397 (t80) REVERT: f 94 GLU cc_start: 0.6322 (pm20) cc_final: 0.5739 (pm20) REVERT: f 96 MET cc_start: 0.7165 (ptm) cc_final: 0.6953 (ptp) REVERT: f 148 ARG cc_start: 0.6040 (mmt90) cc_final: 0.5719 (mmm160) REVERT: h 12 LEU cc_start: 0.7540 (OUTLIER) cc_final: 0.7195 (pp) REVERT: j 11 VAL cc_start: 0.8244 (p) cc_final: 0.8026 (m) REVERT: j 34 ARG cc_start: 0.8407 (OUTLIER) cc_final: 0.7576 (ttp-110) REVERT: j 118 MET cc_start: 0.8894 (OUTLIER) cc_final: 0.8639 (mtp) REVERT: k 32 TYR cc_start: 0.9203 (m-80) cc_final: 0.8824 (m-80) REVERT: k 53 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.7940 (mmtt) REVERT: k 113 MET cc_start: 0.7824 (OUTLIER) cc_final: 0.7409 (ptp) REVERT: l 51 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7628 (mt-10) REVERT: l 129 LYS cc_start: 0.8175 (OUTLIER) cc_final: 0.7395 (mtpt) REVERT: l 141 LYS cc_start: 0.7993 (ptmm) cc_final: 0.7725 (ttpp) REVERT: o 32 PRO cc_start: 0.8716 (Cg_exo) cc_final: 0.8501 (Cg_exo) REVERT: o 34 HIS cc_start: 0.7860 (m90) cc_final: 0.6847 (m90) REVERT: p 6 LYS cc_start: 0.8551 (OUTLIER) cc_final: 0.8185 (tppp) REVERT: p 38 LYS cc_start: 0.8457 (ttpp) cc_final: 0.8209 (ttpt) REVERT: p 78 SER cc_start: 0.8901 (OUTLIER) cc_final: 0.8697 (t) REVERT: p 89 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7476 (mmm-85) REVERT: p 106 LYS cc_start: 0.6441 (OUTLIER) cc_final: 0.4120 (mptt) REVERT: q 112 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8375 (ttmt) REVERT: r 62 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7227 (mm-30) REVERT: r 95 ASP cc_start: 0.8522 (m-30) cc_final: 0.8209 (m-30) REVERT: s 22 ASP cc_start: 0.8076 (m-30) cc_final: 0.7770 (m-30) REVERT: t 18 GLU cc_start: 0.7638 (tm-30) cc_final: 0.7317 (tp30) REVERT: t 26 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8577 (mmpt) REVERT: w 24 ASN cc_start: 0.7970 (m-40) cc_final: 0.7594 (t0) REVERT: y 70 GLU cc_start: 0.7448 (OUTLIER) cc_final: 0.7240 (tp30) outliers start: 134 outliers final: 78 residues processed: 603 average time/residue: 1.8723 time to fit residues: 1511.1833 Evaluate side-chains 618 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 518 time to evaluate : 3.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 25 THR Chi-restraints excluded: chain 1 residue 16 THR Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 3 residue 28 LEU Chi-restraints excluded: chain 6 residue 29 GLN Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 94 VAL Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 252 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 60 VAL Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 141 MET Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 197 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 25 VAL Chi-restraints excluded: chain f residue 32 GLU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 108 VAL Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 36 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 34 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain j residue 118 MET Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 82 ASN Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 129 LYS Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain n residue 14 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 36 THR Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 49 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 112 LYS Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain t residue 42 GLU Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 51 GLN Chi-restraints excluded: chain w residue 61 LEU Chi-restraints excluded: chain w residue 70 ILE Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 360 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 348 optimal weight: 0.9990 chunk 175 optimal weight: 4.9990 chunk 114 optimal weight: 5.9990 chunk 112 optimal weight: 6.9990 chunk 370 optimal weight: 1.9990 chunk 397 optimal weight: 0.8980 chunk 288 optimal weight: 7.9990 chunk 54 optimal weight: 4.9990 chunk 458 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 38 GLN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS n 13 ASN q 56 GLN r 18 GLN r 86 GLN s 31 GLN u 66 GLN w 51 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 98947 Z= 0.177 Angle : 0.574 8.909 148858 Z= 0.300 Chirality : 0.035 0.323 19139 Planarity : 0.004 0.052 7375 Dihedral : 24.505 178.601 51531 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 4.26 % Allowed : 25.75 % Favored : 69.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.15), residues: 3091 helix: -0.15 (0.19), residues: 824 sheet: -0.72 (0.20), residues: 663 loop : -1.17 (0.15), residues: 1604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 0 39 HIS 0.006 0.001 HIS o 100 PHE 0.022 0.001 PHE f 20 TYR 0.010 0.001 TYR h 25 ARG 0.008 0.000 ARG c 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 551 time to evaluate : 3.799 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8273 (p0) cc_final: 0.7922 (p0) REVERT: 0 64 ILE cc_start: 0.9021 (tp) cc_final: 0.8740 (tp) REVERT: 1 44 LYS cc_start: 0.8529 (ttmt) cc_final: 0.8224 (ttpp) REVERT: 2 40 ASP cc_start: 0.8465 (t0) cc_final: 0.8199 (t0) REVERT: 2 44 ILE cc_start: 0.9351 (mm) cc_final: 0.9072 (mt) REVERT: 6 25 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8539 (ttpp) REVERT: 6 29 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.8048 (mt0) REVERT: 7 28 ASN cc_start: 0.9001 (m110) cc_final: 0.8583 (m110) REVERT: 8 24 ARG cc_start: 0.8518 (OUTLIER) cc_final: 0.7948 (mtt-85) REVERT: c 140 THR cc_start: 0.8913 (t) cc_final: 0.8671 (m) REVERT: d 18 ASP cc_start: 0.7693 (OUTLIER) cc_final: 0.7153 (t0) REVERT: d 40 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8119 (tm) REVERT: d 89 GLU cc_start: 0.7349 (mm-30) cc_final: 0.7130 (tp30) REVERT: d 128 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7925 (mmt180) REVERT: e 2 GLU cc_start: 0.6360 (OUTLIER) cc_final: 0.5502 (mm-30) REVERT: e 90 GLN cc_start: 0.8491 (pt0) cc_final: 0.8183 (pt0) REVERT: e 122 GLU cc_start: 0.7413 (pp20) cc_final: 0.6898 (pp20) REVERT: e 137 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8191 (tmtm) REVERT: e 144 GLU cc_start: 0.7115 (OUTLIER) cc_final: 0.6733 (pt0) REVERT: e 197 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7292 (tp30) REVERT: f 7 TYR cc_start: 0.6555 (t80) cc_final: 0.6307 (t80) REVERT: f 16 LEU cc_start: 0.7403 (OUTLIER) cc_final: 0.7170 (mt) REVERT: f 19 GLU cc_start: 0.6014 (pm20) cc_final: 0.5597 (pm20) REVERT: f 94 GLU cc_start: 0.5951 (pm20) cc_final: 0.5532 (pm20) REVERT: f 96 MET cc_start: 0.7003 (ptm) cc_final: 0.6792 (ptp) REVERT: f 101 GLU cc_start: 0.6844 (tt0) cc_final: 0.6190 (mt-10) REVERT: f 148 ARG cc_start: 0.6033 (mmt90) cc_final: 0.5720 (mmm160) REVERT: h 12 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.6960 (pp) REVERT: j 11 VAL cc_start: 0.8192 (p) cc_final: 0.7939 (m) REVERT: j 34 ARG cc_start: 0.8308 (OUTLIER) cc_final: 0.7551 (ttp-110) REVERT: k 32 TYR cc_start: 0.9043 (m-80) cc_final: 0.8835 (m-80) REVERT: k 53 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7957 (mmtt) REVERT: k 113 MET cc_start: 0.7720 (OUTLIER) cc_final: 0.7516 (ptp) REVERT: l 51 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.7529 (mt-10) REVERT: l 129 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7466 (mtpt) REVERT: l 141 LYS cc_start: 0.7925 (ptmm) cc_final: 0.7722 (ttpp) REVERT: o 32 PRO cc_start: 0.8654 (Cg_exo) cc_final: 0.8450 (Cg_exo) REVERT: o 34 HIS cc_start: 0.7836 (m90) cc_final: 0.6992 (m90) REVERT: p 6 LYS cc_start: 0.8476 (OUTLIER) cc_final: 0.8140 (tppp) REVERT: p 38 LYS cc_start: 0.8391 (ttpp) cc_final: 0.8173 (ttpt) REVERT: p 78 SER cc_start: 0.8585 (OUTLIER) cc_final: 0.8371 (t) REVERT: p 89 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7536 (mmm-85) REVERT: p 106 LYS cc_start: 0.6354 (OUTLIER) cc_final: 0.4122 (mptt) REVERT: r 62 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7149 (mm-30) REVERT: r 95 ASP cc_start: 0.8488 (m-30) cc_final: 0.8150 (m-30) REVERT: u 27 ASN cc_start: 0.8300 (p0) cc_final: 0.7990 (p0) REVERT: u 86 ARG cc_start: 0.8156 (ptp90) cc_final: 0.7929 (ptt90) REVERT: w 24 ASN cc_start: 0.7911 (m-40) cc_final: 0.7616 (t0) REVERT: w 46 LYS cc_start: 0.8816 (ttmm) cc_final: 0.8541 (mttm) outliers start: 97 outliers final: 51 residues processed: 609 average time/residue: 1.8640 time to fit residues: 1521.6485 Evaluate side-chains 602 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 531 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 29 GLN Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 252 THR Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 32 VAL Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 197 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 16 LEU Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 34 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain k residue 113 MET Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 129 LYS Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 53 THR Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 101 SER Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 36 VAL Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 530 optimal weight: 4.9990 chunk 558 optimal weight: 0.0770 chunk 509 optimal weight: 2.9990 chunk 543 optimal weight: 0.2980 chunk 327 optimal weight: 8.9990 chunk 236 optimal weight: 10.0000 chunk 426 optimal weight: 0.0030 chunk 166 optimal weight: 7.9990 chunk 491 optimal weight: 1.9990 chunk 513 optimal weight: 9.9990 chunk 541 optimal weight: 7.9990 overall best weight: 1.0752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 38 GLN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS n 13 ASN q 56 GLN r 18 GLN r 86 GLN s 31 GLN u 66 GLN w 51 GLN ** y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 76 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 98947 Z= 0.148 Angle : 0.556 9.071 148858 Z= 0.291 Chirality : 0.034 0.321 19139 Planarity : 0.004 0.065 7375 Dihedral : 24.497 178.890 51531 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.91 % Allowed : 26.34 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.15), residues: 3091 helix: 0.02 (0.19), residues: 822 sheet: -0.67 (0.20), residues: 647 loop : -1.07 (0.15), residues: 1622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 0 39 HIS 0.006 0.001 HIS o 100 PHE 0.022 0.001 PHE f 20 TYR 0.013 0.001 TYR g 94 ARG 0.018 0.000 ARG 0 74 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 535 time to evaluate : 3.899 Fit side-chains revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8240 (p0) cc_final: 0.7900 (p0) REVERT: 0 64 ILE cc_start: 0.9004 (tp) cc_final: 0.8718 (tp) REVERT: 1 30 MET cc_start: 0.8056 (mmp) cc_final: 0.7817 (mmt) REVERT: 1 44 LYS cc_start: 0.8504 (ttmt) cc_final: 0.8211 (ttpp) REVERT: 2 40 ASP cc_start: 0.8462 (t0) cc_final: 0.8181 (t0) REVERT: 2 44 ILE cc_start: 0.9353 (mm) cc_final: 0.9065 (mt) REVERT: 2 56 LYS cc_start: 0.8501 (ttpt) cc_final: 0.7993 (tttm) REVERT: 2 58 GLU cc_start: 0.5289 (mp0) cc_final: 0.4649 (mp0) REVERT: 6 29 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7958 (mt0) REVERT: 7 28 ASN cc_start: 0.8985 (m110) cc_final: 0.8565 (m110) REVERT: 8 24 ARG cc_start: 0.8543 (OUTLIER) cc_final: 0.7891 (mtt-85) REVERT: c 140 THR cc_start: 0.8926 (t) cc_final: 0.8685 (m) REVERT: d 1 MET cc_start: 0.7748 (OUTLIER) cc_final: 0.6865 (tmt) REVERT: d 18 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7153 (t0) REVERT: d 40 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8108 (tm) REVERT: d 89 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7131 (tp30) REVERT: d 128 ARG cc_start: 0.8127 (mtm-85) cc_final: 0.7916 (mmt180) REVERT: e 90 GLN cc_start: 0.8472 (pt0) cc_final: 0.8156 (pt0) REVERT: e 122 GLU cc_start: 0.7465 (pp20) cc_final: 0.7004 (pp20) REVERT: e 137 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8193 (tmtm) REVERT: e 144 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.6710 (pt0) REVERT: e 152 GLU cc_start: 0.5185 (pm20) cc_final: 0.4785 (pm20) REVERT: e 197 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: f 7 TYR cc_start: 0.6546 (t80) cc_final: 0.6292 (t80) REVERT: f 19 GLU cc_start: 0.5954 (pm20) cc_final: 0.5715 (pm20) REVERT: f 42 GLU cc_start: 0.5908 (mp0) cc_final: 0.5463 (pm20) REVERT: f 94 GLU cc_start: 0.5743 (pm20) cc_final: 0.5487 (pm20) REVERT: f 96 MET cc_start: 0.6919 (ptm) cc_final: 0.6715 (ptp) REVERT: f 101 GLU cc_start: 0.6825 (tt0) cc_final: 0.6177 (mt-10) REVERT: f 148 ARG cc_start: 0.6032 (mmt90) cc_final: 0.5738 (mmm160) REVERT: h 12 LEU cc_start: 0.7250 (OUTLIER) cc_final: 0.6935 (pp) REVERT: j 11 VAL cc_start: 0.8185 (p) cc_final: 0.7933 (m) REVERT: j 34 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.7541 (ttp-110) REVERT: j 125 TYR cc_start: 0.8550 (m-80) cc_final: 0.7963 (m-80) REVERT: k 53 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7954 (mmtt) REVERT: l 51 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7499 (mt-10) REVERT: l 129 LYS cc_start: 0.8061 (OUTLIER) cc_final: 0.7409 (mtpt) REVERT: o 34 HIS cc_start: 0.7807 (m90) cc_final: 0.6968 (m90) REVERT: p 6 LYS cc_start: 0.8480 (OUTLIER) cc_final: 0.8139 (tppp) REVERT: p 38 LYS cc_start: 0.8359 (ttpp) cc_final: 0.8137 (ttpt) REVERT: p 89 ARG cc_start: 0.7834 (mtm180) cc_final: 0.7485 (mmm-85) REVERT: p 106 LYS cc_start: 0.6345 (OUTLIER) cc_final: 0.4120 (mptt) REVERT: q 112 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8264 (ttmt) REVERT: r 60 LYS cc_start: 0.8182 (mtpm) cc_final: 0.7981 (mptt) REVERT: r 62 GLU cc_start: 0.7446 (OUTLIER) cc_final: 0.7203 (mm-30) REVERT: r 95 ASP cc_start: 0.8492 (m-30) cc_final: 0.8161 (m-30) REVERT: u 27 ASN cc_start: 0.8272 (p0) cc_final: 0.7774 (p0) REVERT: u 86 ARG cc_start: 0.8159 (ptp90) cc_final: 0.7834 (ptt90) REVERT: w 24 ASN cc_start: 0.7908 (m-40) cc_final: 0.7627 (t0) REVERT: w 46 LYS cc_start: 0.8810 (ttmm) cc_final: 0.8530 (mttm) outliers start: 87 outliers final: 54 residues processed: 588 average time/residue: 1.8814 time to fit residues: 1478.6887 Evaluate side-chains 591 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 520 time to evaluate : 3.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 6 residue 25 LYS Chi-restraints excluded: chain 6 residue 29 GLN Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 252 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 197 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 34 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 129 LYS Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 112 LYS Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 36 VAL Chi-restraints excluded: chain w residue 41 GLU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 356 optimal weight: 6.9990 chunk 574 optimal weight: 9.9990 chunk 350 optimal weight: 4.9990 chunk 272 optimal weight: 10.0000 chunk 399 optimal weight: 3.9990 chunk 602 optimal weight: 6.9990 chunk 554 optimal weight: 0.9990 chunk 479 optimal weight: 6.9990 chunk 49 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 chunk 294 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 6 GLN 1 38 GLN 1 58 ASN f 23 ASN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS n 13 ASN p 66 ASN q 56 GLN r 18 GLN r 86 GLN s 31 GLN w 51 GLN ** y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 76 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.052 98947 Z= 0.428 Angle : 0.690 9.520 148858 Z= 0.353 Chirality : 0.043 0.355 19139 Planarity : 0.005 0.078 7375 Dihedral : 24.503 179.736 51531 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.91 % Allowed : 26.30 % Favored : 69.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.15), residues: 3091 helix: -0.19 (0.18), residues: 826 sheet: -0.70 (0.20), residues: 672 loop : -1.09 (0.15), residues: 1593 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP 0 39 HIS 0.009 0.001 HIS c 200 PHE 0.022 0.002 PHE q 57 TYR 0.015 0.002 TYR q 32 ARG 0.013 0.001 ARG 0 74 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6182 Ramachandran restraints generated. 3091 Oldfield, 0 Emsley, 3091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 524 time to evaluate : 3.870 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 0 60 ASP cc_start: 0.8312 (p0) cc_final: 0.7950 (p0) REVERT: 0 64 ILE cc_start: 0.9026 (tp) cc_final: 0.8749 (tp) REVERT: 1 30 MET cc_start: 0.8106 (mmp) cc_final: 0.7895 (mmt) REVERT: 1 44 LYS cc_start: 0.8579 (ttmt) cc_final: 0.8268 (ttpp) REVERT: 2 40 ASP cc_start: 0.8467 (t0) cc_final: 0.8222 (t0) REVERT: 2 44 ILE cc_start: 0.9369 (mm) cc_final: 0.9114 (mt) REVERT: 6 29 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.8113 (mt0) REVERT: 7 28 ASN cc_start: 0.9045 (m110) cc_final: 0.8673 (m110) REVERT: c 140 THR cc_start: 0.8946 (t) cc_final: 0.8684 (m) REVERT: d 1 MET cc_start: 0.7815 (OUTLIER) cc_final: 0.7414 (tmm) REVERT: d 18 ASP cc_start: 0.7773 (OUTLIER) cc_final: 0.7165 (t0) REVERT: d 40 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8108 (tm) REVERT: d 89 GLU cc_start: 0.7356 (mm-30) cc_final: 0.7121 (tp30) REVERT: d 128 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7912 (mmt180) REVERT: e 90 GLN cc_start: 0.8538 (pt0) cc_final: 0.8167 (pt0) REVERT: e 137 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8336 (tmtm) REVERT: e 144 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6796 (pt0) REVERT: e 152 GLU cc_start: 0.5155 (pm20) cc_final: 0.4855 (pm20) REVERT: e 197 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7228 (tp30) REVERT: f 7 TYR cc_start: 0.6586 (t80) cc_final: 0.6342 (t80) REVERT: f 19 GLU cc_start: 0.6060 (pm20) cc_final: 0.5828 (pm20) REVERT: f 42 GLU cc_start: 0.5978 (mp0) cc_final: 0.5631 (pm20) REVERT: f 94 GLU cc_start: 0.5930 (pm20) cc_final: 0.5588 (pm20) REVERT: f 96 MET cc_start: 0.7061 (ptm) cc_final: 0.6857 (ptp) REVERT: f 101 GLU cc_start: 0.6826 (tt0) cc_final: 0.6192 (mt-10) REVERT: f 148 ARG cc_start: 0.6048 (mmt90) cc_final: 0.5771 (mmm160) REVERT: h 12 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7032 (pp) REVERT: j 11 VAL cc_start: 0.8311 (p) cc_final: 0.8065 (m) REVERT: j 34 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7611 (ttp-110) REVERT: j 118 MET cc_start: 0.8913 (mtt) cc_final: 0.8655 (mtt) REVERT: k 53 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.7964 (mmtt) REVERT: l 51 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7578 (mt-10) REVERT: l 129 LYS cc_start: 0.8130 (OUTLIER) cc_final: 0.7488 (mtpt) REVERT: o 32 PRO cc_start: 0.8716 (Cg_exo) cc_final: 0.8504 (Cg_exo) REVERT: o 34 HIS cc_start: 0.7903 (m90) cc_final: 0.7024 (m90) REVERT: p 6 LYS cc_start: 0.8561 (OUTLIER) cc_final: 0.8186 (tppp) REVERT: p 38 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8172 (ttpt) REVERT: p 89 ARG cc_start: 0.7853 (mtm180) cc_final: 0.7481 (mmm-85) REVERT: p 106 LYS cc_start: 0.6446 (OUTLIER) cc_final: 0.4148 (mptt) REVERT: q 112 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8314 (ttmt) REVERT: r 62 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7232 (mm-30) REVERT: r 95 ASP cc_start: 0.8539 (m-30) cc_final: 0.8239 (m-30) REVERT: t 18 GLU cc_start: 0.7565 (tm-30) cc_final: 0.7305 (tp30) REVERT: u 86 ARG cc_start: 0.8240 (ptp90) cc_final: 0.7908 (ptt90) REVERT: w 24 ASN cc_start: 0.7951 (m-40) cc_final: 0.7616 (t0) REVERT: w 46 LYS cc_start: 0.8857 (ttmm) cc_final: 0.8586 (mttm) REVERT: w 68 LYS cc_start: 0.7744 (tptt) cc_final: 0.7206 (ttpm) REVERT: y 70 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.7238 (tp30) outliers start: 87 outliers final: 61 residues processed: 577 average time/residue: 1.9275 time to fit residues: 1479.2758 Evaluate side-chains 590 residues out of total 2516 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 512 time to evaluate : 3.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 8 THR Chi-restraints excluded: chain 2 residue 36 VAL Chi-restraints excluded: chain 3 residue 18 SER Chi-restraints excluded: chain 3 residue 25 VAL Chi-restraints excluded: chain 6 residue 29 GLN Chi-restraints excluded: chain 6 residue 43 THR Chi-restraints excluded: chain 7 residue 6 THR Chi-restraints excluded: chain 8 residue 2 LYS Chi-restraints excluded: chain 8 residue 24 ARG Chi-restraints excluded: chain c residue 137 VAL Chi-restraints excluded: chain c residue 173 THR Chi-restraints excluded: chain c residue 184 VAL Chi-restraints excluded: chain c residue 185 GLU Chi-restraints excluded: chain c residue 252 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 18 ASP Chi-restraints excluded: chain d residue 21 SER Chi-restraints excluded: chain d residue 40 LEU Chi-restraints excluded: chain d residue 106 LYS Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 151 THR Chi-restraints excluded: chain d residue 179 ARG Chi-restraints excluded: chain d residue 207 VAL Chi-restraints excluded: chain e residue 2 GLU Chi-restraints excluded: chain e residue 137 LYS Chi-restraints excluded: chain e residue 144 GLU Chi-restraints excluded: chain e residue 197 GLU Chi-restraints excluded: chain f residue 13 VAL Chi-restraints excluded: chain f residue 67 ILE Chi-restraints excluded: chain f residue 90 THR Chi-restraints excluded: chain f residue 104 ILE Chi-restraints excluded: chain f residue 135 GLN Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain g residue 41 VAL Chi-restraints excluded: chain g residue 121 ILE Chi-restraints excluded: chain h residue 12 LEU Chi-restraints excluded: chain j residue 34 ARG Chi-restraints excluded: chain j residue 45 THR Chi-restraints excluded: chain k residue 20 MET Chi-restraints excluded: chain k residue 35 VAL Chi-restraints excluded: chain k residue 53 LYS Chi-restraints excluded: chain k residue 58 LEU Chi-restraints excluded: chain k residue 75 SER Chi-restraints excluded: chain k residue 104 THR Chi-restraints excluded: chain l residue 51 GLU Chi-restraints excluded: chain l residue 120 VAL Chi-restraints excluded: chain l residue 129 LYS Chi-restraints excluded: chain m residue 54 THR Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 89 SER Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 47 VAL Chi-restraints excluded: chain o residue 69 ASP Chi-restraints excluded: chain o residue 100 HIS Chi-restraints excluded: chain p residue 5 ILE Chi-restraints excluded: chain p residue 6 LYS Chi-restraints excluded: chain p residue 33 VAL Chi-restraints excluded: chain p residue 41 GLN Chi-restraints excluded: chain p residue 76 THR Chi-restraints excluded: chain p residue 80 VAL Chi-restraints excluded: chain p residue 106 LYS Chi-restraints excluded: chain q residue 18 LEU Chi-restraints excluded: chain q residue 112 LYS Chi-restraints excluded: chain r residue 62 GLU Chi-restraints excluded: chain r residue 72 VAL Chi-restraints excluded: chain r residue 96 VAL Chi-restraints excluded: chain s residue 29 VAL Chi-restraints excluded: chain s residue 109 ASP Chi-restraints excluded: chain t residue 5 GLU Chi-restraints excluded: chain t residue 29 THR Chi-restraints excluded: chain u residue 36 VAL Chi-restraints excluded: chain w residue 42 LEU Chi-restraints excluded: chain w residue 65 VAL Chi-restraints excluded: chain w residue 70 ILE Chi-restraints excluded: chain w residue 92 VAL Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 70 GLU Chi-restraints excluded: chain y residue 81 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 605 random chunks: chunk 381 optimal weight: 3.9990 chunk 511 optimal weight: 3.9990 chunk 147 optimal weight: 3.9990 chunk 442 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 480 optimal weight: 0.6980 chunk 201 optimal weight: 10.0000 chunk 493 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 88 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 6 GLN 1 38 GLN ** f 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 115 HIS n 13 ASN p 66 ASN q 52 GLN q 56 GLN r 18 GLN r 86 GLN s 31 GLN u 66 GLN w 51 GLN ** y 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.145814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105334 restraints weight = 119812.822| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 0.99 r_work: 0.2893 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2744 r_free = 0.2744 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.4741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 98947 Z= 0.256 Angle : 0.614 9.090 148858 Z= 0.320 Chirality : 0.038 0.327 19139 Planarity : 0.005 0.060 7375 Dihedral : 24.522 179.434 51531 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.14 % Allowed : 26.14 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.15), residues: 3091 helix: -0.12 (0.18), residues: 827 sheet: -0.68 (0.20), residues: 676 loop : -1.08 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 248 HIS 0.006 0.001 HIS c 200 PHE 0.017 0.002 PHE f 20 TYR 0.014 0.002 TYR o 36 ARG 0.011 0.000 ARG 0 74 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24433.74 seconds wall clock time: 429 minutes 41.54 seconds (25781.54 seconds total)