Starting phenix.real_space_refine on Wed Mar 20 14:12:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv2_14158/03_2024/7qv2_14158.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv2_14158/03_2024/7qv2_14158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv2_14158/03_2024/7qv2_14158.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv2_14158/03_2024/7qv2_14158.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv2_14158/03_2024/7qv2_14158.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qv2_14158/03_2024/7qv2_14158.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.028 sd= 1.347 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 4722 5.49 5 S 132 5.16 5 C 71179 2.51 5 N 26521 2.21 5 O 40302 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 GLU 35": "OE1" <-> "OE2" Residue "1 ASP 28": "OD1" <-> "OD2" Residue "1 TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 TYR 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "4 GLU 12": "OE1" <-> "OE2" Residue "6 GLU 30": "OE1" <-> "OE2" Residue "C ASP 70": "OD1" <-> "OD2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 123": "OD1" <-> "OD2" Residue "C ARG 217": "NH1" <-> "NH2" Residue "C ARG 221": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 125": "NH1" <-> "NH2" Residue "D TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 153": "NH1" <-> "NH2" Residue "D ARG 163": "NH1" <-> "NH2" Residue "E PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 45": "NH1" <-> "NH2" Residue "E ARG 62": "NH1" <-> "NH2" Residue "E ARG 84": "NH1" <-> "NH2" Residue "E ARG 95": "NH1" <-> "NH2" Residue "E TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 128": "OD1" <-> "OD2" Residue "E ARG 168": "NH1" <-> "NH2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F GLU 81": "OE1" <-> "OE2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F ARG 125": "NH1" <-> "NH2" Residue "F ASP 142": "OD1" <-> "OD2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ASP 14": "OD1" <-> "OD2" Residue "G ASP 48": "OD1" <-> "OD2" Residue "G ARG 55": "NH1" <-> "NH2" Residue "G ARG 172": "NH1" <-> "NH2" Residue "J GLU 32": "OE1" <-> "OE2" Residue "J ASP 72": "OD1" <-> "OD2" Residue "J ARG 77": "NH1" <-> "NH2" Residue "J TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 130": "OE1" <-> "OE2" Residue "J ARG 144": "NH1" <-> "NH2" Residue "K GLU 18": "OE1" <-> "OE2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "K GLU 81": "OE1" <-> "OE2" Residue "L GLU 10": "OE1" <-> "OE2" Residue "L PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 66": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 144": "OE1" <-> "OE2" Residue "M GLU 112": "OE1" <-> "OE2" Residue "N GLU 73": "OE1" <-> "OE2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 108": "NH1" <-> "NH2" Residue "O ASP 62": "OD1" <-> "OD2" Residue "O GLU 66": "OE1" <-> "OE2" Residue "O GLU 79": "OE1" <-> "OE2" Residue "O ARG 97": "NH1" <-> "NH2" Residue "O ARG 114": "NH1" <-> "NH2" Residue "P ARG 14": "NH1" <-> "NH2" Residue "P PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 39": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 93": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 16": "OE1" <-> "OE2" Residue "R GLU 36": "OE1" <-> "OE2" Residue "R GLU 54": "OE1" <-> "OE2" Residue "R ARG 67": "NH1" <-> "NH2" Residue "R ARG 75": "NH1" <-> "NH2" Residue "R TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 89": "NH1" <-> "NH2" Residue "S ARG 86": "NH1" <-> "NH2" Residue "T TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 89": "OE1" <-> "OE2" Residue "T GLU 91": "OE1" <-> "OE2" Residue "U GLU 36": "OE1" <-> "OE2" Residue "U ASP 87": "OD1" <-> "OD2" Residue "W ARG 28": "NH1" <-> "NH2" Residue "W PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ASP 83": "OD1" <-> "OD2" Residue "Y PHE 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "b ARG 29": "NH1" <-> "NH2" Residue "b GLU 52": "OE1" <-> "OE2" Residue "b ARG 110": "NH1" <-> "NH2" Residue "b ASP 116": "OD1" <-> "OD2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b GLU 145": "OE1" <-> "OE2" Residue "b ASP 159": "OD1" <-> "OD2" Residue "b PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 167": "NH1" <-> "NH2" Residue "b ARG 170": "NH1" <-> "NH2" Residue "b ARG 177": "NH1" <-> "NH2" Residue "b ASP 192": "OD1" <-> "OD2" Residue "b GLU 195": "OE1" <-> "OE2" Residue "b ASP 197": "OD1" <-> "OD2" Residue "c TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 104": "OE1" <-> "OE2" Residue "c PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ASP 160": "OD1" <-> "OD2" Residue "c ASP 189": "OD1" <-> "OD2" Residue "c ARG 203": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "d TYR 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 146": "NH1" <-> "NH2" Residue "d GLU 163": "OE1" <-> "OE2" Residue "d GLU 173": "OE1" <-> "OE2" Residue "d GLU 188": "OE1" <-> "OE2" Residue "e GLU 10": "OE1" <-> "OE2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e ARG 20": "NH1" <-> "NH2" Residue "e ARG 32": "NH1" <-> "NH2" Residue "e ARG 112": "NH1" <-> "NH2" Residue "e ASP 152": "OD1" <-> "OD2" Residue "f ARG 11": "NH1" <-> "NH2" Residue "f GLU 24": "OE1" <-> "OE2" Residue "f GLU 36": "OE1" <-> "OE2" Residue "f ARG 46": "NH1" <-> "NH2" Residue "f ARG 77": "NH1" <-> "NH2" Residue "g ASP 11": "OD1" <-> "OD2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 92": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g GLU 117": "OE1" <-> "OE2" Residue "g ARG 119": "NH1" <-> "NH2" Residue "g ARG 138": "NH1" <-> "NH2" Residue "h GLU 26": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h ARG 61": "NH1" <-> "NH2" Residue "h ARG 96": "NH1" <-> "NH2" Residue "h ARG 119": "NH1" <-> "NH2" Residue "i ARG 12": "NH1" <-> "NH2" Residue "i ARG 20": "NH1" <-> "NH2" Residue "i GLU 25": "OE1" <-> "OE2" Residue "i GLU 89": "OE1" <-> "OE2" Residue "i ARG 106": "NH1" <-> "NH2" Residue "j ARG 7": "NH1" <-> "NH2" Residue "j ARG 9": "NH1" <-> "NH2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "k ARG 26": "NH1" <-> "NH2" Residue "k GLU 70": "OE1" <-> "OE2" Residue "k GLU 108": "OE1" <-> "OE2" Residue "l ARG 9": "NH1" <-> "NH2" Residue "l ARG 44": "NH1" <-> "NH2" Residue "l ARG 63": "NH1" <-> "NH2" Residue "l TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l GLU 89": "OE1" <-> "OE2" Residue "l ARG 96": "NH1" <-> "NH2" Residue "l GLU 121": "OE1" <-> "OE2" Residue "l ARG 123": "NH1" <-> "NH2" Residue "l ARG 127": "NH1" <-> "NH2" Residue "m ARG 3": "NH1" <-> "NH2" Residue "m ASP 12": "OD1" <-> "OD2" Residue "m ARG 27": "NH1" <-> "NH2" Residue "m ASP 42": "OD1" <-> "OD2" Residue "m ARG 44": "NH1" <-> "NH2" Residue "m GLU 50": "OE1" <-> "OE2" Residue "m GLU 51": "OE1" <-> "OE2" Residue "m ASP 68": "OD1" <-> "OD2" Residue "m ARG 79": "NH1" <-> "NH2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "m ARG 93": "NH1" <-> "NH2" Residue "m ARG 107": "NH1" <-> "NH2" Residue "m ARG 109": "NH1" <-> "NH2" Residue "n GLU 25": "OE1" <-> "OE2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o GLU 6": "OE1" <-> "OE2" Residue "o GLU 19": "OE1" <-> "OE2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 29": "NH1" <-> "NH2" Residue "p ARG 32": "NH1" <-> "NH2" Residue "p PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 53": "OE1" <-> "OE2" Residue "p GLU 54": "OE1" <-> "OE2" Residue "p ARG 71": "NH1" <-> "NH2" Residue "q ARG 39": "NH1" <-> "NH2" Residue "q ARG 67": "NH1" <-> "NH2" Residue "q GLU 83": "OE1" <-> "OE2" Residue "r PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ASP 27": "OD1" <-> "OD2" Residue "r ARG 48": "NH1" <-> "NH2" Residue "t ARG 18": "NH1" <-> "NH2" Residue "t GLU 43": "OE1" <-> "OE2" Residue "t GLU 53": "OE1" <-> "OE2" Residue "t ARG 78": "NH1" <-> "NH2" Residue "u ARG 37": "NH1" <-> "NH2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 142856 Number of models: 1 Model: "" Number of chains: 53 Chain: "0" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 426 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "1" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 401 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "2" Number of atoms: 368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 368 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "3" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 512 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Chain: "4" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 33} Chain: "6" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 413 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 630 Classifications: {'RNA': 29} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 5} Link IDs: {'rna2p': 7, 'rna3p': 21} Chain: "B" Number of atoms: 2392 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 2392 Classifications: {'RNA': 112} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 8, 'rna3p_pur': 50, 'rna3p_pyr': 44} Link IDs: {'rna2p': 18, 'rna3p': 93} Chain: "C" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2083 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 17, 'TRANS': 254} Chain: "D" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1569 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 10, 'TRANS': 195} Chain: "E" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1561 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 7, 'TRANS': 197} Chain: "F" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1386 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "G" Number of atoms: 1342 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1342 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 9, 'TRANS': 165} Chain: "H" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1643 Classifications: {'RNA': 77} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 11, 'rna3p_pur': 29, 'rna3p_pyr': 28} Link IDs: {'rna2p': 19, 'rna3p': 57} Chain: "I" Number of atoms: 121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 121 Classifications: {'peptide': 24} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'TRANS': 23} Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'UNK:plan-1': 23} Unresolved non-hydrogen planarities: 23 Chain: "J" Number of atoms: 1124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1124 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 921 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "L" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1082 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "M" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1076 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 7, 'TRANS': 127} Chain: "N" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 954 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 913 Classifications: {'peptide': 120} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 118} Chain: "P" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 945 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "Q" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 940 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 787 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "S" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 842 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "T" Number of atoms: 725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 725 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "U" Number of atoms: 762 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 762 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 6, 'TRANS': 94} Chain: "V" Number of atoms: 61999 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2887, 61999 Inner-chain residues flagged as termini: ['pdbres=" G V 328 "', 'pdbres=" G V1220 "'] Classifications: {'RNA': 2887} Modifications used: {'5*END': 3, 'rna2p_pur': 302, 'rna2p_pyr': 156, 'rna3p_pur': 1376, 'rna3p_pyr': 1053} Link IDs: {'rna2p': 458, 'rna3p': 2428} Chain breaks: 3 Chain: "W" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 630 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "Y" Number of atoms: 530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 530 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Chain: "Z" Number of atoms: 456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 456 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "a" Number of atoms: 33138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1545, 33138 Classifications: {'RNA': 1545} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 86, 'rna3p_pur': 755, 'rna3p_pyr': 586} Link IDs: {'rna2p': 204, 'rna3p': 1340} Chain: "b" Number of atoms: 1757 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1757 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 7, 'TRANS': 210} Chain: "c" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 3, 'TRANS': 202} Chain: "d" Number of atoms: 1569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1569 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain: "e" Number of atoms: 1219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1219 Classifications: {'peptide': 164} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 156} Chain: "f" Number of atoms: 755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 755 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "g" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1181 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 6, 'TRANS': 142} Chain: "h" Number of atoms: 1037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1037 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "i" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 784 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 4, 'TRANS': 98} Chain: "j" Number of atoms: 761 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 761 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 6, 'TRANS': 88} Chain: "k" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 839 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 107} Chain: "l" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1052 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 868 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "n" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 498 Classifications: {'peptide': 60} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 56} Chain: "o" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 710 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "p" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 695 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 5, 'TRANS': 82} Chain: "q" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 691 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "s" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 633 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 637 Classifications: {'peptide': 83} Link IDs: {'TRANS': 82} Chain: "u" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 444 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "x" Number of atoms: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1621 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 9, 'rna3p_pur': 31, 'rna3p_pyr': 30} Link IDs: {'rna2p': 14, 'rna3p': 61} Time building chain proxies: 54.79, per 1000 atoms: 0.38 Number of scatterers: 142856 At special positions: 0 Unit cell: (264.825, 231.12, 285.69, 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 132 16.00 P 4722 15.00 O 40302 8.00 N 26521 7.00 C 71179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 63.54 Conformation dependent library (CDL) restraints added in 6.2 seconds 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9688 Finding SS restraints... Secondary structure from input PDB file: 173 helices and 65 sheets defined 35.8% alpha, 18.5% beta 1545 base pairs and 2375 stacking pairs defined. Time for finding SS restraints: 51.35 Creating SS restraints... Processing helix chain '0' and resid 9 through 17 Processing helix chain '0' and resid 18 through 20 No H-bonds generated for 'chain '0' and resid 18 through 20' Processing helix chain '2' and resid 8 through 17 Processing helix chain '2' and resid 17 through 23 Processing helix chain '2' and resid 24 through 37 Processing helix chain '3' and resid 7 through 12 removed outlier: 3.786A pdb=" N LYS 3 12 " --> pdb=" O ARG 3 8 " (cutoff:3.500A) Processing helix chain '3' and resid 18 through 20 No H-bonds generated for 'chain '3' and resid 18 through 20' Processing helix chain '3' and resid 32 through 36 Processing helix chain '3' and resid 37 through 45 Processing helix chain '3' and resid 51 through 59 removed outlier: 3.728A pdb=" N ARG 3 57 " --> pdb=" O GLY 3 53 " (cutoff:3.500A) Processing helix chain '4' and resid 29 through 32 Processing helix chain '6' and resid 48 through 54 removed outlier: 3.954A pdb=" N ALA 6 52 " --> pdb=" O LYS 6 48 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASP 6 53 " --> pdb=" O PHE 6 49 " (cutoff:3.500A) 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 177 through 179 No H-bonds generated for 'chain 'C' and resid 177 through 179' Processing helix chain 'C' and resid 207 through 214 removed outlier: 3.658A pdb=" N SER C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 266 through 268 No H-bonds generated for 'chain 'C' and resid 266 through 268' Processing helix chain 'D' and resid 57 through 61 Processing helix chain 'D' and resid 62 through 71 removed outlier: 4.126A pdb=" N LYS D 71 " --> pdb=" O GLY D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 91 removed outlier: 3.583A pdb=" N ALA D 90 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 102 Processing helix chain 'D' and resid 121 through 127 Processing helix chain 'E' and resid 20 through 25 Processing helix chain 'E' and resid 29 through 45 removed outlier: 3.503A pdb=" N ARG E 45 " --> pdb=" O ARG E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 121 Processing helix chain 'E' and resid 135 through 146 removed outlier: 4.019A pdb=" N MET E 139 " --> pdb=" O LYS E 135 " (cutoff:3.500A) Processing helix chain 'E' and resid 160 through 166 Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.640A pdb=" N GLU E 190 " --> pdb=" O VAL E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 206 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.726A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 21 removed outlier: 3.855A pdb=" N ALA F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 41 through 45 Processing helix chain 'F' and resid 46 through 51 Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 92 through 97 removed outlier: 4.251A pdb=" N MET F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 98 through 105 Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 138 through 142 removed outlier: 3.707A pdb=" N ILE F 141 " --> pdb=" O PHE F 138 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP F 142 " --> pdb=" O PRO F 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 138 through 142' Processing helix chain 'F' and resid 162 through 174 Processing helix chain 'G' and resid 59 through 82 removed outlier: 3.638A pdb=" N ARG G 70 " --> pdb=" O HIS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 138 through 151 removed outlier: 3.664A pdb=" N ALA G 144 " --> pdb=" O GLU G 140 " (cutoff:3.500A) Processing helix chain 'J' and resid 25 through 38 Processing helix chain 'J' and resid 60 through 63 Processing helix chain 'J' and resid 68 through 73 Processing helix chain 'J' and resid 89 through 97 Processing helix chain 'J' and resid 97 through 108 Processing helix chain 'J' and resid 113 through 122 removed outlier: 3.769A pdb=" N LYS J 122 " --> pdb=" O GLN J 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 131 through 137 removed outlier: 3.749A pdb=" N GLU J 134 " --> pdb=" O HIS J 131 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA J 135 " --> pdb=" O PRO J 132 " (cutoff:3.500A) Processing helix chain 'K' and resid 104 through 109 removed outlier: 3.778A pdb=" N GLU K 108 " --> pdb=" O ARG K 104 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN K 109 " --> pdb=" O GLU K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 104 through 109' Processing helix chain 'K' and resid 111 through 117 removed outlier: 3.676A pdb=" N LEU K 117 " --> pdb=" O LYS K 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 6 removed outlier: 3.901A pdb=" N LEU L 6 " --> pdb=" O LEU L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 41 Processing helix chain 'L' and resid 80 through 85 Processing helix chain 'L' and resid 92 through 100 Processing helix chain 'L' and resid 129 through 139 removed outlier: 3.935A pdb=" N GLU L 134 " --> pdb=" O ALA L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 59 Processing helix chain 'M' and resid 110 through 124 removed outlier: 3.630A pdb=" N LYS M 124 " --> pdb=" O LEU M 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 9 through 28 Processing helix chain 'N' and resid 34 through 54 removed outlier: 3.816A pdb=" N SER N 42 " --> pdb=" O LYS N 38 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG N 53 " --> pdb=" O THR N 49 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLY N 54 " --> pdb=" O LEU N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 66 Processing helix chain 'N' and resid 79 through 92 Processing helix chain 'O' and resid 6 through 20 removed outlier: 3.774A pdb=" N ALA O 10 " --> pdb=" O SER O 6 " (cutoff:3.500A) Processing helix chain 'O' and resid 70 through 88 Processing helix chain 'O' and resid 104 through 117 Processing helix chain 'P' and resid 2 through 9 Processing helix chain 'P' and resid 53 through 56 Processing helix chain 'P' and resid 97 through 102 Processing helix chain 'Q' and resid 7 through 20 removed outlier: 3.743A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 25 through 30 Processing helix chain 'Q' and resid 31 through 71 removed outlier: 4.017A pdb=" N ARG Q 51 " --> pdb=" O PHE Q 47 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N MET Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 86 Processing helix chain 'Q' and resid 92 through 101 removed outlier: 3.776A pdb=" N ASN Q 101 " --> pdb=" O ASP Q 97 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 117 Processing helix chain 'S' and resid 13 through 22 removed outlier: 3.502A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.559A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 62 removed outlier: 4.346A pdb=" N ILE S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 67 No H-bonds generated for 'chain 'S' and resid 65 through 67' Processing helix chain 'S' and resid 88 through 92 removed outlier: 3.642A pdb=" N GLY S 91 " --> pdb=" O ARG S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 6 Processing helix chain 'T' and resid 14 through 22 Processing helix chain 'T' and resid 35 through 47 removed outlier: 3.553A pdb=" N PHE T 47 " --> pdb=" O VAL T 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 removed outlier: 3.804A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 35 Processing helix chain 'Y' and resid 40 through 65 removed outlier: 4.251A pdb=" N ARG Y 44 " --> pdb=" O THR Y 40 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N MET Y 53 " --> pdb=" O ALA Y 49 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR Y 55 " --> pdb=" O ALA Y 51 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL Y 56 " --> pdb=" O ARG Y 52 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ILE Y 57 " --> pdb=" O MET Y 53 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ARG Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 26 removed outlier: 3.721A pdb=" N LEU Z 26 " --> pdb=" O THR Z 22 " (cutoff:3.500A) Processing helix chain 'Z' and resid 40 through 51 Processing helix chain 'b' and resid 24 through 31 removed outlier: 5.333A pdb=" N ARG b 29 " --> pdb=" O LYS b 26 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR b 30 " --> pdb=" O MET b 27 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE b 31 " --> pdb=" O LYS b 28 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 63 removed outlier: 4.007A pdb=" N GLU b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLU b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) Processing helix chain 'b' and resid 73 through 88 removed outlier: 4.787A pdb=" N ASP b 78 " --> pdb=" O LYS b 74 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N SER b 79 " --> pdb=" O GLN b 75 " (cutoff:3.500A) Processing helix chain 'b' and resid 103 through 124 removed outlier: 4.614A pdb=" N GLU b 122 " --> pdb=" O GLU b 118 " (cutoff:3.500A) Processing helix chain 'b' and resid 131 through 149 removed outlier: 4.873A pdb=" N LYS b 138 " --> pdb=" O VAL b 134 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N LYS b 139 " --> pdb=" O VAL b 135 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 152 No H-bonds generated for 'chain 'b' and resid 150 through 152' Processing helix chain 'b' and resid 169 through 179 Processing helix chain 'b' and resid 206 through 223 Processing helix chain 'b' and resid 224 through 226 No H-bonds generated for 'chain 'b' and resid 224 through 226' Processing helix chain 'c' and resid 6 through 12 Processing helix chain 'c' and resid 27 through 47 Processing helix chain 'c' and resid 48 through 50 No H-bonds generated for 'chain 'c' and resid 48 through 50' Processing helix chain 'c' and resid 71 through 77 removed outlier: 3.858A pdb=" N VAL c 75 " --> pdb=" O LYS c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 95 removed outlier: 3.864A pdb=" N ALA c 89 " --> pdb=" O ALA c 85 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 110 Processing helix chain 'c' and resid 111 through 125 Processing helix chain 'c' and resid 128 through 145 removed outlier: 4.174A pdb=" N LYS c 134 " --> pdb=" O ARG c 130 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA c 145 " --> pdb=" O MET c 141 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 16 Processing helix chain 'd' and resid 23 through 27 Processing helix chain 'd' and resid 45 through 62 Processing helix chain 'd' and resid 64 through 78 Processing helix chain 'd' and resid 81 through 92 removed outlier: 3.571A pdb=" N ASN d 85 " --> pdb=" O LYS d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 117 Processing helix chain 'd' and resid 148 through 157 Processing helix chain 'd' and resid 181 through 185 Processing helix chain 'd' and resid 193 through 199 Processing helix chain 'e' and resid 55 through 69 Processing helix chain 'e' and resid 76 through 80 removed outlier: 3.518A pdb=" N THR e 79 " --> pdb=" O MET e 76 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 118 Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'e' and resid 160 through 165 Processing helix chain 'f' and resid 15 through 32 removed outlier: 3.534A pdb=" N LEU f 30 " --> pdb=" O PHE f 26 " (cutoff:3.500A) Processing helix chain 'f' and resid 70 through 80 Processing helix chain 'g' and resid 20 through 29 Processing helix chain 'g' and resid 31 through 34 removed outlier: 3.739A pdb=" N GLY g 34 " --> pdb=" O MET g 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 31 through 34' Processing helix chain 'g' and resid 35 through 54 Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 80 through 84 removed outlier: 4.163A pdb=" N ASN g 84 " --> pdb=" O GLY g 81 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.224A pdb=" N GLY g 112 " --> pdb=" O ALA g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 129 removed outlier: 3.511A pdb=" N ARG g 119 " --> pdb=" O THR g 115 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 Processing helix chain 'h' and resid 6 through 21 Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 97 through 101 Processing helix chain 'h' and resid 115 through 122 Processing helix chain 'i' and resid 34 through 39 removed outlier: 3.538A pdb=" N HIS i 38 " --> pdb=" O GLU i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 41 through 55 removed outlier: 3.875A pdb=" N ILE i 45 " --> pdb=" O SER i 41 " (cutoff:3.500A) Proline residue: i 51 - end of helix removed outlier: 3.917A pdb=" N THR i 55 " --> pdb=" O PRO i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 71 through 91 Processing helix chain 'i' and resid 94 through 102 removed outlier: 3.641A pdb=" N LEU i 98 " --> pdb=" O TYR i 94 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 31 removed outlier: 4.508A pdb=" N GLN j 20 " --> pdb=" O ARG j 16 " (cutoff:3.500A) Processing helix chain 'j' and resid 80 through 89 removed outlier: 3.832A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 53 Processing helix chain 'k' and resid 56 through 60 Processing helix chain 'k' and resid 61 through 80 Processing helix chain 'k' and resid 94 through 105 Processing helix chain 'l' and resid 3 through 10 removed outlier: 3.553A pdb=" N LEU l 7 " --> pdb=" O THR l 3 " (cutoff:3.500A) Processing helix chain 'l' and resid 21 through 24 Processing helix chain 'm' and resid 14 through 19 removed outlier: 3.608A pdb=" N LEU m 19 " --> pdb=" O VAL m 15 " (cutoff:3.500A) Processing helix chain 'm' and resid 20 through 22 No H-bonds generated for 'chain 'm' and resid 20 through 22' Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.528A pdb=" N ALA m 30 " --> pdb=" O GLY m 26 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU m 36 " --> pdb=" O GLN m 32 " (cutoff:3.500A) Processing helix chain 'm' and resid 49 through 62 Processing helix chain 'm' and resid 68 through 82 removed outlier: 3.809A pdb=" N SER m 74 " --> pdb=" O ARG m 70 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 94 Processing helix chain 'n' and resid 3 through 12 Processing helix chain 'n' and resid 16 through 20 Processing helix chain 'n' and resid 40 through 50 Processing helix chain 'o' and resid 6 through 15 Processing helix chain 'o' and resid 24 through 44 Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.610A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 Processing helix chain 'p' and resid 52 through 61 Processing helix chain 'p' and resid 67 through 78 removed outlier: 3.529A pdb=" N GLN p 77 " --> pdb=" O LEU p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 78 through 89 Processing helix chain 'r' and resid 16 through 22 Processing helix chain 'r' and resid 31 through 38 removed outlier: 4.213A pdb=" N LYS r 36 " --> pdb=" O ASP r 32 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N PHE r 37 " --> pdb=" O LEU r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 removed outlier: 3.598A pdb=" N MET r 70 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing helix chain 's' and resid 12 through 24 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.673A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 63 through 67 removed outlier: 3.631A pdb=" N VAL s 67 " --> pdb=" O GLU s 64 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 75 removed outlier: 3.516A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 41 Processing helix chain 't' and resid 44 through 65 Processing helix chain 't' and resid 69 through 85 Processing helix chain 'u' and resid 20 through 22 No H-bonds generated for 'chain 'u' and resid 20 through 22' Processing helix chain 'u' and resid 50 through 55 removed outlier: 3.649A pdb=" N LYS u 55 " --> pdb=" O ALA u 51 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain '0' and resid 27 through 29 Processing sheet with id=AA2, first strand: chain '1' and resid 17 through 22 Processing sheet with id=AA3, first strand: chain '3' and resid 15 through 16 Processing sheet with id=AA4, first strand: chain '4' and resid 2 through 3 removed outlier: 5.911A pdb=" N LYS 4 2 " --> pdb=" O LYS 4 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '6' and resid 22 through 26 removed outlier: 3.958A pdb=" N THR 6 24 " --> pdb=" O ALA 6 12 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ALA 6 12 " --> pdb=" O THR 6 24 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N SER 6 26 " --> pdb=" O LYS 6 10 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N VAL 6 31 " --> pdb=" O LYS 6 11 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N THR 6 13 " --> pdb=" O VAL 6 31 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 3 through 5 Processing sheet with id=AA7, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA8, first strand: chain 'C' and resid 101 through 105 removed outlier: 6.875A pdb=" N ILE C 91 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N VAL C 81 " --> pdb=" O ILE C 91 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LEU C 93 " --> pdb=" O ALA C 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 129 through 131 removed outlier: 6.234A pdb=" N LEU C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG C 272 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N MET C 183 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ILE C 270 " --> pdb=" O MET C 183 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 4 through 16 removed outlier: 6.803A pdb=" N VAL D 27 " --> pdb=" O ILE D 10 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N MET D 12 " --> pdb=" O VAL D 25 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL D 25 " --> pdb=" O MET D 12 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLN D 14 " --> pdb=" O ILE D 23 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N ILE D 23 " --> pdb=" O GLN D 14 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LEU D 185 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL D 179 " --> pdb=" O LEU D 185 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N LEU D 187 " --> pdb=" O VAL D 177 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU D 175 " --> pdb=" O LYS D 189 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N THR D 170 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N GLY D 112 " --> pdb=" O THR D 170 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN D 172 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N VAL D 110 " --> pdb=" O GLN D 172 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N VAL D 113 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N LEU D 199 " --> pdb=" O VAL D 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 77 through 84 removed outlier: 6.306A pdb=" N LYS D 77 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ASP D 55 " --> pdb=" O LYS D 77 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ILE D 49 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N GLY D 52 " --> pdb=" O VAL D 35 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL D 35 " --> pdb=" O GLY D 52 " (cutoff:3.500A) removed outlier: 9.007A pdb=" N ASP D 54 " --> pdb=" O ASN D 33 " (cutoff:3.500A) removed outlier: 10.611A pdb=" N ASN D 33 " --> pdb=" O ASP D 54 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 118 through 120 removed outlier: 3.786A pdb=" N GLY D 118 " --> pdb=" O MET D 164 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 6 through 7 removed outlier: 4.401A pdb=" N LEU E 6 " --> pdb=" O ALA E 14 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 123 through 125 removed outlier: 6.381A pdb=" N LEU E 153 " --> pdb=" O LEU E 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.539A pdb=" N LYS F 33 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 66 through 67 removed outlier: 3.708A pdb=" N LYS F 88 " --> pdb=" O VAL F 66 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 9 through 10 removed outlier: 4.094A pdb=" N LEU G 9 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLU G 43 " --> pdb=" O ALA G 54 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 16 through 19 Processing sheet with id=AC1, first strand: chain 'G' and resid 123 through 125 Processing sheet with id=AC2, first strand: chain 'G' and resid 97 through 100 Processing sheet with id=AC3, first strand: chain 'J' and resid 17 through 20 Processing sheet with id=AC4, first strand: chain 'J' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'K' and resid 7 through 10 removed outlier: 6.371A pdb=" N ARG K 17 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ALA K 16 " --> pdb=" O ALA K 46 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ALA K 46 " --> pdb=" O ALA K 16 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N GLU K 18 " --> pdb=" O LYS K 44 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N VAL K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N VAL K 24 " --> pdb=" O VAL K 38 " (cutoff:3.500A) removed outlier: 8.248A pdb=" N VAL K 38 " --> pdb=" O VAL K 24 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA K 83 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N CYS K 84 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LYS K 9 " --> pdb=" O CYS K 84 " (cutoff:3.500A) removed outlier: 8.393A pdb=" N ILE K 86 " --> pdb=" O LYS K 9 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 69 through 70 removed outlier: 3.538A pdb=" N THR P 60 " --> pdb=" O LYS P 49 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LYS P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ARG P 62 " --> pdb=" O VAL P 47 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL P 47 " --> pdb=" O ARG P 62 " (cutoff:3.500A) removed outlier: 8.823A pdb=" N ILE P 64 " --> pdb=" O GLY P 45 " (cutoff:3.500A) removed outlier: 8.780A pdb=" N GLY P 45 " --> pdb=" O ILE P 64 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR P 25 " --> pdb=" O VAL P 87 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS P 83 " --> pdb=" O HIS P 29 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LYS P 31 " --> pdb=" O ILE P 81 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE P 81 " --> pdb=" O LYS P 31 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'L' and resid 75 through 77 removed outlier: 5.808A pdb=" N ALA L 75 " --> pdb=" O LYS L 110 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N VAL L 109 " --> pdb=" O LYS L 127 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'L' and resid 90 through 91 removed outlier: 6.262A pdb=" N VAL L 91 " --> pdb=" O LYS L 124 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'M' and resid 102 through 106 removed outlier: 6.580A pdb=" N VAL M 102 " --> pdb=" O ALA M 36 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ALA M 36 " --> pdb=" O VAL M 102 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N PHE M 104 " --> pdb=" O ILE M 34 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 40 through 43 removed outlier: 3.537A pdb=" N SER M 40 " --> pdb=" O VAL M 97 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL M 97 " --> pdb=" O SER M 40 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLY M 92 " --> pdb=" O TYR M 74 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 29 through 33 removed outlier: 4.462A pdb=" N MET N 114 " --> pdb=" O LEU N 104 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'N' and resid 70 through 72 removed outlier: 7.351A pdb=" N GLN N 77 " --> pdb=" O ALA N 71 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'O' and resid 52 through 57 removed outlier: 3.671A pdb=" N ALA O 54 " --> pdb=" O ILE O 44 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ARG O 30 " --> pdb=" O ILE O 45 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'R' and resid 11 through 14 Processing sheet with id=AD6, first strand: chain 'R' and resid 19 through 22 removed outlier: 6.744A pdb=" N TYR R 92 " --> pdb=" O GLN R 65 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N GLN R 65 " --> pdb=" O TYR R 92 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LYS R 94 " --> pdb=" O GLU R 63 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR R 59 " --> pdb=" O GLU R 98 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE R 100 " --> pdb=" O THR R 57 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N THR R 57 " --> pdb=" O ILE R 100 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA R 60 " --> pdb=" O VAL R 33 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'R' and resid 71 through 76 Processing sheet with id=AD8, first strand: chain 'S' and resid 3 through 6 removed outlier: 5.975A pdb=" N HIS S 102 " --> pdb=" O VAL S 76 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N VAL S 76 " --> pdb=" O HIS S 102 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N THR S 104 " --> pdb=" O ALA S 74 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ALA S 74 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N VAL S 106 " --> pdb=" O SER S 72 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'S' and resid 82 through 86 Processing sheet with id=AE1, first strand: chain 'T' and resid 8 through 11 removed outlier: 3.630A pdb=" N ARG T 10 " --> pdb=" O GLU T 29 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARG T 77 " --> pdb=" O VAL T 30 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ARG T 76 " --> pdb=" O TYR T 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS T 53 " --> pdb=" O LYS T 82 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'U' and resid 63 through 64 Processing sheet with id=AE3, first strand: chain 'U' and resid 40 through 44 Processing sheet with id=AE4, first strand: chain 'U' and resid 81 through 86 Processing sheet with id=AE5, first strand: chain 'W' and resid 30 through 31 removed outlier: 6.555A pdb=" N LEU W 67 " --> pdb=" O LEU W 45 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'W' and resid 53 through 55 Processing sheet with id=AE7, first strand: chain 'Z' and resid 35 through 38 Processing sheet with id=AE8, first strand: chain 'b' and resid 91 through 92 removed outlier: 6.430A pdb=" N PHE b 69 " --> pdb=" O VAL b 92 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N LEU b 161 " --> pdb=" O ILE b 184 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.862A pdb=" N ARG c 58 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS c 53 " --> pdb=" O HIS c 68 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N VAL c 63 " --> pdb=" O HIS c 99 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N ASN c 101 " --> pdb=" O VAL c 63 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ILE c 65 " --> pdb=" O ASN c 101 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU c 103 " --> pdb=" O ILE c 65 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ILE c 67 " --> pdb=" O LEU c 103 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'c' and resid 163 through 170 removed outlier: 3.870A pdb=" N ARG c 163 " --> pdb=" O GLY c 154 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TRP c 200 " --> pdb=" O LYS c 149 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 119 through 121 Processing sheet with id=AF3, first strand: chain 'e' and resid 14 through 25 removed outlier: 4.850A pdb=" N LEU e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL e 38 " --> pdb=" O LEU e 15 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N THR e 17 " --> pdb=" O LEU e 36 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU e 36 " --> pdb=" O THR e 17 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N HIS e 45 " --> pdb=" O ASP e 41 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'e' and resid 85 through 88 Processing sheet with id=AF5, first strand: chain 'f' and resid 36 through 47 removed outlier: 5.913A pdb=" N ILE f 37 " --> pdb=" O GLN f 66 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N GLN f 66 " --> pdb=" O ILE f 37 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLY f 39 " --> pdb=" O ASN f 64 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N TYR f 60 " --> pdb=" O TRP f 43 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N LYS f 45 " --> pdb=" O GLY f 58 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLY f 58 " --> pdb=" O LYS f 45 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N MET f 7 " --> pdb=" O ILE f 89 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ARG f 87 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'g' and resid 73 through 78 Processing sheet with id=AF7, first strand: chain 'h' and resid 25 through 28 removed outlier: 3.502A pdb=" N PHE h 63 " --> pdb=" O ASP h 48 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'h' and resid 77 through 79 removed outlier: 3.853A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'h' and resid 77 through 79 removed outlier: 3.853A pdb=" N LYS h 78 " --> pdb=" O TYR h 130 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N VAL h 127 " --> pdb=" O SER h 107 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N SER h 107 " --> pdb=" O VAL h 127 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ALA h 129 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY h 111 " --> pdb=" O THR h 108 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'i' and resid 6 through 11 removed outlier: 6.253A pdb=" N VAL i 29 " --> pdb=" O VAL i 65 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL i 67 " --> pdb=" O VAL i 29 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'j' and resid 7 through 12 removed outlier: 3.616A pdb=" N THR j 69 " --> pdb=" O GLU j 45 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU j 45 " --> pdb=" O THR j 69 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'j' and resid 40 through 41 Processing sheet with id=AG4, first strand: chain 'k' and resid 43 through 48 removed outlier: 6.911A pdb=" N ILE k 36 " --> pdb=" O ILE k 44 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N TRP k 46 " --> pdb=" O VAL k 34 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL k 34 " --> pdb=" O TRP k 46 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N SER k 48 " --> pdb=" O THR k 32 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N THR k 32 " --> pdb=" O SER k 48 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU k 84 " --> pdb=" O VAL k 109 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ALA k 111 " --> pdb=" O LEU k 84 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'l' and resid 26 through 29 removed outlier: 3.691A pdb=" N GLU l 34 " --> pdb=" O ASN l 29 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'l' and resid 43 through 53 removed outlier: 5.983A pdb=" N CYS l 47 " --> pdb=" O ARG l 69 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARG l 69 " --> pdb=" O CYS l 47 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL l 76 " --> pdb=" O VAL l 68 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N ILE l 110 " --> pdb=" O THR l 77 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N TYR l 79 " --> pdb=" O ILE l 110 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'p' and resid 3 through 6 removed outlier: 3.844A pdb=" N SER p 15 " --> pdb=" O ALA p 12 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ALA p 12 " --> pdb=" O SER p 15 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'p' and resid 3 through 6 removed outlier: 7.332A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ILE p 20 " --> pdb=" O VAL p 37 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLU p 35 " --> pdb=" O VAL p 22 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'q' and resid 39 through 49 removed outlier: 5.111A pdb=" N GLU q 28 " --> pdb=" O GLN q 11 " (cutoff:3.500A) removed outlier: 8.883A pdb=" N GLN q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 12.354A pdb=" N TYR q 30 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 15.385A pdb=" N VAL q 9 " --> pdb=" O TYR q 30 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ILE q 60 " --> pdb=" O VAL q 80 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N VAL q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N ARG q 74 " --> pdb=" O THR q 66 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 's' and resid 31 through 33 removed outlier: 6.073A pdb=" N VAL s 31 " --> pdb=" O ALA s 50 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N TYR s 52 " --> pdb=" O VAL s 31 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N THR s 33 " --> pdb=" O TYR s 52 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'u' and resid 13 through 19 removed outlier: 3.510A pdb=" N SER u 25 " --> pdb=" O ASN u 17 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN u 23 " --> pdb=" O SER u 19 " (cutoff:3.500A) 1659 hydrogen bonds defined for protein. 4635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3920 hydrogen bonds 6310 hydrogen bond angles 0 basepair planarities 1545 basepair parallelities 2375 stacking parallelities Total time for adding SS restraints: 230.17 Time building geometry restraints manager: 68.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 14055 1.32 - 1.44: 69091 1.44 - 1.57: 62737 1.57 - 1.69: 9437 1.69 - 1.81: 238 Bond restraints: 155558 Sorted by residual: bond pdb=" C1' U A 29 " pdb=" N1 U A 29 " ideal model delta sigma weight residual 1.480 1.552 -0.072 1.50e-02 4.44e+03 2.27e+01 bond pdb=" N ARG D 142 " pdb=" CA ARG D 142 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.17e-02 7.31e+03 1.18e+01 bond pdb=" N GLY D 144 " pdb=" CA GLY D 144 " ideal model delta sigma weight residual 1.448 1.477 -0.029 9.00e-03 1.23e+04 1.05e+01 bond pdb=" CA SER D 145 " pdb=" CB SER D 145 " ideal model delta sigma weight residual 1.531 1.480 0.051 1.65e-02 3.67e+03 9.48e+00 bond pdb=" C PRO D 143 " pdb=" O PRO D 143 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 9.18e+00 ... (remaining 155553 not shown) Histogram of bond angle deviations from ideal: 97.06 - 104.45: 20963 104.45 - 111.84: 84773 111.84 - 119.22: 51881 119.22 - 126.61: 61986 126.61 - 134.00: 13837 Bond angle restraints: 233440 Sorted by residual: angle pdb=" C3' C A 21 " pdb=" O3' C A 21 " pdb=" P G A 22 " ideal model delta sigma weight residual 120.20 105.11 15.09 1.50e+00 4.44e-01 1.01e+02 angle pdb=" C3' G V 181 " pdb=" O3' G V 181 " pdb=" P C V 182 " ideal model delta sigma weight residual 120.20 108.00 12.20 1.50e+00 4.44e-01 6.61e+01 angle pdb=" C3' C V 76 " pdb=" O3' C V 76 " pdb=" P U V 77 " ideal model delta sigma weight residual 120.20 108.10 12.10 1.50e+00 4.44e-01 6.51e+01 angle pdb=" C3' A A 27 " pdb=" O3' A A 27 " pdb=" P U A 28 " ideal model delta sigma weight residual 120.20 109.12 11.08 1.50e+00 4.44e-01 5.46e+01 angle pdb=" C3' C V1842 " pdb=" O3' C V1842 " pdb=" P G V1843 " ideal model delta sigma weight residual 120.20 109.19 11.01 1.50e+00 4.44e-01 5.38e+01 ... (remaining 233435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.80: 87264 35.80 - 71.60: 11143 71.60 - 107.40: 1389 107.40 - 143.20: 60 143.20 - 179.00: 58 Dihedral angle restraints: 99914 sinusoidal: 84854 harmonic: 15060 Sorted by residual: dihedral pdb=" C4' G a 482 " pdb=" C3' G a 482 " pdb=" C2' G a 482 " pdb=" C1' G a 482 " ideal model delta sinusoidal sigma weight residual -35.00 35.71 -70.71 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C4' U V2127 " pdb=" C3' U V2127 " pdb=" C2' U V2127 " pdb=" C1' U V2127 " ideal model delta sinusoidal sigma weight residual -35.00 35.43 -70.43 1 8.00e+00 1.56e-02 9.98e+01 dihedral pdb=" C4' G B 48 " pdb=" C3' G B 48 " pdb=" C2' G B 48 " pdb=" C1' G B 48 " ideal model delta sinusoidal sigma weight residual -35.00 34.00 -69.00 1 8.00e+00 1.56e-02 9.62e+01 ... (remaining 99911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 29429 0.102 - 0.204: 451 0.204 - 0.306: 20 0.306 - 0.407: 31 0.407 - 0.509: 13 Chirality restraints: 29944 Sorted by residual: chirality pdb=" P C V 182 " pdb=" OP1 C V 182 " pdb=" OP2 C V 182 " pdb=" O5' C V 182 " both_signs ideal model delta sigma weight residual True 2.41 -2.92 -0.51 2.00e-01 2.50e+01 6.48e+00 chirality pdb=" P C V1449 " pdb=" OP1 C V1449 " pdb=" OP2 C V1449 " pdb=" O5' C V1449 " both_signs ideal model delta sigma weight residual True 2.41 -2.91 -0.50 2.00e-01 2.50e+01 6.21e+00 chirality pdb=" P G A 25 " pdb=" OP1 G A 25 " pdb=" OP2 G A 25 " pdb=" O5' G A 25 " both_signs ideal model delta sigma weight residual True 2.41 -2.88 -0.47 2.00e-01 2.50e+01 5.42e+00 ... (remaining 29941 not shown) Planarity restraints: 11973 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A H 37 " -0.036 2.00e-02 2.50e+03 1.69e-02 7.87e+00 pdb=" N9 A H 37 " 0.040 2.00e-02 2.50e+03 pdb=" C8 A H 37 " -0.002 2.00e-02 2.50e+03 pdb=" N7 A H 37 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A H 37 " -0.000 2.00e-02 2.50e+03 pdb=" C6 A H 37 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A H 37 " -0.009 2.00e-02 2.50e+03 pdb=" N1 A H 37 " -0.003 2.00e-02 2.50e+03 pdb=" C2 A H 37 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A H 37 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A H 37 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C H 74 " 0.009 2.00e-02 2.50e+03 1.61e-02 5.82e+00 pdb=" N1 C H 74 " -0.010 2.00e-02 2.50e+03 pdb=" C2 C H 74 " 0.037 2.00e-02 2.50e+03 pdb=" O2 C H 74 " -0.027 2.00e-02 2.50e+03 pdb=" N3 C H 74 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C H 74 " 0.001 2.00e-02 2.50e+03 pdb=" N4 C H 74 " 0.001 2.00e-02 2.50e+03 pdb=" C5 C H 74 " -0.006 2.00e-02 2.50e+03 pdb=" C6 C H 74 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A V 199 " 0.031 2.00e-02 2.50e+03 1.44e-02 5.69e+00 pdb=" N9 A V 199 " -0.035 2.00e-02 2.50e+03 pdb=" C8 A V 199 " -0.001 2.00e-02 2.50e+03 pdb=" N7 A V 199 " 0.001 2.00e-02 2.50e+03 pdb=" C5 A V 199 " 0.000 2.00e-02 2.50e+03 pdb=" C6 A V 199 " 0.004 2.00e-02 2.50e+03 pdb=" N6 A V 199 " 0.007 2.00e-02 2.50e+03 pdb=" N1 A V 199 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A V 199 " -0.002 2.00e-02 2.50e+03 pdb=" N3 A V 199 " -0.005 2.00e-02 2.50e+03 pdb=" C4 A V 199 " -0.001 2.00e-02 2.50e+03 ... (remaining 11970 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 850 2.45 - 3.06: 87559 3.06 - 3.67: 269663 3.67 - 4.29: 389813 4.29 - 4.90: 544627 Nonbonded interactions: 1292512 Sorted by model distance: nonbonded pdb=" O2' A V1243 " pdb=" OP1 A V1244 " model vdw 1.833 2.440 nonbonded pdb=" O2' G a1175 " pdb=" OP1 A a1176 " model vdw 1.848 2.440 nonbonded pdb=" O2' G V 688 " pdb=" O2' G V2378 " model vdw 1.896 2.440 nonbonded pdb=" O ALA t 61 " pdb=" OG1 THR t 64 " model vdw 1.903 2.440 nonbonded pdb=" O2' G a 455 " pdb=" O5' A a 456 " model vdw 1.910 2.440 ... (remaining 1292507 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'H' and resid 1 through 75) selection = chain 'x' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.140 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: 0.110 Extract box with map and model: 16.120 Check model and map are aligned: 1.570 Set scattering table: 1.010 Process input model: 501.070 Find NCS groups from input model: 2.700 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 527.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 155558 Z= 0.128 Angle : 0.483 15.093 233440 Z= 0.269 Chirality : 0.034 0.509 29944 Planarity : 0.002 0.033 11973 Dihedral : 23.761 179.002 90226 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.12 % Allowed : 4.66 % Favored : 95.23 % Rotamer: Outliers : 0.25 % Allowed : 4.80 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.90 (0.11), residues: 5176 helix: 0.13 (0.13), residues: 1608 sheet: -1.46 (0.15), residues: 935 loop : -2.12 (0.11), residues: 2633 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP M 65 HIS 0.006 0.001 HIS b 18 PHE 0.010 0.001 PHE b 69 TYR 0.009 0.001 TYR o 78 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2202 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2191 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 54 ILE cc_start: 0.8350 (mt) cc_final: 0.8068 (mp) REVERT: 1 19 SER cc_start: 0.8811 (m) cc_final: 0.8503 (p) REVERT: 1 26 ASN cc_start: 0.8693 (m-40) cc_final: 0.8448 (m110) REVERT: 1 48 THR cc_start: 0.8220 (p) cc_final: 0.7930 (p) REVERT: 2 13 SER cc_start: 0.8572 (m) cc_final: 0.8179 (p) REVERT: 2 40 LYS cc_start: 0.8304 (ttpp) cc_final: 0.7974 (ttmm) REVERT: 3 56 LYS cc_start: 0.8377 (ttpp) cc_final: 0.8160 (tttt) REVERT: 4 19 ARG cc_start: 0.7559 (ttm170) cc_final: 0.5955 (ttm170) REVERT: 6 1 MET cc_start: 0.5970 (mtt) cc_final: 0.3436 (ptt) REVERT: C 108 LYS cc_start: 0.8734 (tppt) cc_final: 0.8521 (tppt) REVERT: D 23 ILE cc_start: 0.8711 (mt) cc_final: 0.8355 (mm) REVERT: D 159 LEU cc_start: 0.8797 (mt) cc_final: 0.8323 (mt) REVERT: E 7 TYR cc_start: 0.8659 (m-80) cc_final: 0.8419 (m-80) REVERT: E 13 THR cc_start: 0.9093 (p) cc_final: 0.8846 (t) REVERT: E 16 ASP cc_start: 0.8437 (m-30) cc_final: 0.8169 (m-30) REVERT: E 39 MET cc_start: 0.8734 (tmm) cc_final: 0.8366 (tmm) REVERT: E 126 LEU cc_start: 0.8920 (mt) cc_final: 0.8693 (tt) REVERT: F 120 LYS cc_start: 0.9000 (mtpt) cc_final: 0.8651 (tptt) REVERT: F 122 PHE cc_start: 0.7627 (m-80) cc_final: 0.7043 (m-80) REVERT: F 170 LEU cc_start: 0.9434 (mt) cc_final: 0.9135 (pp) REVERT: G 23 ASN cc_start: 0.6822 (m110) cc_final: 0.6278 (m-40) REVERT: G 106 LEU cc_start: 0.9652 (mt) cc_final: 0.9357 (mp) REVERT: G 116 ILE cc_start: 0.9472 (mt) cc_final: 0.9254 (mp) REVERT: G 131 LYS cc_start: 0.9241 (mttt) cc_final: 0.9023 (mmmm) REVERT: J 50 ASP cc_start: 0.7469 (t0) cc_final: 0.7195 (t0) REVERT: J 53 ASP cc_start: 0.7805 (m-30) cc_final: 0.7489 (m-30) REVERT: J 76 TYR cc_start: 0.8607 (m-80) cc_final: 0.8336 (m-80) REVERT: J 118 GLN cc_start: 0.8258 (tp40) cc_final: 0.7552 (tp40) REVERT: J 127 ARG cc_start: 0.8153 (ttm-80) cc_final: 0.7938 (ttm170) REVERT: K 8 LEU cc_start: 0.8835 (mt) cc_final: 0.8252 (mt) REVERT: K 22 ILE cc_start: 0.9207 (mt) cc_final: 0.8805 (mt) REVERT: K 43 VAL cc_start: 0.9449 (t) cc_final: 0.9213 (t) REVERT: K 59 LYS cc_start: 0.8842 (mtpp) cc_final: 0.8613 (mtmm) REVERT: K 66 LYS cc_start: 0.6365 (pttm) cc_final: 0.5836 (ptmt) REVERT: K 116 SER cc_start: 0.9577 (p) cc_final: 0.9214 (p) REVERT: L 41 ARG cc_start: 0.8841 (mmt180) cc_final: 0.8612 (mpt180) REVERT: L 74 TYR cc_start: 0.8415 (m-80) cc_final: 0.8097 (m-80) REVERT: L 89 THR cc_start: 0.9089 (t) cc_final: 0.8677 (p) REVERT: L 118 GLU cc_start: 0.8577 (mp0) cc_final: 0.8207 (pm20) REVERT: M 37 LEU cc_start: 0.9202 (mt) cc_final: 0.8661 (mp) REVERT: M 44 ASN cc_start: 0.8463 (m-40) cc_final: 0.7954 (m-40) REVERT: M 106 ILE cc_start: 0.8598 (mt) cc_final: 0.8340 (mt) REVERT: M 116 GLU cc_start: 0.8427 (tp30) cc_final: 0.8161 (tp30) REVERT: M 119 ARG cc_start: 0.9079 (ttt-90) cc_final: 0.8816 (ttt-90) REVERT: N 10 SER cc_start: 0.8009 (p) cc_final: 0.7786 (m) REVERT: N 20 LEU cc_start: 0.9122 (mt) cc_final: 0.8524 (mt) REVERT: N 23 ASP cc_start: 0.6581 (m-30) cc_final: 0.6285 (m-30) REVERT: N 45 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7524 (mt-10) REVERT: N 46 LYS cc_start: 0.9186 (mttt) cc_final: 0.8984 (mttp) REVERT: O 32 ASN cc_start: 0.8414 (t0) cc_final: 0.7559 (t0) REVERT: O 34 PHE cc_start: 0.6324 (t80) cc_final: 0.5272 (t80) REVERT: O 41 TYR cc_start: 0.8905 (m-80) cc_final: 0.8562 (m-80) REVERT: O 44 ILE cc_start: 0.9692 (mt) cc_final: 0.9449 (mm) REVERT: O 70 ASP cc_start: 0.8664 (t70) cc_final: 0.8444 (t0) REVERT: O 80 LEU cc_start: 0.9727 (tp) cc_final: 0.9280 (tt) REVERT: P 6 GLU cc_start: 0.7733 (mt-10) cc_final: 0.7428 (mt-10) REVERT: P 91 LYS cc_start: 0.9038 (ttmt) cc_final: 0.8384 (tttt) REVERT: Q 16 LYS cc_start: 0.8913 (mttt) cc_final: 0.8620 (mtpt) REVERT: Q 27 SER cc_start: 0.8439 (m) cc_final: 0.8035 (p) REVERT: Q 76 TYR cc_start: 0.7956 (t80) cc_final: 0.7262 (t80) REVERT: Q 84 LYS cc_start: 0.8480 (mttt) cc_final: 0.8212 (ptmt) REVERT: Q 103 LEU cc_start: 0.9365 (mp) cc_final: 0.9091 (tp) REVERT: Q 107 ASN cc_start: 0.9163 (m-40) cc_final: 0.8951 (m110) REVERT: R 18 GLN cc_start: 0.9006 (tt0) cc_final: 0.8759 (mt0) REVERT: R 40 PHE cc_start: 0.7998 (t80) cc_final: 0.7536 (t80) REVERT: S 37 ASN cc_start: 0.8447 (t0) cc_final: 0.8124 (t0) REVERT: S 99 ARG cc_start: 0.7891 (mmt180) cc_final: 0.7395 (mmt-90) REVERT: T 31 ASP cc_start: 0.8068 (t0) cc_final: 0.7784 (t0) REVERT: U 7 ASP cc_start: 0.7116 (m-30) cc_final: 0.6874 (m-30) REVERT: U 92 ARG cc_start: 0.7701 (mtm180) cc_final: 0.6873 (ptm160) REVERT: W 23 ASP cc_start: 0.8402 (t0) cc_final: 0.8189 (t0) REVERT: W 35 ASP cc_start: 0.7085 (t0) cc_final: 0.6193 (t0) REVERT: W 76 LYS cc_start: 0.8613 (mttt) cc_final: 0.8182 (mmmt) REVERT: Y 8 ASP cc_start: 0.8391 (m-30) cc_final: 0.8167 (m-30) REVERT: Y 27 ASN cc_start: 0.8866 (m-40) cc_final: 0.8090 (m110) REVERT: Z 4 LEU cc_start: 0.7723 (pt) cc_final: 0.7354 (pp) REVERT: Z 5 GLU cc_start: 0.7062 (mp0) cc_final: 0.6749 (mp0) REVERT: b 49 LYS cc_start: 0.9634 (mmmt) cc_final: 0.9390 (tppt) REVERT: b 52 GLU cc_start: 0.8606 (mp0) cc_final: 0.8236 (pm20) REVERT: b 77 GLN cc_start: 0.8466 (mt0) cc_final: 0.8236 (mp10) REVERT: b 82 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8933 (pt0) REVERT: b 93 ASN cc_start: 0.9149 (p0) cc_final: 0.8750 (p0) REVERT: b 94 GLN cc_start: 0.8640 (mm-40) cc_final: 0.8058 (pm20) REVERT: b 108 GLN cc_start: 0.8924 (tt0) cc_final: 0.8632 (tp40) REVERT: b 141 LEU cc_start: 0.9178 (mt) cc_final: 0.8812 (mm) REVERT: b 156 ASP cc_start: 0.8699 (t0) cc_final: 0.8477 (t0) REVERT: b 180 ASN cc_start: 0.8799 (p0) cc_final: 0.8560 (p0) REVERT: b 211 LYS cc_start: 0.9321 (tptt) cc_final: 0.9042 (tppt) REVERT: b 214 THR cc_start: 0.9254 (p) cc_final: 0.8962 (t) REVERT: b 217 MET cc_start: 0.9242 (mmm) cc_final: 0.8710 (mmm) REVERT: c 36 LEU cc_start: 0.9106 (mm) cc_final: 0.8045 (mm) REVERT: c 41 TYR cc_start: 0.9232 (t80) cc_final: 0.8994 (t80) REVERT: c 82 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8339 (mp0) REVERT: c 136 GLN cc_start: 0.8502 (tp-100) cc_final: 0.7514 (tp-100) REVERT: c 138 GLN cc_start: 0.8305 (mt0) cc_final: 0.7981 (mt0) REVERT: c 165 GLU cc_start: 0.6990 (mm-30) cc_final: 0.6410 (mm-30) REVERT: c 198 LYS cc_start: 0.8379 (mttt) cc_final: 0.7965 (mttt) REVERT: d 19 LEU cc_start: 0.8130 (tp) cc_final: 0.7682 (mm) REVERT: d 61 TYR cc_start: 0.7817 (m-80) cc_final: 0.7427 (m-80) REVERT: d 100 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8373 (mmtt) REVERT: d 115 ASN cc_start: 0.8990 (t0) cc_final: 0.7093 (t0) REVERT: e 13 GLU cc_start: 0.7918 (pm20) cc_final: 0.7315 (pp20) REVERT: e 36 LEU cc_start: 0.9078 (pp) cc_final: 0.8655 (tt) REVERT: e 52 LYS cc_start: 0.8495 (mtpt) cc_final: 0.8152 (mtpt) REVERT: e 68 LYS cc_start: 0.9261 (mttt) cc_final: 0.9020 (mtpp) REVERT: f 6 VAL cc_start: 0.9312 (t) cc_final: 0.8771 (p) REVERT: f 24 GLU cc_start: 0.9243 (mm-30) cc_final: 0.8755 (tp30) REVERT: f 28 ASN cc_start: 0.9130 (m-40) cc_final: 0.8086 (m-40) REVERT: f 59 PHE cc_start: 0.8823 (m-80) cc_final: 0.8474 (m-10) REVERT: f 64 ASN cc_start: 0.9301 (m-40) cc_final: 0.8780 (m-40) REVERT: g 40 GLN cc_start: 0.8939 (mt0) cc_final: 0.8573 (mt0) REVERT: g 41 THR cc_start: 0.9667 (m) cc_final: 0.9436 (p) REVERT: g 66 LEU cc_start: 0.9575 (mt) cc_final: 0.8995 (mt) REVERT: g 122 ASN cc_start: 0.9317 (m-40) cc_final: 0.9075 (m110) REVERT: h 32 LEU cc_start: 0.8984 (tp) cc_final: 0.8752 (tp) REVERT: h 36 ILE cc_start: 0.9518 (mt) cc_final: 0.9258 (mt) REVERT: h 41 LYS cc_start: 0.9296 (tptp) cc_final: 0.8905 (tptm) REVERT: h 46 ILE cc_start: 0.7753 (mt) cc_final: 0.7161 (mt) REVERT: h 74 ILE cc_start: 0.9277 (mt) cc_final: 0.8881 (mt) REVERT: j 9 ARG cc_start: 0.7778 (mtp85) cc_final: 0.7351 (mtp180) REVERT: j 66 GLU cc_start: 0.7354 (tt0) cc_final: 0.6662 (tt0) REVERT: j 68 ARG cc_start: 0.7463 (mtt180) cc_final: 0.6732 (mmm-85) REVERT: k 44 ILE cc_start: 0.8849 (mt) cc_final: 0.8500 (mp) REVERT: k 63 PHE cc_start: 0.8545 (t80) cc_final: 0.8007 (t80) REVERT: k 66 GLN cc_start: 0.9278 (tt0) cc_final: 0.8530 (tm-30) REVERT: m 13 LYS cc_start: 0.8296 (mptt) cc_final: 0.8074 (mttt) REVERT: m 21 TYR cc_start: 0.8584 (m-80) cc_final: 0.8127 (m-80) REVERT: m 23 PHE cc_start: 0.8368 (t80) cc_final: 0.7917 (t80) REVERT: m 28 THR cc_start: 0.9242 (p) cc_final: 0.8708 (p) REVERT: n 50 LYS cc_start: 0.8468 (ptmt) cc_final: 0.8192 (mtmm) REVERT: n 57 LYS cc_start: 0.8495 (ptpt) cc_final: 0.8241 (ptmm) REVERT: o 36 ILE cc_start: 0.9330 (mt) cc_final: 0.9115 (mm) REVERT: o 58 LYS cc_start: 0.8723 (mttt) cc_final: 0.8409 (mttp) REVERT: o 68 THR cc_start: 0.9123 (m) cc_final: 0.8637 (p) REVERT: o 69 TYR cc_start: 0.8929 (t80) cc_final: 0.8527 (t80) REVERT: p 9 ARG cc_start: 0.8162 (tpt-90) cc_final: 0.7708 (tpt90) REVERT: p 34 ILE cc_start: 0.9147 (mt) cc_final: 0.8922 (tp) REVERT: p 42 PRO cc_start: 0.9128 (Cg_endo) cc_final: 0.8833 (Cg_exo) REVERT: r 38 VAL cc_start: 0.9289 (t) cc_final: 0.9057 (p) REVERT: s 12 ASP cc_start: 0.7479 (m-30) cc_final: 0.7083 (m-30) REVERT: s 16 MET cc_start: 0.8974 (mmm) cc_final: 0.8610 (tpp) REVERT: s 51 VAL cc_start: 0.8814 (t) cc_final: 0.8549 (p) REVERT: t 12 LYS cc_start: 0.9196 (tttt) cc_final: 0.8887 (ttpp) REVERT: t 15 ASN cc_start: 0.8908 (m110) cc_final: 0.8601 (m110) REVERT: t 19 VAL cc_start: 0.9612 (t) cc_final: 0.9291 (p) REVERT: t 29 ARG cc_start: 0.9358 (mtt90) cc_final: 0.9033 (mtm-85) REVERT: u 50 SER cc_start: 0.8691 (t) cc_final: 0.8305 (m) outliers start: 11 outliers final: 2 residues processed: 2196 average time/residue: 1.4005 time to fit residues: 5220.9848 Evaluate side-chains 1488 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1486 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain c residue 37 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 824 optimal weight: 10.0000 chunk 739 optimal weight: 20.0000 chunk 410 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 499 optimal weight: 50.0000 chunk 395 optimal weight: 50.0000 chunk 764 optimal weight: 3.9990 chunk 296 optimal weight: 20.0000 chunk 465 optimal weight: 10.0000 chunk 569 optimal weight: 10.0000 chunk 886 optimal weight: 10.0000 overall best weight: 8.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 4 ASN 3 40 GLN C 153 GLN C 232 HIS ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 14 GLN D 33 ASN D 140 HIS D 173 ASN E 8 ASN G 39 HIS ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 48 HIS J 54 HIS J 59 ASN J 81 HIS K 4 GLN K 34 ASN L 38 GLN M 13 HIS ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 77 GLN P 77 HIS Q 72 ASN R 11 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 81 ASN S 73 GLN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 55 ASN U 58 ASN U 59 GLN U 67 ASN Y 39 ASN Z 32 ASN b 94 GLN c 122 GLN c 175 HIS d 82 HIS e 93 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 22 HIS i 38 HIS k 24 HIS k 30 ASN l 37 ASN l 122 ASN n 31 HIS ** o 9 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 10 GLN o 18 HIS o 51 HIS o 83 ASN q 5 ASN ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 155558 Z= 0.433 Angle : 0.802 11.535 233440 Z= 0.405 Chirality : 0.042 0.366 29944 Planarity : 0.006 0.079 11973 Dihedral : 24.411 179.952 79605 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.89 % Rotamer: Outliers : 6.09 % Allowed : 18.14 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.43 (0.11), residues: 5176 helix: 0.40 (0.12), residues: 1635 sheet: -1.18 (0.15), residues: 1021 loop : -1.76 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 65 HIS 0.014 0.002 HIS b 18 PHE 0.032 0.003 PHE s 10 TYR 0.027 0.003 TYR b 54 ARG 0.018 0.001 ARG c 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1862 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 1593 time to evaluate : 6.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 20 PHE cc_start: 0.8628 (t80) cc_final: 0.8367 (t80) REVERT: 0 52 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8620 (ptpt) REVERT: 1 15 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8083 (mtt90) REVERT: 1 20 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.8829 (mttm) REVERT: 1 32 PHE cc_start: 0.8565 (m-80) cc_final: 0.8342 (m-10) REVERT: 1 33 LYS cc_start: 0.8892 (ttpt) cc_final: 0.8287 (ttmm) REVERT: 1 35 TYR cc_start: 0.8519 (t80) cc_final: 0.8277 (t80) REVERT: 1 41 LYS cc_start: 0.9282 (ptpp) cc_final: 0.9028 (pttm) REVERT: 4 18 ARG cc_start: 0.8861 (mtp-110) cc_final: 0.8657 (ttm-80) REVERT: 4 19 ARG cc_start: 0.7731 (ttm170) cc_final: 0.6342 (ttm-80) REVERT: 4 20 LYS cc_start: 0.8757 (pttt) cc_final: 0.8437 (ttmt) REVERT: 6 1 MET cc_start: 0.5922 (mtt) cc_final: 0.4089 (ttm) REVERT: C 201 GLU cc_start: 0.8266 (tm-30) cc_final: 0.8038 (tm-30) REVERT: D 54 ASP cc_start: 0.7143 (t70) cc_final: 0.6869 (t70) REVERT: D 120 GLN cc_start: 0.8572 (mm-40) cc_final: 0.8301 (mm110) REVERT: D 128 GLN cc_start: 0.8885 (mt0) cc_final: 0.8654 (mt0) REVERT: D 168 GLN cc_start: 0.8800 (tt0) cc_final: 0.8513 (tt0) REVERT: E 13 THR cc_start: 0.8977 (p) cc_final: 0.8687 (t) REVERT: E 39 MET cc_start: 0.8964 (tmm) cc_final: 0.8467 (tmm) REVERT: E 192 LEU cc_start: 0.8907 (tt) cc_final: 0.8700 (tp) REVERT: F 83 MET cc_start: 0.8518 (mtp) cc_final: 0.8294 (mtt) REVERT: F 97 TYR cc_start: 0.7402 (t80) cc_final: 0.6923 (t80) REVERT: F 122 PHE cc_start: 0.8283 (m-80) cc_final: 0.7460 (m-80) REVERT: F 170 LEU cc_start: 0.9481 (mt) cc_final: 0.9150 (pp) REVERT: G 42 MET cc_start: 0.6614 (tpp) cc_final: 0.6295 (tpp) REVERT: G 84 PHE cc_start: 0.7503 (m-80) cc_final: 0.7219 (m-10) REVERT: J 50 ASP cc_start: 0.7521 (t0) cc_final: 0.7081 (t70) REVERT: J 109 MET cc_start: 0.8539 (mmm) cc_final: 0.7884 (mtt) REVERT: J 127 ARG cc_start: 0.8599 (ttm-80) cc_final: 0.8376 (ptp-110) REVERT: K 44 LYS cc_start: 0.9035 (mmtt) cc_final: 0.8654 (mmtt) REVERT: K 54 LYS cc_start: 0.9310 (ttmm) cc_final: 0.9057 (ttmm) REVERT: K 59 LYS cc_start: 0.9085 (mtpp) cc_final: 0.8834 (mttm) REVERT: K 116 SER cc_start: 0.9376 (p) cc_final: 0.9081 (p) REVERT: K 120 GLU cc_start: 0.8587 (tt0) cc_final: 0.7759 (tt0) REVERT: L 15 THR cc_start: 0.9129 (OUTLIER) cc_final: 0.8857 (t) REVERT: L 38 GLN cc_start: 0.7437 (OUTLIER) cc_final: 0.7127 (tt0) REVERT: L 70 ASN cc_start: 0.9092 (m-40) cc_final: 0.8879 (m110) REVERT: L 80 ASP cc_start: 0.7671 (m-30) cc_final: 0.7009 (m-30) REVERT: L 89 THR cc_start: 0.9081 (t) cc_final: 0.8665 (p) REVERT: L 106 ASN cc_start: 0.7879 (t0) cc_final: 0.7649 (t0) REVERT: M 44 ASN cc_start: 0.8761 (m-40) cc_final: 0.8090 (t0) REVERT: N 31 GLU cc_start: 0.8094 (mt-10) cc_final: 0.7650 (mp0) REVERT: N 45 GLU cc_start: 0.8381 (mt-10) cc_final: 0.7951 (mt-10) REVERT: N 114 MET cc_start: 0.8719 (mmm) cc_final: 0.7649 (mmp) REVERT: O 32 ASN cc_start: 0.8778 (t0) cc_final: 0.8075 (t0) REVERT: O 41 TYR cc_start: 0.8862 (m-80) cc_final: 0.7928 (m-80) REVERT: O 70 ASP cc_start: 0.8730 (t70) cc_final: 0.8363 (t0) REVERT: O 101 LEU cc_start: 0.9341 (tp) cc_final: 0.9015 (tt) REVERT: P 1 MET cc_start: 0.7823 (ptt) cc_final: 0.7422 (ptt) REVERT: P 78 THR cc_start: 0.9020 (OUTLIER) cc_final: 0.8633 (m) REVERT: Q 16 LYS cc_start: 0.9215 (mttt) cc_final: 0.8631 (mtpt) REVERT: Q 27 SER cc_start: 0.8781 (m) cc_final: 0.8301 (p) REVERT: Q 76 TYR cc_start: 0.8656 (t80) cc_final: 0.7770 (t80) REVERT: Q 102 ASP cc_start: 0.8794 (t0) cc_final: 0.8577 (t0) REVERT: Q 108 GLN cc_start: 0.9065 (mt0) cc_final: 0.8862 (mt0) REVERT: R 18 GLN cc_start: 0.8791 (tt0) cc_final: 0.8488 (tt0) REVERT: R 36 GLU cc_start: 0.8337 (pm20) cc_final: 0.8086 (pm20) REVERT: R 67 ARG cc_start: 0.8944 (mmm-85) cc_final: 0.8425 (mtp180) REVERT: R 101 ASN cc_start: 0.8324 (m110) cc_final: 0.7994 (m110) REVERT: S 37 ASN cc_start: 0.8931 (t0) cc_final: 0.8713 (t0) REVERT: S 48 GLU cc_start: 0.8311 (tm-30) cc_final: 0.8041 (tm-30) REVERT: S 65 ASP cc_start: 0.5820 (t0) cc_final: 0.5026 (t0) REVERT: S 101 SER cc_start: 0.9579 (p) cc_final: 0.9348 (m) REVERT: T 26 TYR cc_start: 0.8435 (m-80) cc_final: 0.8191 (m-80) REVERT: T 31 ASP cc_start: 0.8302 (t0) cc_final: 0.7689 (t0) REVERT: T 41 ASP cc_start: 0.8888 (m-30) cc_final: 0.8586 (m-30) REVERT: T 56 ILE cc_start: 0.9057 (mt) cc_final: 0.8840 (mt) REVERT: T 73 THR cc_start: 0.9164 (m) cc_final: 0.8707 (p) REVERT: W 35 ASP cc_start: 0.7652 (t0) cc_final: 0.7417 (t0) REVERT: W 48 GLN cc_start: 0.8272 (OUTLIER) cc_final: 0.7927 (pt0) REVERT: W 51 THR cc_start: 0.8880 (OUTLIER) cc_final: 0.8470 (p) REVERT: W 52 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8680 (mtpp) REVERT: W 76 LYS cc_start: 0.8539 (mttt) cc_final: 0.8225 (mmmt) REVERT: W 78 GLU cc_start: 0.7496 (mt-10) cc_final: 0.7220 (mp0) REVERT: W 83 ASP cc_start: 0.7983 (t70) cc_final: 0.7682 (t70) REVERT: Y 5 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8706 (mm-30) REVERT: Y 27 ASN cc_start: 0.8935 (m-40) cc_final: 0.8687 (m-40) REVERT: Y 29 ARG cc_start: 0.7034 (mtm110) cc_final: 0.6790 (mtm180) REVERT: Z 5 GLU cc_start: 0.7736 (mp0) cc_final: 0.7383 (mp0) REVERT: Z 39 ASP cc_start: 0.8778 (t0) cc_final: 0.8005 (t0) REVERT: Z 57 LYS cc_start: 0.8983 (tppt) cc_final: 0.8686 (tppt) REVERT: b 23 TRP cc_start: 0.8420 (p-90) cc_final: 0.7845 (p-90) REVERT: b 24 ASN cc_start: 0.8543 (t0) cc_final: 0.7736 (t0) REVERT: b 54 TYR cc_start: 0.7291 (m-80) cc_final: 0.6858 (m-80) REVERT: b 89 MET cc_start: 0.7441 (mmm) cc_final: 0.7219 (tpt) REVERT: b 93 ASN cc_start: 0.8909 (p0) cc_final: 0.8617 (p0) REVERT: b 104 PHE cc_start: 0.8807 (t80) cc_final: 0.7669 (t80) REVERT: b 141 LEU cc_start: 0.9331 (mt) cc_final: 0.8880 (tp) REVERT: b 156 ASP cc_start: 0.8723 (t0) cc_final: 0.8510 (t0) REVERT: b 170 ARG cc_start: 0.8742 (ptp-170) cc_final: 0.8217 (ptp90) REVERT: b 180 ASN cc_start: 0.9116 (p0) cc_final: 0.8879 (p0) REVERT: b 217 MET cc_start: 0.9206 (mmm) cc_final: 0.8884 (mmm) REVERT: c 3 GLN cc_start: 0.7065 (mm-40) cc_final: 0.6770 (mm-40) REVERT: c 32 LEU cc_start: 0.8898 (OUTLIER) cc_final: 0.8604 (mt) REVERT: c 122 GLN cc_start: 0.9263 (tp-100) cc_final: 0.8672 (mm-40) REVERT: c 138 GLN cc_start: 0.8382 (mt0) cc_final: 0.7998 (mt0) REVERT: c 187 GLU cc_start: 0.7654 (mt-10) cc_final: 0.7111 (pt0) REVERT: d 47 TYR cc_start: 0.9062 (t80) cc_final: 0.8783 (t80) REVERT: d 67 GLN cc_start: 0.8390 (mp10) cc_final: 0.8151 (mp10) REVERT: d 68 PHE cc_start: 0.9273 (t80) cc_final: 0.8610 (m-80) REVERT: d 100 LYS cc_start: 0.9097 (mmtt) cc_final: 0.8758 (mmtm) REVERT: d 173 GLU cc_start: 0.7255 (tp30) cc_final: 0.6805 (tp30) REVERT: e 13 GLU cc_start: 0.7929 (pm20) cc_final: 0.7478 (pp20) REVERT: e 41 ASP cc_start: 0.8834 (p0) cc_final: 0.8440 (p0) REVERT: e 55 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7847 (mm-30) REVERT: f 24 GLU cc_start: 0.9219 (mm-30) cc_final: 0.8720 (tp30) REVERT: f 25 ARG cc_start: 0.9358 (ptm-80) cc_final: 0.9058 (ttp80) REVERT: f 28 ASN cc_start: 0.9201 (m-40) cc_final: 0.7672 (m-40) REVERT: g 31 MET cc_start: 0.8337 (ttp) cc_final: 0.7530 (ttp) REVERT: g 46 SER cc_start: 0.8944 (m) cc_final: 0.8536 (p) REVERT: g 49 ILE cc_start: 0.9703 (tp) cc_final: 0.9180 (pt) REVERT: g 62 PHE cc_start: 0.9146 (t80) cc_final: 0.8795 (t80) REVERT: g 66 LEU cc_start: 0.9331 (mt) cc_final: 0.8872 (mt) REVERT: g 75 VAL cc_start: 0.7858 (OUTLIER) cc_final: 0.6454 (t) REVERT: g 122 ASN cc_start: 0.9325 (m-40) cc_final: 0.9068 (m110) REVERT: g 125 LEU cc_start: 0.9154 (mt) cc_final: 0.8932 (mt) REVERT: h 36 ILE cc_start: 0.9606 (mt) cc_final: 0.9367 (mt) REVERT: h 42 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8676 (ptp90) REVERT: i 6 TYR cc_start: 0.8503 (m-80) cc_final: 0.8073 (m-80) REVERT: i 35 ILE cc_start: 0.9241 (mp) cc_final: 0.8999 (mp) REVERT: j 24 LYS cc_start: 0.9546 (mmtm) cc_final: 0.9130 (mmtm) REVERT: j 42 LEU cc_start: 0.9402 (OUTLIER) cc_final: 0.8893 (tt) REVERT: j 46 LYS cc_start: 0.9018 (ptpp) cc_final: 0.8800 (ptmt) REVERT: j 64 GLN cc_start: 0.8849 (mm-40) cc_final: 0.8300 (mm-40) REVERT: j 97 ASP cc_start: 0.8133 (t0) cc_final: 0.7888 (t0) REVERT: k 29 PHE cc_start: 0.9118 (OUTLIER) cc_final: 0.8784 (t80) REVERT: k 63 PHE cc_start: 0.8774 (t80) cc_final: 0.8278 (t80) REVERT: k 66 GLN cc_start: 0.9376 (tt0) cc_final: 0.8843 (tm-30) REVERT: k 70 GLU cc_start: 0.8821 (mm-30) cc_final: 0.8459 (mm-30) REVERT: l 42 GLN cc_start: 0.9174 (OUTLIER) cc_final: 0.8681 (mp10) REVERT: l 90 HIS cc_start: 0.7999 (m170) cc_final: 0.7660 (m-70) REVERT: m 13 LYS cc_start: 0.8534 (mptt) cc_final: 0.8162 (mtmt) REVERT: m 23 PHE cc_start: 0.8749 (t80) cc_final: 0.8455 (t80) REVERT: m 66 GLU cc_start: 0.7066 (tp30) cc_final: 0.6753 (tp30) REVERT: n 9 LYS cc_start: 0.8709 (mmtp) cc_final: 0.8346 (mmtt) REVERT: n 19 GLN cc_start: 0.8808 (OUTLIER) cc_final: 0.8408 (mp10) REVERT: n 36 LYS cc_start: 0.9037 (tptm) cc_final: 0.8828 (tppp) REVERT: n 57 LYS cc_start: 0.9192 (ptpt) cc_final: 0.8894 (ptmm) REVERT: o 48 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8228 (mtmm) REVERT: o 68 THR cc_start: 0.9377 (m) cc_final: 0.8976 (p) REVERT: o 69 TYR cc_start: 0.9269 (t80) cc_final: 0.9038 (t80) REVERT: o 80 GLU cc_start: 0.8479 (mt-10) cc_final: 0.7869 (pt0) REVERT: p 24 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7839 (p0) REVERT: q 10 TYR cc_start: 0.7534 (m-80) cc_final: 0.7247 (m-80) REVERT: q 31 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.8026 (ptpt) REVERT: q 83 GLU cc_start: 0.7343 (tp30) cc_final: 0.6857 (tp30) REVERT: r 56 TYR cc_start: 0.8264 (m-80) cc_final: 0.7762 (m-80) REVERT: t 13 THR cc_start: 0.9398 (m) cc_final: 0.9184 (p) REVERT: t 16 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8621 (mm-30) REVERT: t 18 ARG cc_start: 0.8903 (tmm-80) cc_final: 0.8691 (ttp80) REVERT: t 29 ARG cc_start: 0.9320 (mtt90) cc_final: 0.8976 (mmm-85) REVERT: t 35 VAL cc_start: 0.9541 (t) cc_final: 0.9199 (m) REVERT: t 42 ASN cc_start: 0.8520 (m-40) cc_final: 0.8207 (m-40) REVERT: u 50 SER cc_start: 0.9126 (t) cc_final: 0.8425 (p) outliers start: 269 outliers final: 161 residues processed: 1710 average time/residue: 1.2120 time to fit residues: 3587.3240 Evaluate side-chains 1547 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 1370 time to evaluate : 5.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 20 LYS Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 2 residue 23 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 44 LEU Chi-restraints excluded: chain E residue 57 VAL Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 47 THR Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 65 THR Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 86 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 120 VAL Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 42 ILE Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 12 ILE Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 67 ASN Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 59 GLN Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain c residue 32 LEU Chi-restraints excluded: chain c residue 37 LYS Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain d residue 57 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 130 SER Chi-restraints excluded: chain d residue 152 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 74 VAL Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 155 LYS Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 75 VAL Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 42 ARG Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 38 HIS Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 42 LEU Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 85 ASP Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 103 GLN Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain k residue 115 VAL Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 70 LEU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 51 HIS Chi-restraints excluded: chain p residue 24 ASP Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 31 LYS Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain s residue 79 THR Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 24 ILE Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 41 ASN Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 38 ILE Chi-restraints excluded: chain u residue 39 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 492 optimal weight: 6.9990 chunk 275 optimal weight: 1.9990 chunk 737 optimal weight: 20.0000 chunk 603 optimal weight: 10.0000 chunk 244 optimal weight: 5.9990 chunk 887 optimal weight: 6.9990 chunk 959 optimal weight: 7.9990 chunk 790 optimal weight: 5.9990 chunk 880 optimal weight: 2.9990 chunk 302 optimal weight: 20.0000 chunk 712 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 23 ASN C 163 GLN C 199 GLN C 264 ASN D 50 GLN F 27 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN N 27 ASN N 61 GLN N 77 GLN Q 37 GLN ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 108 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN b 103 ASN f 64 ASN ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 15 HIS l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 91 HIS o 9 ASN o 83 ASN p 72 ASN p 77 GLN p 88 GLN ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 155558 Z= 0.272 Angle : 0.634 10.127 233440 Z= 0.326 Chirality : 0.036 0.310 29944 Planarity : 0.004 0.060 11973 Dihedral : 24.282 179.464 79603 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.30 % Favored : 93.62 % Rotamer: Outliers : 6.07 % Allowed : 21.88 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.05 (0.11), residues: 5176 helix: 0.75 (0.13), residues: 1634 sheet: -0.84 (0.16), residues: 1003 loop : -1.62 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP d 9 HIS 0.015 0.002 HIS b 18 PHE 0.025 0.002 PHE b 56 TYR 0.025 0.002 TYR b 54 ARG 0.008 0.001 ARG T 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1792 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 268 poor density : 1524 time to evaluate : 6.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 52 LYS cc_start: 0.8915 (mtpt) cc_final: 0.8702 (ptpt) REVERT: 1 15 ARG cc_start: 0.8313 (mtt90) cc_final: 0.7930 (mtt90) REVERT: 1 32 PHE cc_start: 0.8358 (m-80) cc_final: 0.8104 (m-10) REVERT: 1 35 TYR cc_start: 0.8664 (t80) cc_final: 0.8210 (t80) REVERT: 1 41 LYS cc_start: 0.9272 (ptpp) cc_final: 0.9049 (pttm) REVERT: 4 13 LYS cc_start: 0.9358 (mtmt) cc_final: 0.8956 (mtpp) REVERT: 4 18 ARG cc_start: 0.8874 (mtp-110) cc_final: 0.8544 (ttm-80) REVERT: 6 1 MET cc_start: 0.6184 (mtt) cc_final: 0.3894 (ptt) REVERT: C 192 ILE cc_start: 0.8949 (OUTLIER) cc_final: 0.8724 (mm) REVERT: D 54 ASP cc_start: 0.7165 (t70) cc_final: 0.6879 (t70) REVERT: D 83 LEU cc_start: 0.8928 (OUTLIER) cc_final: 0.8436 (tt) REVERT: D 95 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: D 120 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8193 (mm110) REVERT: D 128 GLN cc_start: 0.8652 (mt0) cc_final: 0.8422 (mt0) REVERT: D 168 GLN cc_start: 0.8749 (tt0) cc_final: 0.8385 (tt0) REVERT: E 13 THR cc_start: 0.8964 (p) cc_final: 0.8715 (t) REVERT: E 39 MET cc_start: 0.8901 (tmm) cc_final: 0.8429 (tmm) REVERT: E 192 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8494 (tp) REVERT: F 83 MET cc_start: 0.8631 (mtp) cc_final: 0.8419 (mtt) REVERT: F 97 TYR cc_start: 0.7664 (t80) cc_final: 0.7430 (t80) REVERT: F 122 PHE cc_start: 0.8371 (m-80) cc_final: 0.7518 (m-80) REVERT: F 170 LEU cc_start: 0.9464 (mt) cc_final: 0.8995 (pp) REVERT: G 84 PHE cc_start: 0.7535 (m-80) cc_final: 0.7309 (m-10) REVERT: J 32 GLU cc_start: 0.8484 (mt-10) cc_final: 0.7938 (tt0) REVERT: J 50 ASP cc_start: 0.7605 (t0) cc_final: 0.7095 (t70) REVERT: J 58 ILE cc_start: 0.9194 (OUTLIER) cc_final: 0.8956 (tp) REVERT: J 109 MET cc_start: 0.8494 (mmm) cc_final: 0.8026 (mtt) REVERT: K 59 LYS cc_start: 0.9088 (mtpp) cc_final: 0.8829 (mttm) REVERT: K 113 LYS cc_start: 0.8931 (tppt) cc_final: 0.8716 (tppt) REVERT: K 116 SER cc_start: 0.9446 (p) cc_final: 0.9167 (p) REVERT: K 120 GLU cc_start: 0.8519 (tt0) cc_final: 0.7689 (tt0) REVERT: L 15 THR cc_start: 0.9128 (OUTLIER) cc_final: 0.8863 (t) REVERT: L 70 ASN cc_start: 0.9060 (m-40) cc_final: 0.8811 (m110) REVERT: L 80 ASP cc_start: 0.7613 (m-30) cc_final: 0.7357 (m-30) REVERT: L 89 THR cc_start: 0.8981 (t) cc_final: 0.8518 (p) REVERT: M 44 ASN cc_start: 0.8794 (m-40) cc_final: 0.8323 (t0) REVERT: N 28 GLU cc_start: 0.7491 (mp0) cc_final: 0.7117 (mp0) REVERT: N 31 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7453 (mp0) REVERT: N 45 GLU cc_start: 0.8330 (mt-10) cc_final: 0.7965 (mt-10) REVERT: N 69 GLU cc_start: 0.8039 (mp0) cc_final: 0.7322 (mp0) REVERT: N 114 MET cc_start: 0.8653 (mmm) cc_final: 0.8254 (tpp) REVERT: O 1 MET cc_start: 0.7696 (tpt) cc_final: 0.6954 (tpp) REVERT: O 32 ASN cc_start: 0.8786 (t0) cc_final: 0.7963 (t0) REVERT: O 41 TYR cc_start: 0.8763 (m-80) cc_final: 0.8033 (m-80) REVERT: O 59 LEU cc_start: 0.9321 (tp) cc_final: 0.8803 (tt) REVERT: O 70 ASP cc_start: 0.8698 (t70) cc_final: 0.8329 (t0) REVERT: O 101 LEU cc_start: 0.9357 (tp) cc_final: 0.9039 (tt) REVERT: P 1 MET cc_start: 0.7724 (ptt) cc_final: 0.7332 (ptt) REVERT: P 78 THR cc_start: 0.8928 (OUTLIER) cc_final: 0.8696 (m) REVERT: P 88 ARG cc_start: 0.8407 (mtp85) cc_final: 0.8146 (mtp-110) REVERT: Q 10 THR cc_start: 0.9535 (m) cc_final: 0.9319 (p) REVERT: Q 16 LYS cc_start: 0.9048 (mttt) cc_final: 0.8591 (mtpt) REVERT: Q 27 SER cc_start: 0.8651 (m) cc_final: 0.8166 (p) REVERT: Q 76 TYR cc_start: 0.8597 (t80) cc_final: 0.7835 (t80) REVERT: Q 102 ASP cc_start: 0.8662 (t0) cc_final: 0.8098 (t0) REVERT: R 16 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8274 (mm-30) REVERT: R 18 GLN cc_start: 0.8891 (tt0) cc_final: 0.8521 (tt0) REVERT: R 36 GLU cc_start: 0.8253 (pm20) cc_final: 0.8031 (pm20) REVERT: R 67 ARG cc_start: 0.8977 (mmm-85) cc_final: 0.8471 (mtp180) REVERT: S 37 ASN cc_start: 0.8966 (t0) cc_final: 0.8633 (t0) REVERT: S 48 GLU cc_start: 0.8306 (tm-30) cc_final: 0.7961 (tm-30) REVERT: S 53 SER cc_start: 0.9383 (OUTLIER) cc_final: 0.8955 (p) REVERT: S 101 SER cc_start: 0.9362 (p) cc_final: 0.9145 (m) REVERT: T 44 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7875 (mm-30) REVERT: T 56 ILE cc_start: 0.9041 (mt) cc_final: 0.8808 (mt) REVERT: T 68 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7357 (ttp-110) REVERT: U 40 MET cc_start: 0.8664 (tpp) cc_final: 0.8383 (tpp) REVERT: U 92 ARG cc_start: 0.8152 (mtm180) cc_final: 0.7611 (ptp-170) REVERT: W 35 ASP cc_start: 0.7551 (t0) cc_final: 0.7323 (t0) REVERT: W 48 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8241 (pt0) REVERT: W 51 THR cc_start: 0.8790 (OUTLIER) cc_final: 0.8462 (p) REVERT: W 52 LYS cc_start: 0.8961 (mmmm) cc_final: 0.8629 (mtpp) REVERT: Y 5 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8706 (mm-30) REVERT: Y 24 GLU cc_start: 0.8698 (tp30) cc_final: 0.8456 (tp30) REVERT: Y 27 ASN cc_start: 0.9002 (m-40) cc_final: 0.8036 (m110) REVERT: Z 5 GLU cc_start: 0.7732 (mp0) cc_final: 0.7308 (mp0) REVERT: Z 57 LYS cc_start: 0.9030 (tppt) cc_final: 0.8772 (tppt) REVERT: b 24 ASN cc_start: 0.8405 (t0) cc_final: 0.7957 (t0) REVERT: b 75 GLN cc_start: 0.8980 (pm20) cc_final: 0.8345 (pm20) REVERT: b 93 ASN cc_start: 0.8900 (p0) cc_final: 0.8609 (p0) REVERT: b 103 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7663 (m110) REVERT: b 169 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8274 (mp0) REVERT: b 180 ASN cc_start: 0.9070 (p0) cc_final: 0.8817 (p0) REVERT: b 217 MET cc_start: 0.9248 (mmm) cc_final: 0.8831 (mmm) REVERT: c 3 GLN cc_start: 0.7086 (mm-40) cc_final: 0.6721 (mm-40) REVERT: c 40 GLU cc_start: 0.8295 (tm-30) cc_final: 0.7895 (tm-30) REVERT: c 138 GLN cc_start: 0.8457 (mt0) cc_final: 0.8073 (mt0) REVERT: c 187 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7248 (pt0) REVERT: d 47 TYR cc_start: 0.8924 (t80) cc_final: 0.8652 (t80) REVERT: d 67 GLN cc_start: 0.8297 (mp10) cc_final: 0.8029 (mp10) REVERT: d 96 ASN cc_start: 0.8675 (t0) cc_final: 0.8219 (m-40) REVERT: d 100 LYS cc_start: 0.9137 (mmtt) cc_final: 0.8818 (mmtt) REVERT: d 176 PHE cc_start: 0.6023 (t80) cc_final: 0.5647 (t80) REVERT: e 69 LYS cc_start: 0.9026 (mttt) cc_final: 0.8535 (mttm) REVERT: e 159 LYS cc_start: 0.8794 (mmtp) cc_final: 0.8486 (mmtm) REVERT: f 22 VAL cc_start: 0.9759 (m) cc_final: 0.9511 (p) REVERT: f 24 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8690 (tp30) REVERT: f 25 ARG cc_start: 0.9238 (ptm-80) cc_final: 0.8971 (ttp80) REVERT: f 28 ASN cc_start: 0.9385 (m-40) cc_final: 0.8436 (m-40) REVERT: f 47 ARG cc_start: 0.8254 (mmm-85) cc_final: 0.7528 (tpp80) REVERT: f 54 ASP cc_start: 0.8317 (t0) cc_final: 0.8107 (t70) REVERT: f 59 PHE cc_start: 0.8856 (m-10) cc_final: 0.7760 (m-10) REVERT: g 46 SER cc_start: 0.8805 (m) cc_final: 0.8418 (p) REVERT: g 62 PHE cc_start: 0.9024 (t80) cc_final: 0.8694 (t80) REVERT: g 66 LEU cc_start: 0.9254 (mt) cc_final: 0.8735 (mt) REVERT: g 86 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7920 (mm-40) REVERT: g 122 ASN cc_start: 0.9317 (m-40) cc_final: 0.9092 (m110) REVERT: h 36 ILE cc_start: 0.9651 (mt) cc_final: 0.9388 (mt) REVERT: i 6 TYR cc_start: 0.8549 (m-80) cc_final: 0.8063 (m-80) REVERT: i 61 TYR cc_start: 0.8651 (m-80) cc_final: 0.8395 (m-80) REVERT: j 24 LYS cc_start: 0.9494 (mmtm) cc_final: 0.9268 (mmtm) REVERT: j 64 GLN cc_start: 0.8901 (mm-40) cc_final: 0.8383 (mm-40) REVERT: k 63 PHE cc_start: 0.8820 (t80) cc_final: 0.8616 (t80) REVERT: k 96 GLU cc_start: 0.8391 (tp30) cc_final: 0.8174 (tp30) REVERT: l 65 TYR cc_start: 0.7716 (p90) cc_final: 0.7200 (p90) REVERT: l 90 HIS cc_start: 0.8068 (m170) cc_final: 0.7466 (m90) REVERT: m 10 PRO cc_start: 0.8864 (Cg_endo) cc_final: 0.7215 (Cg_exo) REVERT: n 19 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8405 (mp10) REVERT: n 25 GLU cc_start: 0.8024 (mm-30) cc_final: 0.7693 (mm-30) REVERT: n 36 LYS cc_start: 0.8948 (tptm) cc_final: 0.8596 (tppp) REVERT: n 46 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7570 (tm-30) REVERT: o 14 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7871 (tm-30) REVERT: o 15 PHE cc_start: 0.8520 (m-80) cc_final: 0.7821 (m-80) REVERT: o 68 THR cc_start: 0.9343 (m) cc_final: 0.8904 (p) REVERT: o 69 TYR cc_start: 0.9307 (t80) cc_final: 0.9084 (t80) REVERT: o 80 GLU cc_start: 0.8473 (mt-10) cc_final: 0.7932 (pt0) REVERT: p 24 ASP cc_start: 0.8184 (OUTLIER) cc_final: 0.7928 (p0) REVERT: p 26 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.8335 (mtt-85) REVERT: p 61 GLN cc_start: 0.9035 (mm-40) cc_final: 0.8780 (mm-40) REVERT: p 68 ASP cc_start: 0.8625 (p0) cc_final: 0.8410 (p0) REVERT: p 69 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8888 (m) REVERT: p 85 ASN cc_start: 0.7641 (m-40) cc_final: 0.7223 (m110) REVERT: p 87 LYS cc_start: 0.8211 (mmmm) cc_final: 0.8000 (mmtt) REVERT: q 10 TYR cc_start: 0.7161 (m-80) cc_final: 0.6909 (m-80) REVERT: q 63 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8740 (tp) REVERT: r 56 TYR cc_start: 0.8252 (m-80) cc_final: 0.7857 (m-80) REVERT: s 12 ASP cc_start: 0.6826 (m-30) cc_final: 0.6430 (m-30) REVERT: s 17 THR cc_start: 0.9560 (m) cc_final: 0.9127 (p) REVERT: s 51 VAL cc_start: 0.8454 (t) cc_final: 0.8168 (p) REVERT: t 13 THR cc_start: 0.9190 (m) cc_final: 0.8939 (p) REVERT: t 15 ASN cc_start: 0.9124 (m110) cc_final: 0.8832 (m110) REVERT: t 17 ARG cc_start: 0.8242 (ttm110) cc_final: 0.7874 (ttm110) REVERT: t 42 ASN cc_start: 0.8416 (m-40) cc_final: 0.8045 (t0) REVERT: u 50 SER cc_start: 0.8873 (t) cc_final: 0.8261 (p) outliers start: 268 outliers final: 181 residues processed: 1635 average time/residue: 1.2367 time to fit residues: 3513.7259 Evaluate side-chains 1585 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 198 poor density : 1387 time to evaluate : 6.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 2 residue 23 SER Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 15 THR Chi-restraints excluded: chain P residue 16 ASP Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 81 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 97 ASP Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 16 GLU Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain U residue 13 SER Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 59 GLN Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 103 ASN Chi-restraints excluded: chain b residue 106 THR Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 137 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain h residue 39 ILE Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 ASN Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain k residue 115 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 70 ARG Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 52 SER Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 24 ASP Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 26 ARG Chi-restraints excluded: chain p residue 27 SER Chi-restraints excluded: chain p residue 69 THR Chi-restraints excluded: chain q residue 43 SER Chi-restraints excluded: chain q residue 50 ASP Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 45 LEU Chi-restraints excluded: chain r residue 48 ARG Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 24 ILE Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 877 optimal weight: 30.0000 chunk 667 optimal weight: 10.0000 chunk 460 optimal weight: 20.0000 chunk 98 optimal weight: 2.9990 chunk 423 optimal weight: 10.0000 chunk 596 optimal weight: 8.9990 chunk 891 optimal weight: 6.9990 chunk 943 optimal weight: 0.0570 chunk 465 optimal weight: 10.0000 chunk 844 optimal weight: 5.9990 chunk 254 optimal weight: 0.1980 overall best weight: 3.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 4 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN L 38 GLN N 27 ASN N 61 GLN N 77 GLN Q 37 GLN Q 108 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN Z 37 HIS ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 122 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 129 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 16 ASN ** h 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 GLN q 11 GLN ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 155558 Z= 0.200 Angle : 0.594 16.305 233440 Z= 0.305 Chirality : 0.034 0.296 29944 Planarity : 0.004 0.062 11973 Dihedral : 24.202 179.922 79599 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.36 % Favored : 93.55 % Rotamer: Outliers : 5.82 % Allowed : 23.28 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.11), residues: 5176 helix: 0.80 (0.13), residues: 1645 sheet: -0.64 (0.16), residues: 1011 loop : -1.47 (0.12), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP f 43 HIS 0.013 0.001 HIS b 18 PHE 0.026 0.002 PHE F 177 TYR 0.036 0.002 TYR b 54 ARG 0.038 0.001 ARG m 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1735 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1478 time to evaluate : 6.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 6 ARG cc_start: 0.8525 (mmm-85) cc_final: 0.8036 (mmm-85) REVERT: 0 10 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8673 (mttt) REVERT: 0 52 LYS cc_start: 0.8905 (mtpt) cc_final: 0.8688 (ptpt) REVERT: 1 15 ARG cc_start: 0.8281 (mtt90) cc_final: 0.7940 (mtt90) REVERT: 1 32 PHE cc_start: 0.8417 (m-80) cc_final: 0.8171 (m-10) REVERT: 1 33 LYS cc_start: 0.8827 (ttpt) cc_final: 0.8332 (ttmm) REVERT: 1 35 TYR cc_start: 0.8642 (t80) cc_final: 0.8123 (t80) REVERT: 1 41 LYS cc_start: 0.9250 (ptpp) cc_final: 0.9010 (pttm) REVERT: 2 23 SER cc_start: 0.8832 (OUTLIER) cc_final: 0.8599 (m) REVERT: 4 1 MET cc_start: 0.8627 (ttm) cc_final: 0.8414 (ttp) REVERT: 4 13 LYS cc_start: 0.9298 (mtmt) cc_final: 0.8925 (mtpp) REVERT: 4 18 ARG cc_start: 0.8823 (mtp-110) cc_final: 0.8509 (ttm-80) REVERT: 6 1 MET cc_start: 0.5817 (mtt) cc_final: 0.3812 (ptt) REVERT: C 192 ILE cc_start: 0.8963 (OUTLIER) cc_final: 0.8733 (mm) REVERT: D 54 ASP cc_start: 0.7110 (t70) cc_final: 0.6774 (t70) REVERT: D 83 LEU cc_start: 0.8914 (OUTLIER) cc_final: 0.8448 (tt) REVERT: D 95 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7232 (tm-30) REVERT: D 120 GLN cc_start: 0.8383 (mm-40) cc_final: 0.7946 (mm110) REVERT: D 168 GLN cc_start: 0.8625 (tt0) cc_final: 0.8232 (tt0) REVERT: E 39 MET cc_start: 0.8889 (tmm) cc_final: 0.8469 (tmm) REVERT: E 192 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8336 (tp) REVERT: F 83 MET cc_start: 0.8781 (mtp) cc_final: 0.8441 (mtt) REVERT: F 97 TYR cc_start: 0.7823 (t80) cc_final: 0.7483 (t80) REVERT: F 122 PHE cc_start: 0.8388 (m-80) cc_final: 0.7595 (m-80) REVERT: F 170 LEU cc_start: 0.9473 (mt) cc_final: 0.9163 (pp) REVERT: G 24 THR cc_start: 0.9243 (m) cc_final: 0.8971 (p) REVERT: J 32 GLU cc_start: 0.8328 (mt-10) cc_final: 0.7734 (tt0) REVERT: J 76 TYR cc_start: 0.8449 (m-80) cc_final: 0.8240 (m-80) REVERT: J 93 MET cc_start: 0.8231 (OUTLIER) cc_final: 0.7997 (ttp) REVERT: K 116 SER cc_start: 0.9506 (p) cc_final: 0.9304 (p) REVERT: L 15 THR cc_start: 0.9106 (m) cc_final: 0.8859 (t) REVERT: L 70 ASN cc_start: 0.9028 (m-40) cc_final: 0.8762 (m110) REVERT: L 80 ASP cc_start: 0.7395 (m-30) cc_final: 0.7170 (m-30) REVERT: L 89 THR cc_start: 0.9058 (t) cc_final: 0.8760 (p) REVERT: L 106 ASN cc_start: 0.8089 (t0) cc_final: 0.7713 (t0) REVERT: M 44 ASN cc_start: 0.8846 (m-40) cc_final: 0.8321 (t0) REVERT: N 14 LYS cc_start: 0.9055 (tttt) cc_final: 0.8744 (tttp) REVERT: N 28 GLU cc_start: 0.7568 (mp0) cc_final: 0.7075 (mp0) REVERT: N 31 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7175 (mp0) REVERT: N 45 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7926 (mt-10) REVERT: N 69 GLU cc_start: 0.7967 (mp0) cc_final: 0.7598 (mp0) REVERT: N 114 MET cc_start: 0.8640 (mmm) cc_final: 0.8260 (tpp) REVERT: O 1 MET cc_start: 0.7660 (tpt) cc_final: 0.6943 (tpp) REVERT: O 32 ASN cc_start: 0.8777 (t0) cc_final: 0.8104 (t0) REVERT: O 34 PHE cc_start: 0.8672 (t80) cc_final: 0.8462 (t80) REVERT: O 40 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8837 (tp) REVERT: O 59 LEU cc_start: 0.9306 (tp) cc_final: 0.8736 (tt) REVERT: O 70 ASP cc_start: 0.8687 (t70) cc_final: 0.8307 (t0) REVERT: O 101 LEU cc_start: 0.9361 (tp) cc_final: 0.9049 (tt) REVERT: P 78 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8654 (m) REVERT: Q 16 LYS cc_start: 0.8973 (mttt) cc_final: 0.8491 (mtpt) REVERT: Q 27 SER cc_start: 0.8465 (m) cc_final: 0.7946 (p) REVERT: Q 40 MET cc_start: 0.8297 (mtp) cc_final: 0.8064 (mtp) REVERT: Q 76 TYR cc_start: 0.8570 (t80) cc_final: 0.7864 (t80) REVERT: R 15 GLU cc_start: 0.8084 (mm-30) cc_final: 0.7713 (mm-30) REVERT: R 16 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8463 (mm-30) REVERT: R 18 GLN cc_start: 0.8870 (tt0) cc_final: 0.8482 (tt0) REVERT: R 36 GLU cc_start: 0.8056 (pm20) cc_final: 0.7853 (pm20) REVERT: S 37 ASN cc_start: 0.8922 (t0) cc_final: 0.8551 (t0) REVERT: S 48 GLU cc_start: 0.8302 (tm-30) cc_final: 0.7892 (tm-30) REVERT: S 53 SER cc_start: 0.9351 (OUTLIER) cc_final: 0.9005 (p) REVERT: S 85 PHE cc_start: 0.8956 (m-80) cc_final: 0.8737 (m-80) REVERT: T 56 ILE cc_start: 0.9035 (mt) cc_final: 0.8815 (mt) REVERT: T 68 ARG cc_start: 0.7866 (mtm110) cc_final: 0.7505 (ttp-110) REVERT: T 72 MET cc_start: 0.8198 (mtp) cc_final: 0.7970 (mmm) REVERT: U 40 MET cc_start: 0.8765 (tpp) cc_final: 0.8510 (tpp) REVERT: U 92 ARG cc_start: 0.8154 (mtm180) cc_final: 0.7588 (ptp-170) REVERT: W 35 ASP cc_start: 0.7584 (t0) cc_final: 0.6760 (t0) REVERT: W 48 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8452 (pt0) REVERT: W 49 ARG cc_start: 0.8578 (mmp80) cc_final: 0.8361 (mmp80) REVERT: W 51 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8554 (p) REVERT: W 52 LYS cc_start: 0.8918 (mmmm) cc_final: 0.8554 (mmmm) REVERT: W 58 ASN cc_start: 0.9064 (m110) cc_final: 0.8785 (m110) REVERT: W 76 LYS cc_start: 0.8690 (mmmt) cc_final: 0.8401 (mmmt) REVERT: W 78 GLU cc_start: 0.7344 (mt-10) cc_final: 0.7104 (mt-10) REVERT: Y 15 GLU cc_start: 0.8427 (pp20) cc_final: 0.8214 (pm20) REVERT: Y 16 GLN cc_start: 0.9113 (tp40) cc_final: 0.8900 (tp40) REVERT: Y 23 GLU cc_start: 0.8296 (pp20) cc_final: 0.7971 (pp20) REVERT: Y 24 GLU cc_start: 0.8781 (tp30) cc_final: 0.8527 (tp30) REVERT: Y 27 ASN cc_start: 0.8811 (m-40) cc_final: 0.7991 (m110) REVERT: Z 5 GLU cc_start: 0.7723 (mp0) cc_final: 0.7272 (mp0) REVERT: Z 46 MET cc_start: 0.8596 (mmt) cc_final: 0.8172 (mmt) REVERT: Z 57 LYS cc_start: 0.9059 (tppt) cc_final: 0.8826 (tppt) REVERT: b 24 ASN cc_start: 0.8357 (t0) cc_final: 0.7960 (t0) REVERT: b 26 LYS cc_start: 0.9458 (mtpt) cc_final: 0.9086 (ttpp) REVERT: b 89 MET cc_start: 0.7470 (mmm) cc_final: 0.7195 (tpt) REVERT: b 93 ASN cc_start: 0.8799 (p0) cc_final: 0.8487 (p0) REVERT: b 142 GLU cc_start: 0.9144 (tp30) cc_final: 0.8898 (tp30) REVERT: b 164 ILE cc_start: 0.9073 (OUTLIER) cc_final: 0.8829 (tp) REVERT: b 169 GLU cc_start: 0.8858 (mm-30) cc_final: 0.8288 (mp0) REVERT: b 180 ASN cc_start: 0.9057 (p0) cc_final: 0.8777 (p0) REVERT: b 217 MET cc_start: 0.9263 (mmm) cc_final: 0.8849 (mmm) REVERT: c 75 VAL cc_start: 0.8863 (m) cc_final: 0.8602 (m) REVERT: c 122 GLN cc_start: 0.9210 (mm-40) cc_final: 0.8903 (tp40) REVERT: c 138 GLN cc_start: 0.8389 (mt0) cc_final: 0.8092 (mt0) REVERT: c 187 GLU cc_start: 0.7688 (mt-10) cc_final: 0.7165 (pt0) REVERT: d 47 TYR cc_start: 0.8898 (t80) cc_final: 0.8697 (t80) REVERT: d 67 GLN cc_start: 0.8224 (mp10) cc_final: 0.7897 (mp10) REVERT: d 100 LYS cc_start: 0.9145 (mmtt) cc_final: 0.8739 (mmtm) REVERT: e 69 LYS cc_start: 0.8993 (mttt) cc_final: 0.8786 (mtmm) REVERT: f 22 VAL cc_start: 0.9750 (m) cc_final: 0.9448 (p) REVERT: f 24 GLU cc_start: 0.9281 (mm-30) cc_final: 0.8441 (tp30) REVERT: f 25 ARG cc_start: 0.9193 (ptm-80) cc_final: 0.8986 (ptm-80) REVERT: f 28 ASN cc_start: 0.9363 (m-40) cc_final: 0.8319 (m-40) REVERT: f 47 ARG cc_start: 0.8325 (mmm-85) cc_final: 0.7368 (tpp80) REVERT: f 48 LEU cc_start: 0.9467 (mp) cc_final: 0.9262 (mp) REVERT: f 74 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8490 (mp0) REVERT: g 30 MET cc_start: 0.8569 (ppp) cc_final: 0.7957 (ppp) REVERT: g 31 MET cc_start: 0.8871 (ttp) cc_final: 0.8286 (tpp) REVERT: g 46 SER cc_start: 0.8714 (m) cc_final: 0.8458 (p) REVERT: g 49 ILE cc_start: 0.9706 (tp) cc_final: 0.9260 (pt) REVERT: g 66 LEU cc_start: 0.9232 (mt) cc_final: 0.8644 (mt) REVERT: g 86 GLN cc_start: 0.8278 (mm-40) cc_final: 0.8046 (mm-40) REVERT: h 32 LEU cc_start: 0.9070 (tp) cc_final: 0.8856 (tp) REVERT: h 36 ILE cc_start: 0.9622 (mt) cc_final: 0.9390 (mt) REVERT: h 41 LYS cc_start: 0.9236 (OUTLIER) cc_final: 0.8780 (tppt) REVERT: i 6 TYR cc_start: 0.8510 (m-80) cc_final: 0.8068 (m-80) REVERT: j 9 ARG cc_start: 0.8576 (mtp180) cc_final: 0.8355 (mtp180) REVERT: j 24 LYS cc_start: 0.9518 (mmtm) cc_final: 0.9302 (mmtm) REVERT: j 64 GLN cc_start: 0.8771 (mm-40) cc_final: 0.8096 (mm-40) REVERT: k 63 PHE cc_start: 0.8780 (t80) cc_final: 0.8285 (t80) REVERT: k 77 ILE cc_start: 0.9466 (mm) cc_final: 0.9265 (mm) REVERT: l 65 TYR cc_start: 0.7570 (p90) cc_final: 0.7156 (p90) REVERT: l 80 ILE cc_start: 0.8908 (mm) cc_final: 0.8605 (mp) REVERT: l 90 HIS cc_start: 0.8074 (m170) cc_final: 0.7491 (m90) REVERT: m 13 LYS cc_start: 0.8283 (mptt) cc_final: 0.7640 (mmtt) REVERT: m 53 LEU cc_start: 0.9634 (mm) cc_final: 0.9356 (mm) REVERT: n 19 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8281 (mp10) REVERT: n 25 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7738 (mm-30) REVERT: n 36 LYS cc_start: 0.8936 (tptm) cc_final: 0.8605 (tppp) REVERT: o 15 PHE cc_start: 0.8450 (m-80) cc_final: 0.7735 (m-80) REVERT: o 68 THR cc_start: 0.9355 (m) cc_final: 0.8938 (p) REVERT: o 69 TYR cc_start: 0.9305 (t80) cc_final: 0.9051 (t80) REVERT: o 88 ARG cc_start: 0.8515 (mmm160) cc_final: 0.8184 (mmm160) REVERT: p 24 ASP cc_start: 0.8079 (OUTLIER) cc_final: 0.7843 (p0) REVERT: p 26 ARG cc_start: 0.8780 (OUTLIER) cc_final: 0.8366 (mtt-85) REVERT: p 85 ASN cc_start: 0.7702 (m-40) cc_final: 0.7500 (m110) REVERT: q 10 TYR cc_start: 0.7384 (m-80) cc_final: 0.7152 (m-80) REVERT: q 63 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8786 (tp) REVERT: r 56 TYR cc_start: 0.8358 (m-80) cc_final: 0.7958 (m-80) REVERT: r 73 LEU cc_start: 0.9042 (tp) cc_final: 0.8768 (mp) REVERT: s 58 VAL cc_start: 0.8993 (m) cc_final: 0.8734 (m) REVERT: t 15 ASN cc_start: 0.9092 (m110) cc_final: 0.8883 (m110) REVERT: t 42 ASN cc_start: 0.8459 (m-40) cc_final: 0.8029 (t0) REVERT: u 50 SER cc_start: 0.8772 (t) cc_final: 0.8127 (p) outliers start: 257 outliers final: 174 residues processed: 1586 average time/residue: 1.2166 time to fit residues: 3368.5065 Evaluate side-chains 1566 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 1375 time to evaluate : 6.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 2 residue 23 SER Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 93 MET Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 3 LYS Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 59 GLN Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 51 THR Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 199 VAL Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 30 ASN Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain k residue 115 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 99 ARG Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain p residue 24 ASP Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 26 ARG Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 50 ASP Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 71 LEU Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 785 optimal weight: 10.0000 chunk 535 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 702 optimal weight: 10.0000 chunk 389 optimal weight: 10.0000 chunk 805 optimal weight: 20.0000 chunk 652 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 481 optimal weight: 10.0000 chunk 846 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 overall best weight: 9.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 23 ASN 1 4 ASN 1 26 ASN C 153 GLN C 163 GLN D 62 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 59 ASN N 61 GLN N 77 GLN Q 37 GLN Q 72 ASN Q 108 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN U 44 HIS U 58 ASN Z 32 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 64 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 129 ASN ** h 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 81 HIS l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 90 HIS p 77 GLN r 57 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 16 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.4810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.138 155558 Z= 0.504 Angle : 0.821 12.915 233440 Z= 0.415 Chirality : 0.044 0.370 29944 Planarity : 0.006 0.087 11973 Dihedral : 24.497 179.911 79599 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 19.42 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.15 % Favored : 91.75 % Rotamer: Outliers : 8.22 % Allowed : 23.17 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.31 (0.11), residues: 5176 helix: 0.26 (0.12), residues: 1657 sheet: -0.81 (0.16), residues: 974 loop : -1.65 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP M 65 HIS 0.015 0.002 HIS b 18 PHE 0.033 0.003 PHE G 84 TYR 0.026 0.003 TYR Q 32 ARG 0.013 0.001 ARG L 41 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1786 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 363 poor density : 1423 time to evaluate : 6.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 6 ARG cc_start: 0.8493 (mmm-85) cc_final: 0.8066 (mmm-85) REVERT: 0 52 LYS cc_start: 0.9123 (mtpt) cc_final: 0.8854 (ptpt) REVERT: 1 15 ARG cc_start: 0.8658 (mtt90) cc_final: 0.8140 (mtt90) REVERT: 1 32 PHE cc_start: 0.8405 (m-80) cc_final: 0.8054 (m-10) REVERT: 1 33 LYS cc_start: 0.8985 (ttpt) cc_final: 0.8439 (ttmm) REVERT: 1 35 TYR cc_start: 0.8499 (t80) cc_final: 0.8260 (t80) REVERT: 1 41 LYS cc_start: 0.9193 (ptpp) cc_final: 0.8940 (pttm) REVERT: 4 1 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8488 (ttp) REVERT: 4 13 LYS cc_start: 0.9415 (mtmt) cc_final: 0.9060 (mtpp) REVERT: 4 18 ARG cc_start: 0.8790 (mtp-110) cc_final: 0.8399 (ttm-80) REVERT: 6 1 MET cc_start: 0.6391 (mtt) cc_final: 0.4232 (ptt) REVERT: C 192 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8786 (mm) REVERT: C 264 ASN cc_start: 0.9001 (OUTLIER) cc_final: 0.8634 (t160) REVERT: D 95 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7449 (tm-30) REVERT: D 120 GLN cc_start: 0.8618 (mm-40) cc_final: 0.8405 (mm-40) REVERT: D 168 GLN cc_start: 0.8815 (tt0) cc_final: 0.8444 (tt0) REVERT: E 39 MET cc_start: 0.8998 (tmm) cc_final: 0.8481 (tmm) REVERT: F 122 PHE cc_start: 0.8625 (m-80) cc_final: 0.7912 (m-80) REVERT: F 140 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5958 (tm-30) REVERT: F 170 LEU cc_start: 0.9516 (mt) cc_final: 0.9086 (pp) REVERT: F 175 MET cc_start: 0.6773 (tmm) cc_final: 0.6065 (tmm) REVERT: G 24 THR cc_start: 0.9326 (m) cc_final: 0.9058 (p) REVERT: J 32 GLU cc_start: 0.8536 (mt-10) cc_final: 0.7964 (tt0) REVERT: J 48 HIS cc_start: 0.7209 (OUTLIER) cc_final: 0.6248 (m170) REVERT: J 50 ASP cc_start: 0.7923 (t0) cc_final: 0.7452 (t70) REVERT: J 109 MET cc_start: 0.8664 (mmm) cc_final: 0.8233 (mtt) REVERT: K 8 LEU cc_start: 0.9163 (mt) cc_final: 0.8805 (mm) REVERT: K 81 GLU cc_start: 0.8725 (pm20) cc_final: 0.8354 (pm20) REVERT: L 15 THR cc_start: 0.9143 (OUTLIER) cc_final: 0.8890 (t) REVERT: L 30 THR cc_start: 0.9010 (p) cc_final: 0.8575 (t) REVERT: L 70 ASN cc_start: 0.9050 (m-40) cc_final: 0.8761 (m110) REVERT: L 80 ASP cc_start: 0.7755 (m-30) cc_final: 0.7442 (m-30) REVERT: L 89 THR cc_start: 0.8950 (t) cc_final: 0.8578 (p) REVERT: L 106 ASN cc_start: 0.8134 (t0) cc_final: 0.7322 (t0) REVERT: M 44 ASN cc_start: 0.8908 (m-40) cc_final: 0.8470 (t0) REVERT: M 45 ARG cc_start: 0.8883 (mmt90) cc_final: 0.8547 (mmt90) REVERT: M 130 LYS cc_start: 0.9246 (pttt) cc_final: 0.8912 (ptmm) REVERT: N 31 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7842 (mp0) REVERT: N 45 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7982 (mt-10) REVERT: N 47 MET cc_start: 0.8688 (mmt) cc_final: 0.8432 (mmm) REVERT: N 69 GLU cc_start: 0.8137 (mp0) cc_final: 0.7545 (mp0) REVERT: N 114 MET cc_start: 0.8622 (mmm) cc_final: 0.7436 (mmp) REVERT: O 32 ASN cc_start: 0.8873 (t0) cc_final: 0.7583 (t0) REVERT: O 34 PHE cc_start: 0.8983 (t80) cc_final: 0.8747 (t80) REVERT: O 40 ILE cc_start: 0.9154 (OUTLIER) cc_final: 0.8930 (tp) REVERT: O 70 ASP cc_start: 0.8927 (t70) cc_final: 0.8597 (t0) REVERT: O 101 LEU cc_start: 0.9499 (tp) cc_final: 0.9117 (tt) REVERT: P 100 LEU cc_start: 0.9246 (tp) cc_final: 0.8938 (tt) REVERT: Q 16 LYS cc_start: 0.9191 (mttt) cc_final: 0.8636 (mtpt) REVERT: Q 27 SER cc_start: 0.9066 (m) cc_final: 0.8526 (p) REVERT: Q 37 GLN cc_start: 0.8972 (mt0) cc_final: 0.8687 (mt0) REVERT: R 36 GLU cc_start: 0.7889 (pm20) cc_final: 0.7674 (pm20) REVERT: S 37 ASN cc_start: 0.9050 (t0) cc_final: 0.8704 (t0) REVERT: S 48 GLU cc_start: 0.8391 (tm-30) cc_final: 0.8012 (tm-30) REVERT: S 65 ASP cc_start: 0.8285 (t0) cc_final: 0.8032 (t0) REVERT: S 69 LEU cc_start: 0.9195 (mm) cc_final: 0.8783 (mm) REVERT: S 85 PHE cc_start: 0.9003 (m-80) cc_final: 0.8789 (m-80) REVERT: T 21 MET cc_start: 0.8256 (tpp) cc_final: 0.7919 (mmm) REVERT: T 72 MET cc_start: 0.8236 (mtp) cc_final: 0.7527 (mmm) REVERT: U 40 MET cc_start: 0.8691 (tpp) cc_final: 0.8385 (tpp) REVERT: U 92 ARG cc_start: 0.8119 (mtm180) cc_final: 0.7776 (ptp-170) REVERT: W 52 LYS cc_start: 0.8909 (mmmm) cc_final: 0.8610 (mmmm) REVERT: W 76 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8544 (mmmt) REVERT: Y 5 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8840 (mm-30) REVERT: Y 17 LYS cc_start: 0.9137 (mmtm) cc_final: 0.8915 (mmtp) REVERT: Y 23 GLU cc_start: 0.8469 (pp20) cc_final: 0.8078 (pp20) REVERT: Y 24 GLU cc_start: 0.8911 (tp30) cc_final: 0.8576 (tp30) REVERT: Y 27 ASN cc_start: 0.8908 (m-40) cc_final: 0.8098 (m110) REVERT: Z 5 GLU cc_start: 0.7812 (mp0) cc_final: 0.7448 (mp0) REVERT: Z 39 ASP cc_start: 0.8639 (t0) cc_final: 0.8325 (t0) REVERT: b 24 ASN cc_start: 0.8652 (t0) cc_final: 0.8260 (t0) REVERT: b 28 LYS cc_start: 0.9162 (ptpt) cc_final: 0.8960 (mptt) REVERT: b 93 ASN cc_start: 0.8886 (p0) cc_final: 0.8417 (p0) REVERT: b 169 GLU cc_start: 0.8721 (mm-30) cc_final: 0.8406 (mp0) REVERT: b 180 ASN cc_start: 0.9175 (p0) cc_final: 0.8904 (p0) REVERT: b 184 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8801 (tt) REVERT: b 217 MET cc_start: 0.9290 (mmm) cc_final: 0.8962 (mmp) REVERT: c 66 THR cc_start: 0.8215 (OUTLIER) cc_final: 0.7971 (p) REVERT: d 96 ASN cc_start: 0.8618 (t0) cc_final: 0.8095 (m-40) REVERT: d 100 LYS cc_start: 0.9107 (mmtt) cc_final: 0.8742 (mmtt) REVERT: d 190 ASN cc_start: 0.9255 (t0) cc_final: 0.8979 (t0) REVERT: e 69 LYS cc_start: 0.9082 (mttt) cc_final: 0.8634 (mttm) REVERT: f 13 ASN cc_start: 0.9171 (m-40) cc_final: 0.8955 (p0) REVERT: f 22 VAL cc_start: 0.9758 (m) cc_final: 0.9467 (p) REVERT: f 25 ARG cc_start: 0.9121 (ptm-80) cc_final: 0.8786 (ptm-80) REVERT: f 36 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8016 (pm20) REVERT: f 47 ARG cc_start: 0.8133 (mmm-85) cc_final: 0.7907 (mmm-85) REVERT: f 51 GLU cc_start: 0.7188 (tt0) cc_final: 0.6939 (tt0) REVERT: f 77 ARG cc_start: 0.9398 (ttp80) cc_final: 0.9118 (ttp80) REVERT: g 28 ASN cc_start: 0.9164 (t0) cc_final: 0.8637 (t0) REVERT: g 30 MET cc_start: 0.8876 (ppp) cc_final: 0.8098 (ppp) REVERT: g 31 MET cc_start: 0.9027 (ttp) cc_final: 0.8474 (tpp) REVERT: g 44 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.7167 (m-80) REVERT: g 46 SER cc_start: 0.8782 (m) cc_final: 0.8524 (p) REVERT: g 49 ILE cc_start: 0.9701 (tp) cc_final: 0.9309 (pt) REVERT: g 86 GLN cc_start: 0.8687 (mm-40) cc_final: 0.8420 (mm-40) REVERT: h 36 ILE cc_start: 0.9676 (mt) cc_final: 0.9458 (mt) REVERT: i 6 TYR cc_start: 0.8706 (m-80) cc_final: 0.8163 (m-80) REVERT: i 38 HIS cc_start: 0.8673 (m-70) cc_final: 0.8028 (m-70) REVERT: j 9 ARG cc_start: 0.8666 (mtp180) cc_final: 0.7813 (mtt180) REVERT: j 24 LYS cc_start: 0.9541 (mmtm) cc_final: 0.9275 (mmtm) REVERT: j 42 LEU cc_start: 0.9501 (tp) cc_final: 0.9182 (mm) REVERT: j 64 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8211 (mm-40) REVERT: k 63 PHE cc_start: 0.8677 (t80) cc_final: 0.8370 (t80) REVERT: l 42 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8543 (mp10) REVERT: l 65 TYR cc_start: 0.8097 (p90) cc_final: 0.7273 (p90) REVERT: l 90 HIS cc_start: 0.8668 (m-70) cc_final: 0.8058 (m-70) REVERT: l 130 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: m 13 LYS cc_start: 0.8637 (mptt) cc_final: 0.8266 (mtpt) REVERT: m 62 LYS cc_start: 0.8929 (mtmm) cc_final: 0.8630 (mtmm) REVERT: n 19 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: n 25 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8032 (mp0) REVERT: n 36 LYS cc_start: 0.8917 (tptm) cc_final: 0.8492 (tppp) REVERT: n 46 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7802 (tm-30) REVERT: o 14 GLU cc_start: 0.8327 (tm-30) cc_final: 0.8114 (tm-30) REVERT: o 15 PHE cc_start: 0.8739 (m-80) cc_final: 0.8094 (m-10) REVERT: o 68 THR cc_start: 0.9423 (m) cc_final: 0.9022 (p) REVERT: o 69 TYR cc_start: 0.9410 (t80) cc_final: 0.9142 (t80) REVERT: p 14 LYS cc_start: 0.9244 (mmmm) cc_final: 0.8835 (mmmt) REVERT: p 48 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: p 69 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.8996 (m) REVERT: q 13 ARG cc_start: 0.8572 (ttp80) cc_final: 0.8341 (ttp80) REVERT: r 47 ARG cc_start: 0.9319 (ttm-80) cc_final: 0.9097 (ttm-80) REVERT: r 56 TYR cc_start: 0.8498 (m-80) cc_final: 0.8152 (m-80) REVERT: r 73 LEU cc_start: 0.9301 (tp) cc_final: 0.9002 (mt) REVERT: s 73 GLU cc_start: 0.8817 (mm-30) cc_final: 0.8220 (tp30) REVERT: t 15 ASN cc_start: 0.9154 (m110) cc_final: 0.8901 (m110) REVERT: t 42 ASN cc_start: 0.8344 (m-40) cc_final: 0.8091 (t0) REVERT: u 50 SER cc_start: 0.9036 (t) cc_final: 0.8477 (p) outliers start: 363 outliers final: 279 residues processed: 1597 average time/residue: 1.2265 time to fit residues: 3443.9183 Evaluate side-chains 1618 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 295 poor density : 1323 time to evaluate : 5.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 5 ILE Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 43 THR Chi-restraints excluded: chain 2 residue 23 SER Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 2 residue 41 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 190 GLU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 195 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 29 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 HIS Chi-restraints excluded: chain J residue 51 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 27 ASN Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 81 GLN Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 23 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 32 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 34 THR Chi-restraints excluded: chain R residue 101 ASN Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 47 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 21 VAL Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 32 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 59 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 135 VAL Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 8 VAL Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 166 TYR Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 152 LYS Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 30 LEU Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 61 GLN Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 24 SER Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 ASN Chi-restraints excluded: chain h residue 99 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 75 GLN Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 35 THR Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 95 ARG Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain k residue 131 VAL Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 35 GLU Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 48 GLU Chi-restraints excluded: chain p residue 69 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 50 ASP Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 57 GLN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 39 THR Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 317 optimal weight: 20.0000 chunk 849 optimal weight: 3.9990 chunk 186 optimal weight: 20.0000 chunk 553 optimal weight: 10.0000 chunk 232 optimal weight: 6.9990 chunk 944 optimal weight: 10.0000 chunk 783 optimal weight: 5.9990 chunk 437 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 312 optimal weight: 4.9990 chunk 495 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 4 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 75 ASN N 77 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 58 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 28 ASN f 64 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 ASN l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 11 GLN ** p 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 70 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 155558 Z= 0.311 Angle : 0.677 12.824 233440 Z= 0.348 Chirality : 0.038 0.323 29944 Planarity : 0.005 0.078 11973 Dihedral : 24.382 179.514 79599 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 7.23 % Allowed : 25.80 % Favored : 66.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.11), residues: 5176 helix: 0.39 (0.13), residues: 1651 sheet: -0.78 (0.16), residues: 986 loop : -1.56 (0.12), residues: 2539 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP g 103 HIS 0.020 0.002 HIS b 18 PHE 0.034 0.002 PHE L 50 TYR 0.027 0.002 TYR g 18 ARG 0.011 0.001 ARG Z 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1762 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 319 poor density : 1443 time to evaluate : 6.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 52 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8862 (ptpt) REVERT: 1 15 ARG cc_start: 0.8674 (mtt90) cc_final: 0.8227 (mtt90) REVERT: 1 32 PHE cc_start: 0.8332 (m-80) cc_final: 0.8111 (m-10) REVERT: 1 35 TYR cc_start: 0.8627 (t80) cc_final: 0.8184 (t80) REVERT: 1 41 LYS cc_start: 0.9201 (ptpp) cc_final: 0.8934 (pttm) REVERT: 2 23 SER cc_start: 0.8852 (OUTLIER) cc_final: 0.8648 (m) REVERT: 4 1 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8542 (ttp) REVERT: 4 13 LYS cc_start: 0.9358 (mtmt) cc_final: 0.9104 (mtpp) REVERT: 4 18 ARG cc_start: 0.8943 (mtp-110) cc_final: 0.8537 (ttm-80) REVERT: 6 1 MET cc_start: 0.6300 (mtt) cc_final: 0.4599 (ttm) REVERT: C 192 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8847 (mm) REVERT: C 264 ASN cc_start: 0.8970 (OUTLIER) cc_final: 0.8630 (t160) REVERT: D 83 LEU cc_start: 0.9059 (OUTLIER) cc_final: 0.8660 (tt) REVERT: D 95 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7437 (tm-30) REVERT: D 120 GLN cc_start: 0.8387 (mm-40) cc_final: 0.8169 (mm-40) REVERT: D 168 GLN cc_start: 0.8776 (tt0) cc_final: 0.8395 (tt0) REVERT: E 39 MET cc_start: 0.8968 (tmm) cc_final: 0.8380 (tmm) REVERT: E 129 LEU cc_start: 0.9459 (tp) cc_final: 0.9217 (tp) REVERT: E 192 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8510 (tp) REVERT: F 122 PHE cc_start: 0.8558 (m-80) cc_final: 0.7975 (m-80) REVERT: F 170 LEU cc_start: 0.9502 (mt) cc_final: 0.9146 (pp) REVERT: G 24 THR cc_start: 0.9323 (m) cc_final: 0.9030 (p) REVERT: J 32 GLU cc_start: 0.8465 (mt-10) cc_final: 0.7868 (tt0) REVERT: J 48 HIS cc_start: 0.7050 (OUTLIER) cc_final: 0.6093 (m170) REVERT: J 58 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8927 (tp) REVERT: K 81 GLU cc_start: 0.8664 (pm20) cc_final: 0.8396 (pm20) REVERT: K 113 LYS cc_start: 0.8900 (tppt) cc_final: 0.8609 (tppt) REVERT: L 15 THR cc_start: 0.9126 (OUTLIER) cc_final: 0.8867 (t) REVERT: L 30 THR cc_start: 0.9011 (p) cc_final: 0.8638 (t) REVERT: L 70 ASN cc_start: 0.9043 (m-40) cc_final: 0.8744 (m110) REVERT: L 80 ASP cc_start: 0.7854 (m-30) cc_final: 0.7635 (m-30) REVERT: L 89 THR cc_start: 0.9065 (t) cc_final: 0.8810 (p) REVERT: M 44 ASN cc_start: 0.8880 (m-40) cc_final: 0.8408 (t0) REVERT: M 45 ARG cc_start: 0.8843 (mmt90) cc_final: 0.8523 (mmt90) REVERT: M 46 GLN cc_start: 0.8678 (mt0) cc_final: 0.8269 (mt0) REVERT: M 83 MET cc_start: 0.7826 (OUTLIER) cc_final: 0.7511 (ttp) REVERT: M 130 LYS cc_start: 0.9413 (pttt) cc_final: 0.9128 (ptmm) REVERT: N 14 LYS cc_start: 0.9103 (tttt) cc_final: 0.8852 (ttpp) REVERT: N 31 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7795 (mp0) REVERT: N 45 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8065 (mt-10) REVERT: N 47 MET cc_start: 0.8668 (mmt) cc_final: 0.8442 (mmm) REVERT: N 69 GLU cc_start: 0.8106 (mp0) cc_final: 0.7551 (mp0) REVERT: N 87 ILE cc_start: 0.9406 (mm) cc_final: 0.9180 (mm) REVERT: N 114 MET cc_start: 0.8745 (mmm) cc_final: 0.8493 (mmt) REVERT: O 32 ASN cc_start: 0.8604 (t0) cc_final: 0.7779 (t0) REVERT: O 34 PHE cc_start: 0.8847 (t80) cc_final: 0.8588 (t80) REVERT: O 40 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8932 (tp) REVERT: O 70 ASP cc_start: 0.8840 (t70) cc_final: 0.8507 (t0) REVERT: O 101 LEU cc_start: 0.9502 (tp) cc_final: 0.9113 (tt) REVERT: P 78 THR cc_start: 0.8926 (OUTLIER) cc_final: 0.8708 (m) REVERT: Q 16 LYS cc_start: 0.9073 (mttt) cc_final: 0.8529 (mtpt) REVERT: Q 27 SER cc_start: 0.9013 (m) cc_final: 0.8432 (p) REVERT: Q 92 ARG cc_start: 0.8265 (OUTLIER) cc_final: 0.7454 (tpm170) REVERT: R 36 GLU cc_start: 0.8076 (pm20) cc_final: 0.7858 (pm20) REVERT: S 37 ASN cc_start: 0.8977 (t0) cc_final: 0.8586 (t0) REVERT: S 48 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7895 (tm-30) REVERT: S 53 SER cc_start: 0.9451 (OUTLIER) cc_final: 0.8957 (p) REVERT: S 65 ASP cc_start: 0.8273 (t0) cc_final: 0.7912 (t0) REVERT: S 69 LEU cc_start: 0.9177 (mm) cc_final: 0.8772 (mm) REVERT: T 21 MET cc_start: 0.8273 (tpp) cc_final: 0.7974 (mmm) REVERT: T 72 MET cc_start: 0.8111 (mtp) cc_final: 0.7850 (mmm) REVERT: U 92 ARG cc_start: 0.8096 (mtm180) cc_final: 0.7741 (ptp-170) REVERT: W 48 GLN cc_start: 0.8661 (OUTLIER) cc_final: 0.8111 (pt0) REVERT: W 52 LYS cc_start: 0.8912 (mmmm) cc_final: 0.8455 (mmmm) REVERT: W 57 GLU cc_start: 0.7850 (tp30) cc_final: 0.7552 (tm-30) REVERT: W 76 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8579 (mmmt) REVERT: Y 17 LYS cc_start: 0.9149 (mmtm) cc_final: 0.8929 (mmtm) REVERT: Y 19 LYS cc_start: 0.9102 (OUTLIER) cc_final: 0.8517 (ptpp) REVERT: Y 24 GLU cc_start: 0.8867 (tp30) cc_final: 0.8490 (tp30) REVERT: Y 27 ASN cc_start: 0.8941 (m-40) cc_final: 0.8474 (m110) REVERT: Z 5 GLU cc_start: 0.7802 (mp0) cc_final: 0.7444 (mp0) REVERT: Z 38 GLU cc_start: 0.8180 (pm20) cc_final: 0.7732 (tm-30) REVERT: b 24 ASN cc_start: 0.8656 (t0) cc_final: 0.8212 (t0) REVERT: b 28 LYS cc_start: 0.9151 (ptpt) cc_final: 0.8893 (mptt) REVERT: b 93 ASN cc_start: 0.8932 (p0) cc_final: 0.8529 (p0) REVERT: b 104 PHE cc_start: 0.8648 (t80) cc_final: 0.8436 (t80) REVERT: b 164 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.9022 (tp) REVERT: b 169 GLU cc_start: 0.8673 (mm-30) cc_final: 0.8364 (mp0) REVERT: b 184 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8795 (tt) REVERT: b 217 MET cc_start: 0.9230 (mmm) cc_final: 0.8840 (mmm) REVERT: c 36 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8747 (mt) REVERT: c 66 THR cc_start: 0.8304 (OUTLIER) cc_final: 0.8027 (p) REVERT: c 135 GLN cc_start: 0.8618 (tm-30) cc_final: 0.8384 (tm-30) REVERT: c 136 GLN cc_start: 0.8578 (tp40) cc_final: 0.8233 (tp40) REVERT: d 47 TYR cc_start: 0.9205 (t80) cc_final: 0.8848 (t80) REVERT: d 61 TYR cc_start: 0.8495 (m-80) cc_final: 0.8023 (m-80) REVERT: d 96 ASN cc_start: 0.8187 (t0) cc_final: 0.7850 (t0) REVERT: d 99 TYR cc_start: 0.8602 (t80) cc_final: 0.8245 (t80) REVERT: d 100 LYS cc_start: 0.9125 (mmtt) cc_final: 0.8912 (mmtt) REVERT: d 109 GLN cc_start: 0.9233 (OUTLIER) cc_final: 0.8996 (mp10) REVERT: d 190 ASN cc_start: 0.9233 (t0) cc_final: 0.9024 (t0) REVERT: e 42 LYS cc_start: 0.9323 (mmmt) cc_final: 0.9094 (tppt) REVERT: f 77 ARG cc_start: 0.9282 (ttp80) cc_final: 0.8633 (ttp80) REVERT: f 78 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.8807 (mt) REVERT: g 30 MET cc_start: 0.8894 (ppp) cc_final: 0.8023 (ppp) REVERT: g 31 MET cc_start: 0.9010 (ttp) cc_final: 0.8394 (tpp) REVERT: g 40 GLN cc_start: 0.9024 (tp-100) cc_final: 0.7998 (tp-100) REVERT: g 44 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.7491 (m-80) REVERT: g 46 SER cc_start: 0.8734 (m) cc_final: 0.8495 (p) REVERT: g 86 GLN cc_start: 0.8666 (mm-40) cc_final: 0.8365 (mm-40) REVERT: h 36 ILE cc_start: 0.9687 (mt) cc_final: 0.9412 (mt) REVERT: h 51 PHE cc_start: 0.7433 (t80) cc_final: 0.7007 (t80) REVERT: i 6 TYR cc_start: 0.8569 (m-80) cc_final: 0.8003 (m-80) REVERT: i 38 HIS cc_start: 0.8636 (m-70) cc_final: 0.7981 (m-70) REVERT: j 9 ARG cc_start: 0.8568 (mtp180) cc_final: 0.7689 (mtt180) REVERT: j 11 LYS cc_start: 0.8856 (OUTLIER) cc_final: 0.8386 (mttt) REVERT: j 24 LYS cc_start: 0.9513 (mmtm) cc_final: 0.9199 (mmtm) REVERT: j 42 LEU cc_start: 0.9527 (tp) cc_final: 0.9208 (mm) REVERT: k 63 PHE cc_start: 0.8632 (t80) cc_final: 0.7812 (t80) REVERT: k 66 GLN cc_start: 0.9147 (tm-30) cc_final: 0.8793 (pp30) REVERT: l 42 GLN cc_start: 0.8961 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: l 65 TYR cc_start: 0.7972 (p90) cc_final: 0.7408 (p90) REVERT: l 90 HIS cc_start: 0.8621 (m-70) cc_final: 0.8025 (m-70) REVERT: m 13 LYS cc_start: 0.8494 (mptt) cc_final: 0.8173 (mttt) REVERT: n 15 LYS cc_start: 0.9168 (mmmt) cc_final: 0.8561 (mttt) REVERT: n 19 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8278 (mp10) REVERT: n 36 LYS cc_start: 0.8900 (tptm) cc_final: 0.8452 (tppp) REVERT: n 46 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7651 (tm-30) REVERT: o 15 PHE cc_start: 0.8712 (m-80) cc_final: 0.7739 (m-80) REVERT: o 68 THR cc_start: 0.9392 (m) cc_final: 0.9068 (p) REVERT: o 69 TYR cc_start: 0.9433 (t80) cc_final: 0.9054 (t80) REVERT: p 19 ARG cc_start: 0.8762 (mtp180) cc_final: 0.8442 (mtt180) REVERT: p 48 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: p 52 ASP cc_start: 0.8621 (t0) cc_final: 0.8324 (t0) REVERT: p 69 THR cc_start: 0.9392 (OUTLIER) cc_final: 0.8809 (m) REVERT: p 87 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7896 (mmmt) REVERT: q 57 ILE cc_start: 0.8665 (mp) cc_final: 0.8226 (mm) REVERT: r 56 TYR cc_start: 0.8134 (m-80) cc_final: 0.7605 (m-80) REVERT: s 73 GLU cc_start: 0.8550 (mm-30) cc_final: 0.7796 (tp30) REVERT: t 15 ASN cc_start: 0.9137 (m110) cc_final: 0.8847 (m110) REVERT: t 42 ASN cc_start: 0.8362 (m-40) cc_final: 0.8129 (t0) REVERT: u 50 SER cc_start: 0.8861 (t) cc_final: 0.8222 (p) outliers start: 319 outliers final: 245 residues processed: 1591 average time/residue: 1.2921 time to fit residues: 3628.5533 Evaluate side-chains 1626 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1352 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 2 residue 23 SER Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 20 ASP Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 123 ILE Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 HIS Chi-restraints excluded: chain J residue 58 ILE Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 MET Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain P residue 81 ILE Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 125 THR Chi-restraints excluded: chain b residue 157 LEU Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 190 THR Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 109 GLN Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 152 LYS Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 73 LEU Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 ASN Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 15 HIS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 30 ASN Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 81 LEU Chi-restraints excluded: chain k residue 82 LYS Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 48 GLU Chi-restraints excluded: chain p residue 69 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 50 ASP Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 41 PHE Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Chi-restraints excluded: chain u residue 40 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 910 optimal weight: 30.0000 chunk 106 optimal weight: 5.9990 chunk 538 optimal weight: 10.0000 chunk 689 optimal weight: 10.0000 chunk 534 optimal weight: 10.0000 chunk 794 optimal weight: 3.9990 chunk 527 optimal weight: 10.0000 chunk 940 optimal weight: 5.9990 chunk 588 optimal weight: 10.0000 chunk 573 optimal weight: 10.0000 chunk 434 optimal weight: 20.0000 overall best weight: 7.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 4 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 ASN E 8 ASN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 77 GLN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 97 ASN Z 32 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 115 ASN d 116 HIS ** e 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 32 ASN ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 GLN ** p 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 57 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 47 HIS ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.5136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 155558 Z= 0.379 Angle : 0.724 13.739 233440 Z= 0.370 Chirality : 0.040 0.334 29944 Planarity : 0.005 0.077 11973 Dihedral : 24.412 179.504 79599 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.10 % Favored : 91.79 % Rotamer: Outliers : 8.18 % Allowed : 25.78 % Favored : 66.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: -1.28 (0.11), residues: 5176 helix: 0.26 (0.13), residues: 1639 sheet: -0.82 (0.16), residues: 986 loop : -1.60 (0.12), residues: 2551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP M 65 HIS 0.016 0.002 HIS b 18 PHE 0.032 0.003 PHE L 50 TYR 0.027 0.002 TYR W 46 ARG 0.013 0.001 ARG k 130 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1746 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 361 poor density : 1385 time to evaluate : 6.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 6 ARG cc_start: 0.8330 (mmm-85) cc_final: 0.7820 (mtp85) REVERT: 0 52 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8852 (ptpt) REVERT: 1 15 ARG cc_start: 0.8669 (mtt90) cc_final: 0.8219 (mtt90) REVERT: 1 32 PHE cc_start: 0.8341 (m-80) cc_final: 0.8101 (m-10) REVERT: 1 33 LYS cc_start: 0.8966 (ttpt) cc_final: 0.8714 (tptp) REVERT: 1 35 TYR cc_start: 0.8692 (t80) cc_final: 0.8431 (t80) REVERT: 1 41 LYS cc_start: 0.9217 (ptpp) cc_final: 0.8969 (pttm) REVERT: 4 1 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8533 (ttp) REVERT: 4 13 LYS cc_start: 0.9484 (mtmt) cc_final: 0.9135 (mtpp) REVERT: 4 18 ARG cc_start: 0.8771 (mtp-110) cc_final: 0.8302 (ttm-80) REVERT: 4 19 ARG cc_start: 0.7890 (ttm170) cc_final: 0.6604 (ttm-80) REVERT: 6 1 MET cc_start: 0.6291 (mtt) cc_final: 0.4393 (ptt) REVERT: C 192 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8851 (mm) REVERT: C 198 GLU cc_start: 0.7885 (mp0) cc_final: 0.7619 (mp0) REVERT: C 201 GLU cc_start: 0.8246 (tp30) cc_final: 0.8017 (tp30) REVERT: C 264 ASN cc_start: 0.8971 (OUTLIER) cc_final: 0.8632 (t160) REVERT: D 95 GLN cc_start: 0.7916 (OUTLIER) cc_final: 0.7465 (tm-30) REVERT: D 168 GLN cc_start: 0.8779 (tt0) cc_final: 0.8406 (tt0) REVERT: E 39 MET cc_start: 0.8993 (tmm) cc_final: 0.8432 (tmm) REVERT: E 129 LEU cc_start: 0.9490 (tp) cc_final: 0.9229 (tp) REVERT: F 97 TYR cc_start: 0.7900 (t80) cc_final: 0.7468 (t80) REVERT: F 122 PHE cc_start: 0.8581 (m-80) cc_final: 0.8099 (m-80) REVERT: F 170 LEU cc_start: 0.9555 (mt) cc_final: 0.9200 (pp) REVERT: F 175 MET cc_start: 0.6863 (tmm) cc_final: 0.6454 (tmm) REVERT: G 24 THR cc_start: 0.9331 (m) cc_final: 0.9064 (p) REVERT: J 32 GLU cc_start: 0.8472 (mt-10) cc_final: 0.7927 (tt0) REVERT: J 48 HIS cc_start: 0.7244 (OUTLIER) cc_final: 0.6205 (m170) REVERT: K 81 GLU cc_start: 0.8729 (pm20) cc_final: 0.8369 (pm20) REVERT: K 112 MET cc_start: 0.8325 (pmm) cc_final: 0.7849 (mmp) REVERT: L 15 THR cc_start: 0.9152 (OUTLIER) cc_final: 0.8875 (t) REVERT: L 30 THR cc_start: 0.9071 (p) cc_final: 0.8672 (t) REVERT: L 70 ASN cc_start: 0.9068 (m-40) cc_final: 0.8775 (m110) REVERT: L 89 THR cc_start: 0.8962 (t) cc_final: 0.8635 (p) REVERT: M 43 THR cc_start: 0.9036 (p) cc_final: 0.7903 (p) REVERT: M 44 ASN cc_start: 0.8897 (m-40) cc_final: 0.7686 (t0) REVERT: M 46 GLN cc_start: 0.8697 (mt0) cc_final: 0.8107 (mt0) REVERT: N 31 GLU cc_start: 0.8145 (mt-10) cc_final: 0.7734 (mp0) REVERT: N 45 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8101 (mt-10) REVERT: N 47 MET cc_start: 0.8700 (mmt) cc_final: 0.8458 (mmm) REVERT: N 69 GLU cc_start: 0.8181 (mp0) cc_final: 0.7487 (mp0) REVERT: N 114 MET cc_start: 0.8734 (mmm) cc_final: 0.8424 (tpp) REVERT: O 32 ASN cc_start: 0.8547 (t0) cc_final: 0.7842 (t0) REVERT: O 34 PHE cc_start: 0.8991 (t80) cc_final: 0.8732 (t80) REVERT: O 40 ILE cc_start: 0.9160 (OUTLIER) cc_final: 0.8936 (tp) REVERT: O 70 ASP cc_start: 0.8735 (t70) cc_final: 0.8382 (t0) REVERT: O 101 LEU cc_start: 0.9550 (tp) cc_final: 0.9102 (tt) REVERT: O 106 VAL cc_start: 0.9546 (OUTLIER) cc_final: 0.9310 (p) REVERT: P 78 THR cc_start: 0.8919 (OUTLIER) cc_final: 0.8644 (m) REVERT: P 112 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8007 (mm-30) REVERT: Q 16 LYS cc_start: 0.9115 (mttt) cc_final: 0.8558 (mtpt) REVERT: Q 27 SER cc_start: 0.9100 (m) cc_final: 0.8592 (p) REVERT: Q 37 GLN cc_start: 0.8941 (mt0) cc_final: 0.8625 (mt0) REVERT: Q 92 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7221 (tpm170) REVERT: R 36 GLU cc_start: 0.8245 (pm20) cc_final: 0.8040 (pm20) REVERT: S 37 ASN cc_start: 0.9025 (t0) cc_final: 0.8648 (t0) REVERT: S 48 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7952 (tm-30) REVERT: S 65 ASP cc_start: 0.8330 (t0) cc_final: 0.7945 (t0) REVERT: S 69 LEU cc_start: 0.9232 (mm) cc_final: 0.8811 (mm) REVERT: T 68 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7434 (mtm110) REVERT: T 72 MET cc_start: 0.8139 (mtp) cc_final: 0.7871 (mmm) REVERT: U 92 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7739 (ptp-170) REVERT: W 48 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8080 (pt0) REVERT: W 52 LYS cc_start: 0.8930 (mmmm) cc_final: 0.8484 (mmmm) REVERT: W 57 GLU cc_start: 0.7947 (tp30) cc_final: 0.7381 (tp30) REVERT: W 58 ASN cc_start: 0.8951 (m-40) cc_final: 0.8040 (m-40) REVERT: W 76 LYS cc_start: 0.8817 (mmmt) cc_final: 0.8511 (mmmt) REVERT: Y 1 MET cc_start: 0.8428 (tpp) cc_final: 0.8214 (tpp) REVERT: Y 19 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8750 (ptpp) REVERT: Y 24 GLU cc_start: 0.8902 (tp30) cc_final: 0.8511 (tp30) REVERT: Y 27 ASN cc_start: 0.9012 (m-40) cc_final: 0.8504 (m110) REVERT: Z 5 GLU cc_start: 0.7797 (mp0) cc_final: 0.7480 (mp0) REVERT: Z 46 MET cc_start: 0.8503 (mmm) cc_final: 0.8068 (mmm) REVERT: b 24 ASN cc_start: 0.8712 (t0) cc_final: 0.8272 (t0) REVERT: b 28 LYS cc_start: 0.9156 (ptpt) cc_final: 0.8898 (mptt) REVERT: b 93 ASN cc_start: 0.8938 (p0) cc_final: 0.8406 (p0) REVERT: b 104 PHE cc_start: 0.8534 (t80) cc_final: 0.8094 (t80) REVERT: b 184 ILE cc_start: 0.9059 (OUTLIER) cc_final: 0.8776 (tt) REVERT: b 217 MET cc_start: 0.9208 (mmm) cc_final: 0.8874 (mmp) REVERT: c 66 THR cc_start: 0.8274 (OUTLIER) cc_final: 0.8031 (p) REVERT: c 74 MET cc_start: 0.8457 (ppp) cc_final: 0.8255 (ppp) REVERT: c 135 GLN cc_start: 0.8589 (tm-30) cc_final: 0.8207 (tm-30) REVERT: c 136 GLN cc_start: 0.8736 (tp40) cc_final: 0.8357 (tp40) REVERT: d 47 TYR cc_start: 0.9326 (t80) cc_final: 0.9017 (t80) REVERT: d 190 ASN cc_start: 0.9265 (t0) cc_final: 0.9032 (t0) REVERT: e 69 LYS cc_start: 0.9041 (mttt) cc_final: 0.8633 (mttm) REVERT: e 142 GLN cc_start: 0.8700 (tm-30) cc_final: 0.8421 (tm-30) REVERT: f 77 ARG cc_start: 0.9230 (ttp80) cc_final: 0.8915 (ttp80) REVERT: g 30 MET cc_start: 0.9009 (ppp) cc_final: 0.8174 (ppp) REVERT: g 31 MET cc_start: 0.9064 (ttp) cc_final: 0.8461 (tpp) REVERT: g 40 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8232 (tp-100) REVERT: g 44 TYR cc_start: 0.8596 (OUTLIER) cc_final: 0.7445 (m-80) REVERT: g 46 SER cc_start: 0.8809 (m) cc_final: 0.8508 (p) REVERT: g 86 GLN cc_start: 0.8805 (mm-40) cc_final: 0.8490 (mm-40) REVERT: g 107 TYR cc_start: 0.9150 (m-80) cc_final: 0.8915 (m-80) REVERT: h 36 ILE cc_start: 0.9691 (mt) cc_final: 0.9481 (mt) REVERT: h 51 PHE cc_start: 0.7547 (t80) cc_final: 0.7284 (t80) REVERT: h 56 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8200 (tppp) REVERT: i 6 TYR cc_start: 0.8650 (m-80) cc_final: 0.7983 (m-80) REVERT: i 38 HIS cc_start: 0.8666 (m-70) cc_final: 0.8007 (m170) REVERT: i 68 HIS cc_start: 0.8113 (m-70) cc_final: 0.7908 (m-70) REVERT: i 94 TYR cc_start: 0.8055 (OUTLIER) cc_final: 0.6998 (p90) REVERT: j 9 ARG cc_start: 0.8625 (mtp180) cc_final: 0.7712 (mtt180) REVERT: j 11 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8443 (mttt) REVERT: j 24 LYS cc_start: 0.9527 (mmtm) cc_final: 0.9206 (mmtm) REVERT: k 63 PHE cc_start: 0.8643 (t80) cc_final: 0.8437 (t80) REVERT: k 77 ILE cc_start: 0.9412 (OUTLIER) cc_final: 0.9110 (pt) REVERT: l 42 GLN cc_start: 0.9093 (OUTLIER) cc_final: 0.8667 (mp10) REVERT: l 65 TYR cc_start: 0.7935 (p90) cc_final: 0.7258 (p90) REVERT: l 90 HIS cc_start: 0.8549 (m-70) cc_final: 0.7753 (m90) REVERT: m 13 LYS cc_start: 0.8554 (mptt) cc_final: 0.8129 (mtmt) REVERT: m 34 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8155 (mp) REVERT: n 15 LYS cc_start: 0.9225 (mmmt) cc_final: 0.8608 (mttt) REVERT: n 19 GLN cc_start: 0.8917 (OUTLIER) cc_final: 0.8237 (mp10) REVERT: n 25 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7878 (mp0) REVERT: n 36 LYS cc_start: 0.8907 (tptm) cc_final: 0.8489 (tppp) REVERT: o 10 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8646 (mt0) REVERT: o 15 PHE cc_start: 0.8418 (m-80) cc_final: 0.8062 (m-10) REVERT: o 68 THR cc_start: 0.9403 (m) cc_final: 0.9012 (p) REVERT: o 69 TYR cc_start: 0.9472 (t80) cc_final: 0.9049 (t80) REVERT: p 14 LYS cc_start: 0.9294 (mmmm) cc_final: 0.8913 (mmmt) REVERT: p 19 ARG cc_start: 0.8784 (mtp180) cc_final: 0.8529 (mtt180) REVERT: p 69 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.8860 (m) REVERT: p 87 LYS cc_start: 0.8288 (mmmm) cc_final: 0.8086 (mmmt) REVERT: q 13 ARG cc_start: 0.8430 (ttp80) cc_final: 0.8220 (ttp80) REVERT: r 56 TYR cc_start: 0.8342 (m-80) cc_final: 0.7956 (m-80) REVERT: r 73 LEU cc_start: 0.9149 (tp) cc_final: 0.8839 (mp) REVERT: s 73 GLU cc_start: 0.8363 (mm-30) cc_final: 0.7922 (tp30) REVERT: t 15 ASN cc_start: 0.9152 (m110) cc_final: 0.8880 (m110) REVERT: u 50 SER cc_start: 0.8884 (t) cc_final: 0.8253 (p) outliers start: 361 outliers final: 283 residues processed: 1553 average time/residue: 1.1912 time to fit residues: 3229.5460 Evaluate side-chains 1658 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1351 time to evaluate : 6.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 0 residue 24 VAL Chi-restraints excluded: chain 0 residue 35 GLU Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 28 ASP Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 47 GLU Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 49 VAL Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 264 ASN Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 172 GLN Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 184 LEU Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 HIS Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 6 THR Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain L residue 69 ILE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 55 THR Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 90 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 8 ILE Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain Q residue 104 THR Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 10 VAL Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain T residue 81 VAL Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 63 ILE Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 50 ILE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 22 THR Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 32 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 27 MET Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 59 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 74 LYS Chi-restraints excluded: chain b residue 141 LEU Chi-restraints excluded: chain b residue 159 ASP Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 183 ILE Chi-restraints excluded: chain b residue 184 ILE Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain b residue 213 LEU Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 166 TYR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 185 THR Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 137 GLN Chi-restraints excluded: chain d residue 152 LYS Chi-restraints excluded: chain d residue 158 ASN Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 134 ILE Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 18 SER Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 54 ASP Chi-restraints excluded: chain f residue 55 PHE Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 78 LEU Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 24 SER Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 89 VAL Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 ASN Chi-restraints excluded: chain h residue 94 VAL Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 32 ASN Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 91 ASP Chi-restraints excluded: chain i residue 94 TYR Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain i residue 103 LEU Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 47 SER Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 30 ASN Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 77 ILE Chi-restraints excluded: chain k residue 82 LYS Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 71 THR Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 34 LEU Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 82 GLU Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 10 GLN Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 29 ILE Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 69 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 50 ASP Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 22 LEU Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 26 SER Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 67 VAL Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Chi-restraints excluded: chain u residue 40 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 581 optimal weight: 0.0170 chunk 375 optimal weight: 10.0000 chunk 561 optimal weight: 20.0000 chunk 283 optimal weight: 8.9990 chunk 184 optimal weight: 6.9990 chunk 182 optimal weight: 0.5980 chunk 598 optimal weight: 10.0000 chunk 640 optimal weight: 20.0000 chunk 465 optimal weight: 8.9990 chunk 87 optimal weight: 7.9990 chunk 739 optimal weight: 20.0000 overall best weight: 4.9224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 4 ASN ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 77 GLN O 15 HIS ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 45 HIS ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 ASN t 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.5168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 155558 Z= 0.272 Angle : 0.659 14.419 233440 Z= 0.339 Chirality : 0.037 0.328 29944 Planarity : 0.005 0.078 11973 Dihedral : 24.357 179.980 79599 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.46 % Favored : 92.43 % Rotamer: Outliers : 6.93 % Allowed : 27.34 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.11), residues: 5176 helix: 0.39 (0.13), residues: 1628 sheet: -0.74 (0.16), residues: 956 loop : -1.53 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP M 65 HIS 0.018 0.001 HIS b 18 PHE 0.033 0.002 PHE b 56 TYR 0.024 0.002 TYR g 18 ARG 0.013 0.001 ARG k 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1737 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 1431 time to evaluate : 6.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 6 ARG cc_start: 0.8283 (mmm-85) cc_final: 0.7806 (mtp85) REVERT: 0 52 LYS cc_start: 0.9117 (mtpt) cc_final: 0.8853 (ptpt) REVERT: 1 15 ARG cc_start: 0.8605 (mtt90) cc_final: 0.8164 (mtt90) REVERT: 1 32 PHE cc_start: 0.8343 (m-80) cc_final: 0.8100 (m-10) REVERT: 1 33 LYS cc_start: 0.8951 (ttpt) cc_final: 0.8391 (tttp) REVERT: 1 35 TYR cc_start: 0.8628 (t80) cc_final: 0.8378 (t80) REVERT: 1 41 LYS cc_start: 0.9213 (ptpp) cc_final: 0.8956 (pttm) REVERT: 4 1 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8481 (ttp) REVERT: 4 18 ARG cc_start: 0.8872 (mtp-110) cc_final: 0.8430 (ttm-80) REVERT: 6 1 MET cc_start: 0.6016 (mtt) cc_final: 0.4878 (ttm) REVERT: C 192 ILE cc_start: 0.9095 (OUTLIER) cc_final: 0.8841 (mm) REVERT: C 201 GLU cc_start: 0.8155 (tp30) cc_final: 0.7920 (tp30) REVERT: D 83 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8652 (tt) REVERT: D 95 GLN cc_start: 0.7914 (OUTLIER) cc_final: 0.7543 (tm-30) REVERT: D 128 GLN cc_start: 0.8810 (mt0) cc_final: 0.8500 (mt0) REVERT: D 168 GLN cc_start: 0.8724 (tt0) cc_final: 0.8355 (tt0) REVERT: E 39 MET cc_start: 0.8975 (tmm) cc_final: 0.8486 (tmm) REVERT: E 56 GLU cc_start: 0.8244 (mp0) cc_final: 0.7958 (pm20) REVERT: E 129 LEU cc_start: 0.9456 (tp) cc_final: 0.9209 (tp) REVERT: E 192 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8422 (tp) REVERT: F 97 TYR cc_start: 0.7944 (t80) cc_final: 0.7404 (t80) REVERT: F 122 PHE cc_start: 0.8621 (m-80) cc_final: 0.8406 (m-80) REVERT: G 24 THR cc_start: 0.9409 (m) cc_final: 0.9189 (p) REVERT: K 81 GLU cc_start: 0.8746 (pm20) cc_final: 0.8367 (pm20) REVERT: K 112 MET cc_start: 0.8121 (pmm) cc_final: 0.7899 (mmt) REVERT: L 15 THR cc_start: 0.9135 (OUTLIER) cc_final: 0.8854 (t) REVERT: L 30 THR cc_start: 0.9043 (p) cc_final: 0.8730 (t) REVERT: L 66 PHE cc_start: 0.8169 (OUTLIER) cc_final: 0.7355 (t80) REVERT: L 70 ASN cc_start: 0.9001 (m-40) cc_final: 0.8697 (m-40) REVERT: L 89 THR cc_start: 0.8951 (t) cc_final: 0.8657 (p) REVERT: M 1 MET cc_start: 0.7931 (mmt) cc_final: 0.7586 (mmt) REVERT: M 43 THR cc_start: 0.9001 (p) cc_final: 0.7852 (p) REVERT: M 44 ASN cc_start: 0.8911 (m-40) cc_final: 0.8480 (t0) REVERT: M 46 GLN cc_start: 0.8652 (mt0) cc_final: 0.8020 (mt0) REVERT: M 65 TRP cc_start: 0.8060 (m100) cc_final: 0.7731 (m100) REVERT: M 66 ILE cc_start: 0.8707 (mm) cc_final: 0.8444 (mm) REVERT: N 14 LYS cc_start: 0.9143 (tttt) cc_final: 0.8870 (tttm) REVERT: N 31 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7288 (mp0) REVERT: N 45 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7306 (mt-10) REVERT: N 47 MET cc_start: 0.8656 (mmt) cc_final: 0.8424 (mmm) REVERT: N 114 MET cc_start: 0.8744 (mmm) cc_final: 0.8499 (mmt) REVERT: O 32 ASN cc_start: 0.8534 (t0) cc_final: 0.7773 (t0) REVERT: O 34 PHE cc_start: 0.8801 (t80) cc_final: 0.8568 (t80) REVERT: O 40 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8947 (tp) REVERT: O 44 ILE cc_start: 0.9234 (mm) cc_final: 0.8952 (tp) REVERT: O 70 ASP cc_start: 0.8844 (t70) cc_final: 0.8513 (t0) REVERT: O 101 LEU cc_start: 0.9547 (tp) cc_final: 0.9185 (tt) REVERT: P 78 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8681 (m) REVERT: P 112 GLU cc_start: 0.8386 (mm-30) cc_final: 0.7575 (mm-30) REVERT: Q 16 LYS cc_start: 0.9078 (mttt) cc_final: 0.8534 (mtpt) REVERT: Q 27 SER cc_start: 0.8910 (m) cc_final: 0.8367 (p) REVERT: Q 37 GLN cc_start: 0.8882 (mt0) cc_final: 0.8585 (mt0) REVERT: Q 92 ARG cc_start: 0.7695 (OUTLIER) cc_final: 0.7011 (tpm170) REVERT: R 18 GLN cc_start: 0.8913 (tt0) cc_final: 0.8374 (tt0) REVERT: R 36 GLU cc_start: 0.8270 (pm20) cc_final: 0.8069 (pm20) REVERT: S 37 ASN cc_start: 0.9000 (t0) cc_final: 0.8612 (t0) REVERT: S 48 GLU cc_start: 0.8330 (tm-30) cc_final: 0.7903 (tm-30) REVERT: S 53 SER cc_start: 0.9456 (OUTLIER) cc_final: 0.8970 (p) REVERT: S 65 ASP cc_start: 0.8279 (t0) cc_final: 0.7920 (t0) REVERT: S 69 LEU cc_start: 0.9223 (mm) cc_final: 0.8802 (mm) REVERT: S 78 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7334 (mt-10) REVERT: S 90 MET cc_start: 0.8120 (mpp) cc_final: 0.7887 (mpp) REVERT: T 68 ARG cc_start: 0.7579 (mtm110) cc_final: 0.7317 (mtm110) REVERT: T 72 MET cc_start: 0.8103 (mtp) cc_final: 0.7844 (mmm) REVERT: U 69 MET cc_start: 0.8698 (mtm) cc_final: 0.8495 (mtt) REVERT: U 92 ARG cc_start: 0.8086 (mtm180) cc_final: 0.7723 (ptp-170) REVERT: W 48 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: W 52 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8646 (mmmm) REVERT: W 57 GLU cc_start: 0.7898 (tp30) cc_final: 0.7323 (tp30) REVERT: W 58 ASN cc_start: 0.8967 (m-40) cc_final: 0.8058 (m-40) REVERT: W 64 ASP cc_start: 0.8757 (p0) cc_final: 0.8555 (p0) REVERT: W 76 LYS cc_start: 0.8878 (mmmt) cc_final: 0.8518 (mmmt) REVERT: Y 17 LYS cc_start: 0.9001 (mmtm) cc_final: 0.8714 (mmtm) REVERT: Y 19 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8772 (ptpp) REVERT: Y 23 GLU cc_start: 0.8529 (pp20) cc_final: 0.8326 (pp20) REVERT: Y 24 GLU cc_start: 0.8876 (tp30) cc_final: 0.8478 (tp30) REVERT: Y 27 ASN cc_start: 0.9002 (m-40) cc_final: 0.8503 (m110) REVERT: Z 5 GLU cc_start: 0.7797 (mp0) cc_final: 0.7458 (mp0) REVERT: Z 40 ASN cc_start: 0.9114 (t0) cc_final: 0.8548 (p0) REVERT: Z 46 MET cc_start: 0.8691 (mmm) cc_final: 0.8365 (mmm) REVERT: Z 57 LYS cc_start: 0.8926 (tppt) cc_final: 0.8655 (tmtt) REVERT: b 24 ASN cc_start: 0.8725 (t0) cc_final: 0.8303 (t0) REVERT: b 28 LYS cc_start: 0.9115 (ptpt) cc_final: 0.8853 (mptt) REVERT: b 89 MET cc_start: 0.7661 (mmm) cc_final: 0.7453 (tpt) REVERT: b 93 ASN cc_start: 0.8891 (p0) cc_final: 0.8390 (p0) REVERT: b 104 PHE cc_start: 0.8426 (t80) cc_final: 0.7938 (t80) REVERT: b 169 GLU cc_start: 0.8704 (mm-30) cc_final: 0.8423 (mp0) REVERT: b 217 MET cc_start: 0.9201 (mmm) cc_final: 0.8856 (mmp) REVERT: c 36 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8855 (mt) REVERT: c 66 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.8092 (p) REVERT: c 74 MET cc_start: 0.8404 (ppp) cc_final: 0.8176 (ppp) REVERT: c 135 GLN cc_start: 0.8674 (tm-30) cc_final: 0.8403 (tm-30) REVERT: d 19 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8491 (mt) REVERT: d 47 TYR cc_start: 0.9238 (t80) cc_final: 0.8962 (t80) REVERT: d 100 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8827 (mmtt) REVERT: e 58 GLU cc_start: 0.8569 (mp0) cc_final: 0.8308 (mp0) REVERT: e 106 ILE cc_start: 0.9014 (mm) cc_final: 0.8757 (mm) REVERT: f 25 ARG cc_start: 0.8821 (ttp80) cc_final: 0.8535 (ttp80) REVERT: f 47 ARG cc_start: 0.7828 (mmm-85) cc_final: 0.7250 (mmm-85) REVERT: f 77 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8594 (ttp80) REVERT: f 78 LEU cc_start: 0.9561 (mt) cc_final: 0.8731 (mt) REVERT: g 30 MET cc_start: 0.9012 (ppp) cc_final: 0.8169 (ppp) REVERT: g 31 MET cc_start: 0.9052 (ttp) cc_final: 0.8408 (tpp) REVERT: g 40 GLN cc_start: 0.8813 (tp-100) cc_final: 0.7907 (tp-100) REVERT: g 44 TYR cc_start: 0.8589 (OUTLIER) cc_final: 0.7291 (m-80) REVERT: g 46 SER cc_start: 0.8794 (m) cc_final: 0.8498 (p) REVERT: g 86 GLN cc_start: 0.8724 (mm-40) cc_final: 0.8141 (mm110) REVERT: h 36 ILE cc_start: 0.9710 (mt) cc_final: 0.9481 (mt) REVERT: h 56 LYS cc_start: 0.8543 (OUTLIER) cc_final: 0.8065 (tppp) REVERT: i 6 TYR cc_start: 0.8544 (m-80) cc_final: 0.7945 (m-80) REVERT: i 38 HIS cc_start: 0.8603 (m-70) cc_final: 0.7956 (m-70) REVERT: j 9 ARG cc_start: 0.8633 (mtp180) cc_final: 0.7745 (mtt180) REVERT: j 11 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8454 (mttt) REVERT: j 24 LYS cc_start: 0.9539 (mmtm) cc_final: 0.9186 (mmtm) REVERT: k 77 ILE cc_start: 0.9390 (tp) cc_final: 0.9096 (pt) REVERT: l 42 GLN cc_start: 0.8931 (OUTLIER) cc_final: 0.8566 (mp10) REVERT: l 65 TYR cc_start: 0.7903 (p90) cc_final: 0.7379 (p90) REVERT: l 90 HIS cc_start: 0.8516 (m-70) cc_final: 0.7742 (m90) REVERT: m 13 LYS cc_start: 0.8447 (mptt) cc_final: 0.8045 (mtmt) REVERT: n 15 LYS cc_start: 0.9311 (mmmt) cc_final: 0.8632 (mttt) REVERT: n 19 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8051 (mp10) REVERT: n 25 GLU cc_start: 0.8483 (mm-30) cc_final: 0.7925 (mp0) REVERT: n 36 LYS cc_start: 0.8751 (tptm) cc_final: 0.8323 (tppp) REVERT: o 15 PHE cc_start: 0.8357 (m-80) cc_final: 0.7941 (m-10) REVERT: o 69 TYR cc_start: 0.9462 (t80) cc_final: 0.8988 (t80) REVERT: p 9 ARG cc_start: 0.8193 (tpt90) cc_final: 0.7769 (tpp80) REVERT: p 14 LYS cc_start: 0.9265 (mmmm) cc_final: 0.8790 (mmmt) REVERT: p 19 ARG cc_start: 0.8691 (mtp180) cc_final: 0.8396 (mtt180) REVERT: q 70 SER cc_start: 0.8828 (p) cc_final: 0.8495 (m) REVERT: r 56 TYR cc_start: 0.8288 (m-80) cc_final: 0.7972 (m-80) REVERT: s 73 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7827 (tp30) REVERT: t 15 ASN cc_start: 0.9120 (m-40) cc_final: 0.8851 (m110) REVERT: u 50 SER cc_start: 0.8586 (t) cc_final: 0.8305 (t) outliers start: 306 outliers final: 235 residues processed: 1565 average time/residue: 1.2194 time to fit residues: 3348.1493 Evaluate side-chains 1620 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1363 time to evaluate : 5.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 30 VAL Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 47 GLU Chi-restraints excluded: chain 2 residue 23 SER Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 2 residue 30 VAL Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 1 MET Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain 4 residue 23 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 82 GLN Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 130 THR Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 101 MET Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain K residue 89 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 66 PHE Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 34 ILE Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 21 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain N residue 117 ILE Chi-restraints excluded: chain N residue 119 LEU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 1 MET Chi-restraints excluded: chain P residue 9 THR Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain P residue 78 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 17 VAL Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 52 GLN Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 19 LEU Chi-restraints excluded: chain S residue 20 VAL Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 53 SER Chi-restraints excluded: chain S residue 78 GLU Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 38 VAL Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain U residue 87 ASP Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 32 ASN Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 68 LEU Chi-restraints excluded: chain b residue 161 LEU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 88 LYS Chi-restraints excluded: chain c residue 101 ASN Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 152 LYS Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 80 THR Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 59 PHE Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 24 SER Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 92 ASN Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain h residue 128 LEU Chi-restraints excluded: chain h residue 132 TRP Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 60 THR Chi-restraints excluded: chain i residue 105 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 47 SER Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 18 ILE Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 29 PHE Chi-restraints excluded: chain k residue 30 ASN Chi-restraints excluded: chain k residue 42 ASN Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 76 SER Chi-restraints excluded: chain k residue 82 LYS Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain l residue 3 THR Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 48 LYS Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 50 ASP Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 12 ASP Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Chi-restraints excluded: chain u residue 40 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 855 optimal weight: 2.9990 chunk 901 optimal weight: 10.0000 chunk 822 optimal weight: 0.7980 chunk 876 optimal weight: 10.0000 chunk 900 optimal weight: 1.9990 chunk 527 optimal weight: 10.0000 chunk 381 optimal weight: 10.0000 chunk 688 optimal weight: 10.0000 chunk 269 optimal weight: 1.9990 chunk 792 optimal weight: 8.9990 chunk 829 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 GLN F 27 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 110 ASN ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 77 GLN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN S 97 ASN ** Y 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 61 GLN p 77 GLN ** p 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 ASN t 70 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 155558 Z= 0.209 Angle : 0.629 15.355 233440 Z= 0.323 Chirality : 0.035 0.307 29944 Planarity : 0.005 0.077 11973 Dihedral : 24.260 179.985 79599 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 14.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.30 % Favored : 92.62 % Rotamer: Outliers : 5.78 % Allowed : 28.88 % Favored : 65.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.11), residues: 5176 helix: 0.33 (0.13), residues: 1629 sheet: -0.67 (0.17), residues: 955 loop : -1.48 (0.12), residues: 2592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP M 65 HIS 0.010 0.001 HIS s 14 PHE 0.032 0.002 PHE b 56 TYR 0.028 0.002 TYR W 46 ARG 0.019 0.001 ARG k 100 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1692 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1437 time to evaluate : 6.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 8 THR cc_start: 0.9352 (OUTLIER) cc_final: 0.9135 (p) REVERT: 0 28 THR cc_start: 0.8336 (m) cc_final: 0.8108 (p) REVERT: 0 52 LYS cc_start: 0.9130 (mtpt) cc_final: 0.8858 (ptpt) REVERT: 1 15 ARG cc_start: 0.8662 (mtt90) cc_final: 0.8170 (mtt90) REVERT: 1 32 PHE cc_start: 0.8380 (m-80) cc_final: 0.8155 (m-10) REVERT: 1 33 LYS cc_start: 0.8992 (ttpt) cc_final: 0.8412 (tttp) REVERT: 1 35 TYR cc_start: 0.8717 (t80) cc_final: 0.8488 (t80) REVERT: 1 41 LYS cc_start: 0.9199 (ptpp) cc_final: 0.8939 (pttm) REVERT: 4 18 ARG cc_start: 0.8980 (mtp-110) cc_final: 0.8559 (ttm-80) REVERT: 6 1 MET cc_start: 0.4894 (mtt) cc_final: 0.3936 (ttm) REVERT: C 192 ILE cc_start: 0.9096 (OUTLIER) cc_final: 0.8866 (mm) REVERT: D 83 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8623 (tt) REVERT: D 95 GLN cc_start: 0.7951 (OUTLIER) cc_final: 0.7484 (tm-30) REVERT: D 120 GLN cc_start: 0.8082 (mm-40) cc_final: 0.7755 (mm110) REVERT: D 128 GLN cc_start: 0.8790 (mt0) cc_final: 0.8554 (mt0) REVERT: D 146 MET cc_start: 0.8263 (mmm) cc_final: 0.7846 (mtt) REVERT: D 168 GLN cc_start: 0.8570 (tt0) cc_final: 0.8177 (tt0) REVERT: E 39 MET cc_start: 0.8954 (tmm) cc_final: 0.8372 (tmm) REVERT: E 129 LEU cc_start: 0.9444 (tp) cc_final: 0.9200 (tp) REVERT: E 161 GLU cc_start: 0.8181 (tp30) cc_final: 0.7894 (tp30) REVERT: E 192 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8349 (tp) REVERT: F 97 TYR cc_start: 0.7867 (t80) cc_final: 0.7209 (t80) REVERT: J 48 HIS cc_start: 0.7297 (OUTLIER) cc_final: 0.6477 (m170) REVERT: J 81 HIS cc_start: 0.8251 (m-70) cc_final: 0.7894 (m-70) REVERT: K 81 GLU cc_start: 0.8747 (pm20) cc_final: 0.8368 (pm20) REVERT: K 112 MET cc_start: 0.7878 (pmm) cc_final: 0.7523 (mpp) REVERT: L 15 THR cc_start: 0.9142 (m) cc_final: 0.8841 (t) REVERT: L 30 THR cc_start: 0.8992 (p) cc_final: 0.8715 (t) REVERT: L 89 THR cc_start: 0.8946 (t) cc_final: 0.8661 (p) REVERT: M 43 THR cc_start: 0.8947 (p) cc_final: 0.8736 (p) REVERT: M 44 ASN cc_start: 0.8864 (m-40) cc_final: 0.8305 (t0) REVERT: M 65 TRP cc_start: 0.8141 (m100) cc_final: 0.7851 (m100) REVERT: M 66 ILE cc_start: 0.8463 (mm) cc_final: 0.8231 (mm) REVERT: N 14 LYS cc_start: 0.9114 (tttt) cc_final: 0.8853 (tttm) REVERT: N 31 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7397 (mp0) REVERT: N 45 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7570 (mt-10) REVERT: N 47 MET cc_start: 0.8587 (mmt) cc_final: 0.8387 (mmm) REVERT: N 69 GLU cc_start: 0.8077 (mp0) cc_final: 0.6922 (mp0) REVERT: O 31 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8943 (mm) REVERT: O 32 ASN cc_start: 0.8559 (t0) cc_final: 0.7683 (t0) REVERT: O 40 ILE cc_start: 0.9196 (OUTLIER) cc_final: 0.8973 (tp) REVERT: O 44 ILE cc_start: 0.9388 (mm) cc_final: 0.8900 (tp) REVERT: O 70 ASP cc_start: 0.8788 (t70) cc_final: 0.8465 (t0) REVERT: O 101 LEU cc_start: 0.9548 (tp) cc_final: 0.9105 (tt) REVERT: O 106 VAL cc_start: 0.9483 (OUTLIER) cc_final: 0.9274 (p) REVERT: P 112 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8114 (tp30) REVERT: Q 16 LYS cc_start: 0.9033 (mttt) cc_final: 0.8506 (mtpt) REVERT: Q 27 SER cc_start: 0.8818 (m) cc_final: 0.8294 (p) REVERT: Q 40 MET cc_start: 0.8363 (mtp) cc_final: 0.7973 (mtp) REVERT: Q 92 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7430 (tpm170) REVERT: R 15 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7743 (mm-30) REVERT: R 18 GLN cc_start: 0.8917 (tt0) cc_final: 0.8341 (tt0) REVERT: R 36 GLU cc_start: 0.8333 (pm20) cc_final: 0.8121 (pm20) REVERT: S 37 ASN cc_start: 0.8978 (t0) cc_final: 0.8575 (t0) REVERT: S 48 GLU cc_start: 0.8325 (tm-30) cc_final: 0.7898 (tm-30) REVERT: S 65 ASP cc_start: 0.8144 (t0) cc_final: 0.7846 (t0) REVERT: S 69 LEU cc_start: 0.9230 (mm) cc_final: 0.8762 (mm) REVERT: T 72 MET cc_start: 0.8088 (mtp) cc_final: 0.7827 (mmm) REVERT: U 69 MET cc_start: 0.8674 (mtm) cc_final: 0.8457 (mtt) REVERT: U 92 ARG cc_start: 0.8094 (mtm180) cc_final: 0.7511 (ptp-170) REVERT: W 48 GLN cc_start: 0.8814 (OUTLIER) cc_final: 0.8564 (pt0) REVERT: W 57 GLU cc_start: 0.7837 (tp30) cc_final: 0.7224 (tp30) REVERT: W 58 ASN cc_start: 0.8978 (m-40) cc_final: 0.8072 (m-40) REVERT: Y 17 LYS cc_start: 0.8984 (mmtm) cc_final: 0.8685 (mmtp) REVERT: Y 19 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8637 (ptpp) REVERT: Y 23 GLU cc_start: 0.8496 (pp20) cc_final: 0.8279 (pp20) REVERT: Y 24 GLU cc_start: 0.8865 (tp30) cc_final: 0.8463 (tp30) REVERT: Y 27 ASN cc_start: 0.8976 (m-40) cc_final: 0.8457 (m110) REVERT: Z 5 GLU cc_start: 0.7808 (mp0) cc_final: 0.7454 (mp0) REVERT: Z 46 MET cc_start: 0.8652 (mmm) cc_final: 0.8297 (mmm) REVERT: b 24 ASN cc_start: 0.8672 (t0) cc_final: 0.8032 (t0) REVERT: b 26 LYS cc_start: 0.9510 (mtpt) cc_final: 0.8940 (ttpt) REVERT: b 28 LYS cc_start: 0.9063 (ptpt) cc_final: 0.8763 (mptt) REVERT: b 93 ASN cc_start: 0.8815 (p0) cc_final: 0.8194 (p0) REVERT: b 104 PHE cc_start: 0.8435 (t80) cc_final: 0.7873 (t80) REVERT: b 169 GLU cc_start: 0.8696 (mm-30) cc_final: 0.8390 (mp0) REVERT: b 217 MET cc_start: 0.9172 (mmm) cc_final: 0.8816 (mmp) REVERT: c 36 LEU cc_start: 0.9227 (OUTLIER) cc_final: 0.8882 (mt) REVERT: c 66 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8349 (p) REVERT: c 74 MET cc_start: 0.8429 (ppp) cc_final: 0.8210 (ppp) REVERT: c 135 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8457 (tm-30) REVERT: d 19 LEU cc_start: 0.8863 (OUTLIER) cc_final: 0.8592 (mm) REVERT: d 47 TYR cc_start: 0.9145 (t80) cc_final: 0.8878 (t80) REVERT: d 100 LYS cc_start: 0.9140 (mmtm) cc_final: 0.8894 (mmtt) REVERT: e 58 GLU cc_start: 0.8557 (mp0) cc_final: 0.8318 (mp0) REVERT: f 4 TYR cc_start: 0.8419 (m-80) cc_final: 0.8045 (m-80) REVERT: f 47 ARG cc_start: 0.7775 (mmm-85) cc_final: 0.7535 (mmm-85) REVERT: f 77 ARG cc_start: 0.9108 (ttp80) cc_final: 0.8525 (ttp80) REVERT: f 78 LEU cc_start: 0.9531 (mt) cc_final: 0.8646 (mt) REVERT: g 30 MET cc_start: 0.9043 (ppp) cc_final: 0.8164 (ppp) REVERT: g 31 MET cc_start: 0.9039 (ttp) cc_final: 0.8394 (tpp) REVERT: g 40 GLN cc_start: 0.8935 (tp-100) cc_final: 0.7962 (tp-100) REVERT: g 44 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.7099 (m-80) REVERT: g 86 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8422 (mm-40) REVERT: h 26 GLU cc_start: 0.7656 (tp30) cc_final: 0.7428 (tp30) REVERT: h 36 ILE cc_start: 0.9743 (mt) cc_final: 0.9488 (mt) REVERT: h 41 LYS cc_start: 0.9403 (tptm) cc_final: 0.9196 (tppp) REVERT: i 6 TYR cc_start: 0.8511 (m-80) cc_final: 0.7909 (m-80) REVERT: i 37 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7451 (tm-30) REVERT: i 38 HIS cc_start: 0.8578 (m-70) cc_final: 0.7719 (m170) REVERT: j 9 ARG cc_start: 0.8624 (mtp180) cc_final: 0.7771 (mtt180) REVERT: j 11 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8499 (mttt) REVERT: j 24 LYS cc_start: 0.9537 (mmtm) cc_final: 0.9256 (mmtm) REVERT: l 42 GLN cc_start: 0.8918 (OUTLIER) cc_final: 0.8532 (mp10) REVERT: l 65 TYR cc_start: 0.7858 (p90) cc_final: 0.7339 (p90) REVERT: l 90 HIS cc_start: 0.8452 (m-70) cc_final: 0.7719 (m90) REVERT: m 13 LYS cc_start: 0.8264 (mptt) cc_final: 0.7879 (mtmt) REVERT: m 21 TYR cc_start: 0.8590 (m-80) cc_final: 0.8244 (m-80) REVERT: m 91 HIS cc_start: 0.8710 (t-90) cc_final: 0.8167 (t70) REVERT: n 10 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8334 (tm-30) REVERT: n 15 LYS cc_start: 0.9325 (mmmt) cc_final: 0.8625 (mttt) REVERT: n 19 GLN cc_start: 0.8718 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: n 36 LYS cc_start: 0.8759 (tptm) cc_final: 0.8342 (tppp) REVERT: o 15 PHE cc_start: 0.8400 (m-80) cc_final: 0.7976 (m-10) REVERT: o 69 TYR cc_start: 0.9362 (t80) cc_final: 0.8981 (t80) REVERT: p 9 ARG cc_start: 0.8170 (tpt90) cc_final: 0.7713 (tpp80) REVERT: p 19 ARG cc_start: 0.8640 (mtp180) cc_final: 0.8383 (mtt180) REVERT: q 70 SER cc_start: 0.8836 (p) cc_final: 0.8414 (m) REVERT: r 56 TYR cc_start: 0.8136 (m-80) cc_final: 0.7672 (m-80) REVERT: r 66 ARG cc_start: 0.8147 (mmm-85) cc_final: 0.7937 (mmm-85) REVERT: s 73 GLU cc_start: 0.8062 (mm-30) cc_final: 0.7791 (tp30) REVERT: s 74 PHE cc_start: 0.9326 (m-10) cc_final: 0.9123 (m-10) REVERT: t 15 ASN cc_start: 0.9103 (m110) cc_final: 0.8772 (m-40) REVERT: u 50 SER cc_start: 0.8584 (t) cc_final: 0.8354 (t) outliers start: 255 outliers final: 204 residues processed: 1554 average time/residue: 1.2331 time to fit residues: 3359.6373 Evaluate side-chains 1598 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 1375 time to evaluate : 6.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 47 GLU Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 HIS Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 78 ASP Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 31 LEU Chi-restraints excluded: chain O residue 40 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 39 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 75 VAL Chi-restraints excluded: chain c residue 166 TYR Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 158 ASN Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 100 SER Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 59 PHE Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 82 SER Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 24 SER Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 55 SER Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 47 SER Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 42 ASN Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 82 LYS Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 23 PHE Chi-restraints excluded: chain m residue 28 THR Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain o residue 80 GLU Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 15 LEU Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain s residue 51 VAL Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain t residue 70 ASN Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Chi-restraints excluded: chain u residue 40 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 873 optimal weight: 0.0980 chunk 575 optimal weight: 30.0000 chunk 926 optimal weight: 0.6980 chunk 565 optimal weight: 20.0000 chunk 439 optimal weight: 30.0000 chunk 644 optimal weight: 10.0000 chunk 972 optimal weight: 10.0000 chunk 894 optimal weight: 2.9990 chunk 774 optimal weight: 9.9990 chunk 80 optimal weight: 8.9990 chunk 598 optimal weight: 10.0000 overall best weight: 4.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 75 GLN E 82 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN N 77 GLN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 67 ASN ** Y 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN b 123 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 147 ASN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 GLN ** q 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 ASN t 70 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 155558 Z= 0.261 Angle : 0.658 15.198 233440 Z= 0.337 Chirality : 0.036 0.317 29944 Planarity : 0.005 0.102 11973 Dihedral : 24.255 179.914 79599 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.08 % Allowed : 7.40 % Favored : 92.52 % Rotamer: Outliers : 5.62 % Allowed : 29.69 % Favored : 64.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -1.12 (0.11), residues: 5176 helix: 0.35 (0.13), residues: 1626 sheet: -0.65 (0.17), residues: 972 loop : -1.49 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP M 65 HIS 0.009 0.001 HIS b 18 PHE 0.035 0.002 PHE L 50 TYR 0.024 0.002 TYR g 18 ARG 0.015 0.001 ARG k 130 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10352 Ramachandran restraints generated. 5176 Oldfield, 0 Emsley, 5176 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1381 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 8 THR cc_start: 0.9360 (OUTLIER) cc_final: 0.9155 (p) REVERT: 0 52 LYS cc_start: 0.9138 (mtpt) cc_final: 0.8916 (ptpt) REVERT: 1 15 ARG cc_start: 0.8598 (mtt90) cc_final: 0.8166 (mtt90) REVERT: 1 32 PHE cc_start: 0.8389 (m-80) cc_final: 0.8124 (m-10) REVERT: 1 35 TYR cc_start: 0.8705 (t80) cc_final: 0.8501 (t80) REVERT: 1 41 LYS cc_start: 0.9208 (ptpp) cc_final: 0.8942 (pttm) REVERT: 4 18 ARG cc_start: 0.8927 (mtp-110) cc_final: 0.8476 (ttm-80) REVERT: 6 1 MET cc_start: 0.4934 (mtt) cc_final: 0.4005 (ttm) REVERT: C 192 ILE cc_start: 0.9089 (OUTLIER) cc_final: 0.8860 (mm) REVERT: D 83 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8637 (tt) REVERT: D 95 GLN cc_start: 0.7967 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: D 128 GLN cc_start: 0.8767 (mt0) cc_final: 0.8520 (mt0) REVERT: D 146 MET cc_start: 0.8332 (mmm) cc_final: 0.7909 (mtt) REVERT: D 168 GLN cc_start: 0.8622 (tt0) cc_final: 0.8261 (tt0) REVERT: E 39 MET cc_start: 0.8978 (tmm) cc_final: 0.8532 (tmm) REVERT: E 192 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8518 (tp) REVERT: F 22 TYR cc_start: 0.6112 (m-10) cc_final: 0.5783 (m-10) REVERT: F 97 TYR cc_start: 0.7807 (t80) cc_final: 0.7138 (t80) REVERT: F 122 PHE cc_start: 0.8923 (m-80) cc_final: 0.8014 (m-80) REVERT: J 48 HIS cc_start: 0.7303 (OUTLIER) cc_final: 0.6426 (m170) REVERT: K 81 GLU cc_start: 0.8747 (pm20) cc_final: 0.8351 (pm20) REVERT: K 120 GLU cc_start: 0.8514 (tt0) cc_final: 0.7924 (tt0) REVERT: L 15 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8862 (t) REVERT: L 30 THR cc_start: 0.8999 (p) cc_final: 0.8714 (t) REVERT: L 89 THR cc_start: 0.8942 (t) cc_final: 0.8652 (p) REVERT: M 43 THR cc_start: 0.8975 (p) cc_final: 0.8756 (p) REVERT: M 44 ASN cc_start: 0.8874 (m-40) cc_final: 0.8192 (t0) REVERT: M 65 TRP cc_start: 0.8208 (m100) cc_final: 0.7967 (m100) REVERT: M 66 ILE cc_start: 0.8517 (mm) cc_final: 0.8276 (mm) REVERT: N 14 LYS cc_start: 0.9127 (tttt) cc_final: 0.8852 (tttm) REVERT: N 31 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7693 (mp0) REVERT: N 45 GLU cc_start: 0.8297 (mt-10) cc_final: 0.7582 (mt-10) REVERT: N 69 GLU cc_start: 0.8110 (mp0) cc_final: 0.6939 (mp0) REVERT: O 32 ASN cc_start: 0.8525 (t0) cc_final: 0.7785 (t0) REVERT: O 34 PHE cc_start: 0.8850 (t80) cc_final: 0.7603 (t80) REVERT: O 70 ASP cc_start: 0.8793 (t70) cc_final: 0.8457 (t0) REVERT: O 101 LEU cc_start: 0.9551 (tp) cc_final: 0.9109 (tt) REVERT: O 106 VAL cc_start: 0.9469 (OUTLIER) cc_final: 0.9218 (p) REVERT: P 6 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7915 (mt-10) REVERT: P 112 GLU cc_start: 0.8373 (mm-30) cc_final: 0.8131 (tp30) REVERT: Q 16 LYS cc_start: 0.9109 (mttt) cc_final: 0.8594 (mtpt) REVERT: Q 27 SER cc_start: 0.8873 (m) cc_final: 0.8327 (p) REVERT: Q 92 ARG cc_start: 0.8003 (OUTLIER) cc_final: 0.7459 (tpm170) REVERT: R 15 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7727 (mm-30) REVERT: R 18 GLN cc_start: 0.8962 (tt0) cc_final: 0.8378 (tt0) REVERT: S 37 ASN cc_start: 0.8991 (t0) cc_final: 0.8590 (t0) REVERT: S 48 GLU cc_start: 0.8324 (tm-30) cc_final: 0.7891 (tm-30) REVERT: S 65 ASP cc_start: 0.8383 (t0) cc_final: 0.7868 (t0) REVERT: S 69 LEU cc_start: 0.9199 (mm) cc_final: 0.8720 (mm) REVERT: S 92 ARG cc_start: 0.7842 (mmt-90) cc_final: 0.7534 (ttm110) REVERT: T 68 ARG cc_start: 0.7626 (mtm110) cc_final: 0.7247 (mtm110) REVERT: T 72 MET cc_start: 0.8133 (mtp) cc_final: 0.7861 (mmm) REVERT: U 69 MET cc_start: 0.8707 (mtm) cc_final: 0.8497 (mtt) REVERT: U 92 ARG cc_start: 0.8099 (mtm180) cc_final: 0.7510 (ptp-170) REVERT: W 48 GLN cc_start: 0.8780 (OUTLIER) cc_final: 0.8533 (pt0) REVERT: W 52 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8405 (mtpp) REVERT: W 57 GLU cc_start: 0.7878 (tp30) cc_final: 0.7306 (tp30) REVERT: W 58 ASN cc_start: 0.9008 (m-40) cc_final: 0.8224 (m-40) REVERT: W 68 PHE cc_start: 0.9463 (p90) cc_final: 0.9091 (p90) REVERT: Y 17 LYS cc_start: 0.8977 (mmtm) cc_final: 0.8702 (mmtp) REVERT: Y 19 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8642 (ptpp) REVERT: Y 23 GLU cc_start: 0.8526 (pp20) cc_final: 0.8316 (pp20) REVERT: Y 24 GLU cc_start: 0.8889 (tp30) cc_final: 0.8496 (tp30) REVERT: Y 27 ASN cc_start: 0.8989 (m-40) cc_final: 0.8475 (m110) REVERT: Z 5 GLU cc_start: 0.7768 (mp0) cc_final: 0.7444 (mp0) REVERT: Z 46 MET cc_start: 0.8683 (mmm) cc_final: 0.8400 (mmm) REVERT: Z 57 LYS cc_start: 0.8911 (tppt) cc_final: 0.8673 (tmtt) REVERT: Z 58 GLU cc_start: 0.8008 (mm-30) cc_final: 0.7806 (mm-30) REVERT: b 15 HIS cc_start: 0.8202 (p-80) cc_final: 0.7926 (p-80) REVERT: b 24 ASN cc_start: 0.8753 (t0) cc_final: 0.8084 (t0) REVERT: b 26 LYS cc_start: 0.9505 (mtpt) cc_final: 0.8933 (ttpt) REVERT: b 28 LYS cc_start: 0.9068 (ptpt) cc_final: 0.8755 (mptt) REVERT: b 52 GLU cc_start: 0.8333 (mp0) cc_final: 0.8120 (pm20) REVERT: b 75 GLN cc_start: 0.8847 (pm20) cc_final: 0.8561 (pm20) REVERT: b 93 ASN cc_start: 0.8854 (p0) cc_final: 0.8314 (p0) REVERT: b 104 PHE cc_start: 0.8355 (t80) cc_final: 0.7867 (t80) REVERT: b 169 GLU cc_start: 0.8708 (mm-30) cc_final: 0.8404 (mp0) REVERT: b 217 MET cc_start: 0.9185 (mmm) cc_final: 0.8814 (mmp) REVERT: c 36 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8889 (mt) REVERT: c 66 THR cc_start: 0.8118 (OUTLIER) cc_final: 0.7875 (p) REVERT: c 135 GLN cc_start: 0.8759 (tm-30) cc_final: 0.8551 (tm-30) REVERT: d 19 LEU cc_start: 0.8852 (OUTLIER) cc_final: 0.8564 (mm) REVERT: d 47 TYR cc_start: 0.9180 (t80) cc_final: 0.8902 (t80) REVERT: d 100 LYS cc_start: 0.9157 (mmtm) cc_final: 0.8783 (mmtt) REVERT: d 198 TYR cc_start: 0.8315 (m-10) cc_final: 0.8109 (m-10) REVERT: e 42 LYS cc_start: 0.8787 (tppt) cc_final: 0.8500 (mmtt) REVERT: e 58 GLU cc_start: 0.8605 (mp0) cc_final: 0.8340 (mp0) REVERT: e 106 ILE cc_start: 0.8965 (mm) cc_final: 0.8687 (mm) REVERT: f 47 ARG cc_start: 0.7844 (mmm-85) cc_final: 0.7382 (mmm-85) REVERT: f 74 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8193 (mp0) REVERT: f 77 ARG cc_start: 0.9156 (ttp80) cc_final: 0.8630 (ttp80) REVERT: f 78 LEU cc_start: 0.9543 (mt) cc_final: 0.8585 (mt) REVERT: g 28 ASN cc_start: 0.9088 (t0) cc_final: 0.8573 (t0) REVERT: g 30 MET cc_start: 0.9069 (ppp) cc_final: 0.8207 (ppp) REVERT: g 31 MET cc_start: 0.9053 (ttp) cc_final: 0.8374 (tpp) REVERT: g 40 GLN cc_start: 0.8942 (tp-100) cc_final: 0.7997 (tp-100) REVERT: g 44 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.7104 (m-80) REVERT: g 86 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8454 (mm-40) REVERT: h 35 GLU cc_start: 0.8086 (tp30) cc_final: 0.7786 (tp30) REVERT: h 36 ILE cc_start: 0.9733 (mt) cc_final: 0.9489 (mt) REVERT: h 56 LYS cc_start: 0.8277 (OUTLIER) cc_final: 0.7734 (tttp) REVERT: i 6 TYR cc_start: 0.8652 (m-80) cc_final: 0.8191 (m-80) REVERT: i 34 GLU cc_start: 0.8317 (pp20) cc_final: 0.7997 (tm-30) REVERT: i 37 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7628 (tm-30) REVERT: i 38 HIS cc_start: 0.8607 (m-70) cc_final: 0.7736 (m170) REVERT: j 9 ARG cc_start: 0.8682 (mtp180) cc_final: 0.7812 (mtt180) REVERT: j 11 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8525 (mttt) REVERT: j 24 LYS cc_start: 0.9532 (mmtm) cc_final: 0.9189 (mmtm) REVERT: j 42 LEU cc_start: 0.9494 (mm) cc_final: 0.9208 (mm) REVERT: k 103 GLN cc_start: 0.9418 (tp40) cc_final: 0.8650 (pp30) REVERT: l 42 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8580 (mp10) REVERT: l 65 TYR cc_start: 0.7871 (p90) cc_final: 0.7318 (p90) REVERT: l 90 HIS cc_start: 0.8473 (m-70) cc_final: 0.7915 (m-70) REVERT: m 91 HIS cc_start: 0.8672 (t-90) cc_final: 0.8167 (t70) REVERT: n 10 GLN cc_start: 0.8655 (tm-30) cc_final: 0.8263 (tm-30) REVERT: n 19 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8168 (mp10) REVERT: n 36 LYS cc_start: 0.8753 (tptm) cc_final: 0.8367 (tppp) REVERT: n 46 GLU cc_start: 0.8080 (tp30) cc_final: 0.7609 (tm-30) REVERT: o 15 PHE cc_start: 0.8518 (m-80) cc_final: 0.8003 (m-10) REVERT: o 69 TYR cc_start: 0.9489 (t80) cc_final: 0.9012 (t80) REVERT: p 9 ARG cc_start: 0.8198 (tpt90) cc_final: 0.7746 (tpp80) REVERT: p 19 ARG cc_start: 0.8668 (mtp180) cc_final: 0.8374 (mtt180) REVERT: p 87 LYS cc_start: 0.8448 (mmmm) cc_final: 0.7959 (mmmt) REVERT: q 19 MET cc_start: 0.7161 (mmp) cc_final: 0.6549 (mmp) REVERT: q 70 SER cc_start: 0.8843 (p) cc_final: 0.8409 (m) REVERT: r 56 TYR cc_start: 0.8038 (m-80) cc_final: 0.7712 (m-80) REVERT: s 73 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7811 (tp30) REVERT: t 15 ASN cc_start: 0.8979 (m-40) cc_final: 0.8616 (m110) outliers start: 248 outliers final: 206 residues processed: 1498 average time/residue: 1.2005 time to fit residues: 3147.4904 Evaluate side-chains 1577 residues out of total 4415 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1352 time to evaluate : 8.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 8 THR Chi-restraints excluded: chain 1 residue 6 THR Chi-restraints excluded: chain 1 residue 42 SER Chi-restraints excluded: chain 1 residue 47 GLU Chi-restraints excluded: chain 2 residue 24 SER Chi-restraints excluded: chain 3 residue 6 THR Chi-restraints excluded: chain 3 residue 37 SER Chi-restraints excluded: chain 3 residue 56 LYS Chi-restraints excluded: chain 4 residue 16 VAL Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 38 HIS Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 40 THR Chi-restraints excluded: chain D residue 69 VAL Chi-restraints excluded: chain D residue 83 LEU Chi-restraints excluded: chain D residue 95 GLN Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 133 MET Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 140 HIS Chi-restraints excluded: chain D residue 201 THR Chi-restraints excluded: chain E residue 13 THR Chi-restraints excluded: chain E residue 182 ASN Chi-restraints excluded: chain E residue 185 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 46 ASN Chi-restraints excluded: chain F residue 107 SER Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 11 ILE Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 44 ILE Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 107 ASN Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain J residue 6 MET Chi-restraints excluded: chain J residue 12 ILE Chi-restraints excluded: chain J residue 26 LEU Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 HIS Chi-restraints excluded: chain J residue 114 SER Chi-restraints excluded: chain K residue 21 THR Chi-restraints excluded: chain K residue 28 SER Chi-restraints excluded: chain K residue 53 LYS Chi-restraints excluded: chain K residue 73 ASP Chi-restraints excluded: chain L residue 15 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 92 THR Chi-restraints excluded: chain M residue 3 LEU Chi-restraints excluded: chain M residue 25 THR Chi-restraints excluded: chain M residue 58 MET Chi-restraints excluded: chain M residue 71 SER Chi-restraints excluded: chain M residue 94 VAL Chi-restraints excluded: chain M residue 122 SER Chi-restraints excluded: chain N residue 9 THR Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 61 GLN Chi-restraints excluded: chain N residue 66 ILE Chi-restraints excluded: chain N residue 116 ILE Chi-restraints excluded: chain O residue 45 ILE Chi-restraints excluded: chain O residue 94 VAL Chi-restraints excluded: chain O residue 96 ASP Chi-restraints excluded: chain O residue 106 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 61 VAL Chi-restraints excluded: chain P residue 65 SER Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 10 THR Chi-restraints excluded: chain Q residue 30 THR Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 42 SER Chi-restraints excluded: chain Q residue 92 ARG Chi-restraints excluded: chain Q residue 100 VAL Chi-restraints excluded: chain R residue 32 THR Chi-restraints excluded: chain S residue 4 LYS Chi-restraints excluded: chain S residue 38 LEU Chi-restraints excluded: chain S residue 97 ASN Chi-restraints excluded: chain S residue 105 ILE Chi-restraints excluded: chain U residue 9 VAL Chi-restraints excluded: chain U residue 16 ASP Chi-restraints excluded: chain U residue 31 ASP Chi-restraints excluded: chain U residue 34 LEU Chi-restraints excluded: chain U residue 41 VAL Chi-restraints excluded: chain U residue 45 SER Chi-restraints excluded: chain U residue 68 VAL Chi-restraints excluded: chain U residue 71 LEU Chi-restraints excluded: chain W residue 15 VAL Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 19 LYS Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Z residue 4 LEU Chi-restraints excluded: chain Z residue 24 ARG Chi-restraints excluded: chain Z residue 48 ASN Chi-restraints excluded: chain b residue 9 LEU Chi-restraints excluded: chain b residue 33 THR Chi-restraints excluded: chain b residue 55 ASN Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 196 ILE Chi-restraints excluded: chain b residue 197 ASP Chi-restraints excluded: chain c residue 30 ASP Chi-restraints excluded: chain c residue 36 LEU Chi-restraints excluded: chain c residue 48 ASP Chi-restraints excluded: chain c residue 66 THR Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 169 GLU Chi-restraints excluded: chain c residue 172 VAL Chi-restraints excluded: chain c residue 178 ARG Chi-restraints excluded: chain c residue 180 ASP Chi-restraints excluded: chain c residue 189 ASP Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 71 LEU Chi-restraints excluded: chain d residue 118 HIS Chi-restraints excluded: chain d residue 121 VAL Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 158 ASN Chi-restraints excluded: chain d residue 166 THR Chi-restraints excluded: chain d residue 185 LEU Chi-restraints excluded: chain d residue 189 ILE Chi-restraints excluded: chain e residue 5 ASP Chi-restraints excluded: chain e residue 15 LEU Chi-restraints excluded: chain e residue 17 THR Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain e residue 48 PHE Chi-restraints excluded: chain e residue 50 THR Chi-restraints excluded: chain e residue 72 ILE Chi-restraints excluded: chain e residue 85 ILE Chi-restraints excluded: chain e residue 114 VAL Chi-restraints excluded: chain e residue 131 ASN Chi-restraints excluded: chain e residue 140 THR Chi-restraints excluded: chain f residue 29 VAL Chi-restraints excluded: chain f residue 31 THR Chi-restraints excluded: chain f residue 53 ASN Chi-restraints excluded: chain f residue 59 PHE Chi-restraints excluded: chain f residue 64 ASN Chi-restraints excluded: chain f residue 72 VAL Chi-restraints excluded: chain g residue 12 VAL Chi-restraints excluded: chain g residue 15 ASP Chi-restraints excluded: chain g residue 20 SER Chi-restraints excluded: chain g residue 24 SER Chi-restraints excluded: chain g residue 27 ILE Chi-restraints excluded: chain g residue 44 TYR Chi-restraints excluded: chain g residue 62 PHE Chi-restraints excluded: chain g residue 84 ASN Chi-restraints excluded: chain g residue 130 ASN Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 43 GLU Chi-restraints excluded: chain h residue 53 GLU Chi-restraints excluded: chain h residue 54 ASP Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 57 GLN Chi-restraints excluded: chain h residue 62 VAL Chi-restraints excluded: chain h residue 64 LEU Chi-restraints excluded: chain h residue 74 ILE Chi-restraints excluded: chain h residue 114 THR Chi-restraints excluded: chain h residue 127 VAL Chi-restraints excluded: chain i residue 9 THR Chi-restraints excluded: chain i residue 21 LEU Chi-restraints excluded: chain i residue 57 THR Chi-restraints excluded: chain i residue 96 THR Chi-restraints excluded: chain j residue 11 LYS Chi-restraints excluded: chain j residue 17 ILE Chi-restraints excluded: chain j residue 44 THR Chi-restraints excluded: chain j residue 47 SER Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 55 VAL Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 25 ILE Chi-restraints excluded: chain k residue 42 ASN Chi-restraints excluded: chain k residue 60 SER Chi-restraints excluded: chain k residue 82 LYS Chi-restraints excluded: chain k residue 112 ILE Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 16 VAL Chi-restraints excluded: chain l residue 29 ASN Chi-restraints excluded: chain l residue 40 SER Chi-restraints excluded: chain l residue 42 GLN Chi-restraints excluded: chain l residue 47 CYS Chi-restraints excluded: chain l residue 48 THR Chi-restraints excluded: chain l residue 62 LEU Chi-restraints excluded: chain l residue 106 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain m residue 31 GLN Chi-restraints excluded: chain m residue 45 VAL Chi-restraints excluded: chain m residue 85 SER Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 18 VAL Chi-restraints excluded: chain n residue 19 GLN Chi-restraints excluded: chain n residue 22 THR Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain o residue 66 LEU Chi-restraints excluded: chain p residue 10 MET Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 25 SER Chi-restraints excluded: chain p residue 30 ASP Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain q residue 16 SER Chi-restraints excluded: chain q residue 24 THR Chi-restraints excluded: chain q residue 26 VAL Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 63 ILE Chi-restraints excluded: chain r residue 16 CYS Chi-restraints excluded: chain r residue 21 ASN Chi-restraints excluded: chain r residue 30 ASP Chi-restraints excluded: chain r residue 53 ASN Chi-restraints excluded: chain r residue 60 LEU Chi-restraints excluded: chain r residue 70 MET Chi-restraints excluded: chain s residue 31 VAL Chi-restraints excluded: chain t residue 14 ASN Chi-restraints excluded: chain t residue 34 GLN Chi-restraints excluded: chain u residue 5 CYS Chi-restraints excluded: chain u residue 12 THR Chi-restraints excluded: chain u residue 25 SER Chi-restraints excluded: chain u residue 39 LEU Chi-restraints excluded: chain u residue 40 VAL Chi-restraints excluded: chain u residue 59 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 976 random chunks: chunk 474 optimal weight: 20.0000 chunk 615 optimal weight: 30.0000 chunk 824 optimal weight: 8.9990 chunk 237 optimal weight: 8.9990 chunk 713 optimal weight: 10.0000 chunk 114 optimal weight: 0.9990 chunk 215 optimal weight: 0.0170 chunk 775 optimal weight: 5.9990 chunk 324 optimal weight: 20.0000 chunk 796 optimal weight: 0.4980 chunk 98 optimal weight: 4.9990 overall best weight: 2.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 60 GLN E 75 GLN E 82 GLN ** G 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** O 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 41 GLN Q 37 GLN ** R 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 68 ASN S 97 ASN U 67 ASN ** Y 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 103 ASN ** c 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN l 59 ASN ** n 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 77 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 15 ASN ** t 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.079983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.057372 restraints weight = 529755.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.058761 restraints weight = 189817.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.058623 restraints weight = 128383.994| |-----------------------------------------------------------------------------| r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 155558 Z= 0.181 Angle : 0.626 16.316 233440 Z= 0.321 Chirality : 0.034 0.304 29944 Planarity : 0.004 0.075 11973 Dihedral : 24.225 179.735 79599 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.99 % Favored : 92.95 % Rotamer: Outliers : 4.89 % Allowed : 30.60 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.06 (0.11), residues: 5176 helix: 0.34 (0.13), residues: 1610 sheet: -0.57 (0.16), residues: 981 loop : -1.41 (0.12), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 65 HIS 0.009 0.001 HIS s 14 PHE 0.034 0.002 PHE L 50 TYR 0.023 0.002 TYR g 18 ARG 0.015 0.001 ARG k 130 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 44617.84 seconds wall clock time: 776 minutes 2.32 seconds (46562.32 seconds total)