Starting phenix.real_space_refine on Wed Mar 20 05:54:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8aye_15712/03_2024/8aye_15712_neut_updated.pdb" } resolution = 1.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.125 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4475 5.49 5 Mg 308 5.21 5 S 147 5.16 5 C 70313 2.51 5 N 26115 2.21 5 O 38845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 20": "OD1" <-> "OD2" Residue "3 GLU 30": "OE1" <-> "OE2" Residue "4 ASP 4": "OD1" <-> "OD2" Residue "B GLU 44": "OE1" <-> "OE2" Residue "B PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 140": "OE1" <-> "OE2" Residue "B GLU 142": "OE1" <-> "OE2" Residue "B GLU 145": "OE1" <-> "OE2" Residue "B ASP 167": "OD1" <-> "OD2" Residue "B GLU 169": "OE1" <-> "OE2" Residue "B ASP 197": "OD1" <-> "OD2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "B GLU 223": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "C ASP 34": "OD1" <-> "OD2" Residue "C GLU 46": "OE1" <-> "OE2" Residue "C GLU 85": "OE1" <-> "OE2" Residue "C GLU 110": "OE1" <-> "OE2" Residue "C ASP 118": "OD1" <-> "OD2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 152": "OE1" <-> "OE2" Residue "C GLU 161": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D GLU 88": "OE1" <-> "OE2" Residue "D TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 160": "OE1" <-> "OE2" Residue "D GLU 163": "OE1" <-> "OE2" Residue "D PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 202": "OE1" <-> "OE2" Residue "E PHE 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 65": "OE1" <-> "OE2" Residue "F TYR 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 73": "OE1" <-> "OE2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "G ASP 15": "OD1" <-> "OD2" Residue "G GLU 40": "OE1" <-> "OE2" Residue "G GLU 48": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "G PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 74": "OE1" <-> "OE2" Residue "G GLU 106": "OE1" <-> "OE2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G ASP 140": "OD1" <-> "OD2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "H GLU 42": "OE1" <-> "OE2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H GLU 52": "OE1" <-> "OE2" Residue "H ASP 54": "OD1" <-> "OD2" Residue "H GLU 58": "OE1" <-> "OE2" Residue "H GLU 124": "OE1" <-> "OE2" Residue "I GLU 89": "OE1" <-> "OE2" Residue "I ASP 107": "OD1" <-> "OD2" Residue "J GLU 27": "OE1" <-> "OE2" Residue "J GLU 47": "OE1" <-> "OE2" Residue "J ASP 60": "OD1" <-> "OD2" Residue "K ASP 18": "OD1" <-> "OD2" Residue "K ASP 36": "OD1" <-> "OD2" Residue "K GLU 76": "OE1" <-> "OE2" Residue "K TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 112": "OD1" <-> "OD2" Residue "L GLU 62": "OE1" <-> "OE2" Residue "L ASP 109": "OD1" <-> "OD2" Residue "M ASP 11": "OD1" <-> "OD2" Residue "M GLU 66": "OE1" <-> "OE2" Residue "M ASP 68": "OD1" <-> "OD2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 14": "OE1" <-> "OE2" Residue "O GLU 45": "OE1" <-> "OE2" Residue "O ASP 68": "OD1" <-> "OD2" Residue "O GLU 83": "OE1" <-> "OE2" Residue "P PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 34": "OE1" <-> "OE2" Residue "P GLU 48": "OE1" <-> "OE2" Residue "P ASP 53": "OD1" <-> "OD2" Residue "Q GLU 26": "OE1" <-> "OE2" Residue "Q GLU 52": "OE1" <-> "OE2" Residue "Q GLU 60": "OE1" <-> "OE2" Residue "R PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "S ASP 27": "OD1" <-> "OD2" Residue "T GLU 15": "OE1" <-> "OE2" Residue "T ASP 59": "OD1" <-> "OD2" Residue "U GLU 39": "OE1" <-> "OE2" Residue "c GLU 35": "OE1" <-> "OE2" Residue "c ASP 72": "OD1" <-> "OD2" Residue "c GLU 79": "OE1" <-> "OE2" Residue "c GLU 82": "OE1" <-> "OE2" Residue "c ASP 168": "OD1" <-> "OD2" Residue "c TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 194": "OE1" <-> "OE2" Residue "c GLU 199": "OE1" <-> "OE2" Residue "d ASP 18": "OD1" <-> "OD2" Residue "d GLU 30": "OE1" <-> "OE2" Residue "d GLU 89": "OE1" <-> "OE2" Residue "d ASP 103": "OD1" <-> "OD2" Residue "d ASP 200": "OD1" <-> "OD2" Residue "e ASP 7": "OD1" <-> "OD2" Residue "e GLU 25": "OE1" <-> "OE2" Residue "e TYR 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 51": "OE1" <-> "OE2" Residue "e ASP 91": "OD1" <-> "OD2" Residue "e GLU 111": "OE1" <-> "OE2" Residue "e GLU 144": "OE1" <-> "OE2" Residue "e ASP 145": "OD1" <-> "OD2" Residue "e GLU 155": "OE1" <-> "OE2" Residue "e PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 19": "OE1" <-> "OE2" Residue "f GLU 32": "OE1" <-> "OE2" Residue "f ASP 56": "OD1" <-> "OD2" Residue "f GLU 98": "OE1" <-> "OE2" Residue "f GLU 101": "OE1" <-> "OE2" Residue "f ASP 113": "OD1" <-> "OD2" Residue "f PHE 122": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ASP 123": "OD1" <-> "OD2" Residue "f TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 140": "OE1" <-> "OE2" Residue "f ASP 147": "OD1" <-> "OD2" Residue "f ASP 163": "OD1" <-> "OD2" Residue "f GLU 164": "OE1" <-> "OE2" Residue "g GLU 42": "OE1" <-> "OE2" Residue "g GLU 155": "OE1" <-> "OE2" Residue "g GLU 173": "OE1" <-> "OE2" Residue "h PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i TYR 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 31": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "i GLU 91": "OE1" <-> "OE2" Residue "i GLU 98": "OE1" <-> "OE2" Residue "i GLU 102": "OE1" <-> "OE2" Residue "i GLU 129": "OE1" <-> "OE2" Residue "j ASP 80": "OD1" <-> "OD2" Residue "j GLU 92": "OE1" <-> "OE2" Residue "j GLU 110": "OE1" <-> "OE2" Residue "j GLU 121": "OE1" <-> "OE2" Residue "k GLU 51": "OE1" <-> "OE2" Residue "k PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k GLU 86": "OE1" <-> "OE2" Residue "l GLU 47": "OE1" <-> "OE2" Residue "l PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "l ASP 70": "OD1" <-> "OD2" Residue "l GLU 75": "OE1" <-> "OE2" Residue "l GLU 104": "OE1" <-> "OE2" Residue "l ASP 106": "OD1" <-> "OD2" Residue "m GLU 74": "OE1" <-> "OE2" Residue "m GLU 82": "OE1" <-> "OE2" Residue "n ASP 2": "OD1" <-> "OD2" Residue "n ASP 69": "OD1" <-> "OD2" Residue "n GLU 84": "OE1" <-> "OE2" Residue "n PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 9": "OE1" <-> "OE2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o GLU 112": "OE1" <-> "OE2" Residue "p TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q GLU 16": "OE1" <-> "OE2" Residue "q GLU 46": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r GLU 78": "OE1" <-> "OE2" Residue "r ASP 109": "OD1" <-> "OD2" Residue "s GLU 25": "OE1" <-> "OE2" Residue "t ASP 8": "OD1" <-> "OD2" Residue "t PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 11": "OE1" <-> "OE2" Residue "u GLU 41": "OE1" <-> "OE2" Residue "u ASP 43": "OD1" <-> "OD2" Residue "u GLU 59": "OE1" <-> "OE2" Residue "u ASP 76": "OD1" <-> "OD2" Residue "v GLU 70": "OE1" <-> "OE2" Residue "w GLU 41": "OE1" <-> "OE2" Residue "w GLU 43": "OE1" <-> "OE2" Residue "w ASP 60": "OD1" <-> "OD2" Residue "x GLU 5": "OE1" <-> "OE2" Residue "x GLU 8": "OE1" <-> "OE2" Residue "x GLU 12": "OE1" <-> "OE2" Residue "x GLU 13": "OE1" <-> "OE2" Residue "x GLU 17": "OE1" <-> "OE2" Residue "x GLU 24": "OE1" <-> "OE2" Residue "y GLU 37": "OE1" <-> "OE2" Residue "y GLU 39": "OE1" <-> "OE2" Residue "y ASP 40": "OD1" <-> "OD2" Residue "y GLU 58": "OE1" <-> "OE2" Residue "z ASP 46": "OD1" <-> "OD2" 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: 140205 Number of models: 1 Model: "" Number of chains: 67 Chain: "0" Number of atoms: 417 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 417 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "2" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "3" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "4" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 480 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 2, 'TRANS': 57} Chain breaks: 1 Chain: "5" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 42 Classifications: {'RNA': 2} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1} Link IDs: {'rna2p': 1} Chain: "A" Number of atoms: 32612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1519, 32612 Classifications: {'RNA': 1519} Modifications used: {'rna2p': 1, 'rna2p_pur': 121, 'rna2p_pyr': 80, 'rna3p': 10, 'rna3p_pur': 741, 'rna3p_pyr': 566} Link IDs: {'rna2p': 202, 'rna3p': 1316} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "D" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "E" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "F" Number of atoms: 839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 839 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "G" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1203 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 5, 'TRANS': 147} Chain: "H" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 92} Chain: "K" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "L" Number of atoms: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 955 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} Chain: "M" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "O" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "P" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "Q" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 641 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "R" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "S" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 668 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 5, 'TRANS': 78} Chain: "T" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 670 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "U" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "X" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 131 Classifications: {'RNA': 6} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna3p': 5} Chain: "Z" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1623 Classifications: {'RNA': 76} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 32, 'rna3p_pyr': 33} Link IDs: {'rna2p': 10, 'rna3p': 65} Chain: "a" Number of atoms: 59129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2753, 59129 Classifications: {'RNA': 2753} Modifications used: {'rna2p': 6, 'rna2p_pur': 267, 'rna2p_pyr': 141, 'rna3p': 16, 'rna3p_pur': 1318, 'rna3p_pyr': 1005} Link IDs: {'rna2p': 413, 'rna3p': 2339} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 9 Chain: "b" Number of atoms: 2549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 2549 Classifications: {'RNA': 119} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 49} Link IDs: {'rna2p': 13, 'rna3p': 105} Chain: "c" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "d" Number of atoms: 1566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1566 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEQ:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "e" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "f" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "g" Number of atoms: 1323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1323 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "h" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 303 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "i" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "j" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "k" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "l" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "m" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 945 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "n" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "o" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "p" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "r" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "s" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "t" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "u" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "v" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 586 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "w" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "x" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "y" Number of atoms: 449 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 449 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "z" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "3" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 133 Unusual residues: {' MG': 89, 'T8B': 1} Classifications: {'undetermined': 90} Link IDs: {None: 89} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 207 Unusual residues: {' MG': 207} Classifications: {'undetermined': 207} Link IDs: {None: 206} Chain: "b" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "k" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1383 SG CYS 3 11 46.991 110.875 136.548 1.00 24.76 S ATOM 1408 SG CYS 3 14 48.622 111.768 132.964 1.00 17.23 S ATOM 1511 SG CYS 3 27 46.435 114.161 135.148 1.00 19.11 S ATOM 1730 SG CYS 4 16 109.410 23.936 166.287 1.00 33.57 S ATOM 1742 SG CYS 4 18 106.736 21.282 167.049 1.00 39.57 S ATOM 1884 SG CYS 4 37 106.282 23.475 163.932 1.00 40.43 S ATOM 1905 SG CYS 4 40 106.156 24.990 167.355 1.00 32.66 S Time building chain proxies: 53.01, per 1000 atoms: 0.38 Number of scatterers: 140205 At special positions: 0 Unit cell: (216.58, 248.234, 272.391, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 147 16.00 P 4475 15.00 Mg 308 11.99 O 38845 8.00 N 26115 7.00 C 70313 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: 61.18 Conformation dependent library (CDL) restraints added in 7.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 3 101 " pdb="ZN ZN 3 101 " - pdb=" ND1 HIS 3 33 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " pdb=" ZN 4 101 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 16 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 40 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 18 " pdb="ZN ZN 4 101 " - pdb=" SG CYS 4 37 " Number of angles added : 9 10964 Ramachandran restraints generated. 5482 Oldfield, 0 Emsley, 5482 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10262 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 176 helices and 71 sheets defined 39.6% alpha, 19.9% beta 1559 base pairs and 2302 stacking pairs defined. Time for finding SS restraints: 70.60 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.154A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N LYS 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) Processing helix chain '1' and resid 26 through 38 Processing helix chain '2' and resid 7 through 14 removed outlier: 3.544A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 32 through 37 removed outlier: 4.543A pdb=" N LYS 2 36 " --> pdb=" O ILE 2 32 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ALA 2 37 " --> pdb=" O LEU 2 33 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 32 through 37' Processing helix chain '2' and resid 38 through 46 Proline residue: 2 46 - end of helix Processing helix chain '2' and resid 51 through 63 removed outlier: 4.558A pdb=" N GLY 2 56 " --> pdb=" O LYS 2 52 " (cutoff:3.500A) removed outlier: 5.146A pdb=" N LEU 2 57 " --> pdb=" O GLY 2 53 " (cutoff:3.500A) Proline residue: 2 63 - end of helix Processing helix chain '4' and resid 41 through 46 Processing helix chain '4' and resid 55 through 65 removed outlier: 3.846A pdb=" N ARG 4 59 " --> pdb=" O GLY 4 55 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN 4 65 " --> pdb=" O ASN 4 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 13 Processing helix chain 'B' and resid 24 through 32 removed outlier: 4.161A pdb=" N LYS B 28 " --> pdb=" O ASN B 24 " (cutoff:3.500A) Proline residue: B 29 - end of helix removed outlier: 5.555A pdb=" N PHE B 32 " --> pdb=" O LYS B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 24 through 32' Processing helix chain 'B' and resid 42 through 64 Proline residue: B 48 - end of helix removed outlier: 3.689A pdb=" N LYS B 64 " --> pdb=" O ILE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 88 Processing helix chain 'B' and resid 103 through 124 removed outlier: 4.513A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 130 removed outlier: 4.138A pdb=" N LEU B 129 " --> pdb=" O THR B 125 " (cutoff:3.500A) removed outlier: 5.621A pdb=" N THR B 130 " --> pdb=" O PHE B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 130' Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 165 through 170 Processing helix chain 'B' and resid 171 through 180 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 6 through 12 removed outlier: 3.857A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 48 Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 113 removed outlier: 4.148A pdb=" N ASP C 112 " --> pdb=" O LYS C 108 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ALA C 113 " --> pdb=" O PRO C 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 108 through 113' Processing helix chain 'C' and resid 114 through 127 Processing helix chain 'C' and resid 129 through 145 Processing helix chain 'D' and resid 7 through 16 removed outlier: 4.364A pdb=" N LEU D 11 " --> pdb=" O PRO D 7 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER D 12 " --> pdb=" O LYS D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 27 through 32 removed outlier: 3.581A pdb=" N LYS D 31 " --> pdb=" O ALA D 27 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 66 Processing helix chain 'D' and resid 68 through 83 removed outlier: 5.286A pdb=" N LYS D 83 " --> pdb=" O ALA D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.583A pdb=" N ARG D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 106 Processing helix chain 'D' and resid 110 through 121 removed outlier: 3.567A pdb=" N LYS D 121 " --> pdb=" O LEU D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 146 through 151 removed outlier: 4.648A pdb=" N LYS D 151 " --> pdb=" O GLU D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 166 removed outlier: 3.572A pdb=" N LYS D 156 " --> pdb=" O GLN D 152 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N GLU D 166 " --> pdb=" O ALA D 162 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 192 removed outlier: 3.828A pdb=" N LEU D 191 " --> pdb=" O GLU D 187 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER D 192 " --> pdb=" O ARG D 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 187 through 192' Processing helix chain 'D' and resid 196 through 206 removed outlier: 3.854A pdb=" N ILE D 200 " --> pdb=" O ASN D 196 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 71 removed outlier: 3.740A pdb=" N MET E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 119 removed outlier: 4.505A pdb=" N ALA E 113 " --> pdb=" O GLY E 109 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL E 114 " --> pdb=" O ALA E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 148 removed outlier: 5.851A pdb=" N ASN E 148 " --> pdb=" O LEU E 144 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 158 Processing helix chain 'E' and resid 160 through 165 Processing helix chain 'F' and resid 14 through 33 removed outlier: 3.803A pdb=" N VAL F 18 " --> pdb=" O GLN F 14 " (cutoff:3.500A) Proline residue: F 19 - end of helix Processing helix chain 'F' and resid 67 through 81 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 70 Processing helix chain 'G' and resid 92 through 112 removed outlier: 5.610A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 130 Processing helix chain 'G' and resid 132 through 153 removed outlier: 5.245A pdb=" N ALA G 150 " --> pdb=" O GLU G 146 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N PHE G 151 " --> pdb=" O ALA G 147 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA G 152 " --> pdb=" O ASN G 148 " (cutoff:3.500A) removed outlier: 5.370A pdb=" N HIS G 153 " --> pdb=" O LYS G 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 21 Processing helix chain 'H' and resid 30 through 44 Processing helix chain 'H' and resid 112 through 120 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 56 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 80 through 91 removed outlier: 3.797A pdb=" N VAL J 84 " --> pdb=" O THR J 80 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU J 90 " --> pdb=" O ALA J 86 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASP J 91 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 46 through 51 removed outlier: 4.329A pdb=" N GLY K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 59 removed outlier: 3.926A pdb=" N SER K 58 " --> pdb=" O GLY K 54 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N THR K 59 " --> pdb=" O SER K 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 54 through 59' Processing helix chain 'K' and resid 60 through 75 Processing helix chain 'K' and resid 92 through 104 removed outlier: 3.935A pdb=" N THR K 96 " --> pdb=" O GLY K 92 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N ILE K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY K 104 " --> pdb=" O LEU K 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 3 through 11 Proline residue: L 11 - end of helix Processing helix chain 'L' and resid 113 through 118 removed outlier: 3.788A pdb=" N TYR L 117 " --> pdb=" O ALA L 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 22 removed outlier: 4.030A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ILE M 22 " --> pdb=" O ALA M 18 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 44 through 49 removed outlier: 3.744A pdb=" N LEU M 48 " --> pdb=" O LYS M 44 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N SER M 49 " --> pdb=" O ILE M 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 44 through 49' Processing helix chain 'M' and resid 50 through 64 removed outlier: 3.755A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL M 64 " --> pdb=" O VAL M 60 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 21 Processing helix chain 'N' and resid 22 through 33 Processing helix chain 'N' and resid 37 through 51 removed outlier: 3.709A pdb=" N THR N 50 " --> pdb=" O LEU N 46 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 80 through 91 Processing helix chain 'N' and resid 52 through 57 Proline residue: N 57 - end of helix Processing helix chain 'O' and resid 4 through 16 Processing helix chain 'O' and resid 24 through 43 removed outlier: 4.232A pdb=" N GLY O 41 " --> pdb=" O ASN O 37 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N HIS O 42 " --> pdb=" O HIS O 38 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 74 removed outlier: 3.775A pdb=" N GLY O 55 " --> pdb=" O HIS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 75 through 86 Processing helix chain 'P' and resid 53 through 64 Processing helix chain 'P' and resid 68 through 80 removed outlier: 3.566A pdb=" N LYS P 80 " --> pdb=" O LYS P 76 " (cutoff:3.500A) Processing helix chain 'R' and resid 11 through 17 removed outlier: 3.634A pdb=" N GLU R 16 " --> pdb=" O ARG R 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 25 through 34 removed outlier: 4.036A pdb=" N ASN R 31 " --> pdb=" O ALA R 27 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N TYR R 32 " --> pdb=" O THR R 28 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N THR R 34 " --> pdb=" O LYS R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 46 Processing helix chain 'R' and resid 48 through 66 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 70 through 76 removed outlier: 4.326A pdb=" N PHE S 74 " --> pdb=" O LYS S 70 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ALA S 75 " --> pdb=" O LEU S 71 " (cutoff:3.500A) Proline residue: S 76 - end of helix No H-bonds generated for 'chain 'S' and resid 70 through 76' Processing helix chain 'T' and resid 4 through 41 Processing helix chain 'T' and resid 44 through 65 Proline residue: T 56 - end of helix Processing helix chain 'T' and resid 68 through 87 removed outlier: 3.581A pdb=" N ALA T 87 " --> pdb=" O ILE T 83 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 27 Processing helix chain 'U' and resid 28 through 37 removed outlier: 4.759A pdb=" N PHE U 37 " --> pdb=" O ARG U 33 " (cutoff:3.500A) Processing helix chain 'U' and resid 40 through 69 removed outlier: 4.266A pdb=" N ARG U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR U 68 " --> pdb=" O ASN U 64 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N ARG U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 15 removed outlier: 4.788A pdb=" N HIS c 15 " --> pdb=" O PRO c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 35 removed outlier: 3.810A pdb=" N LEU c 34 " --> pdb=" O PHE c 30 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N GLU c 35 " --> pdb=" O ALA c 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 30 through 35' Processing helix chain 'c' and resid 131 through 136 removed outlier: 3.760A pdb=" N ILE c 135 " --> pdb=" O PRO c 131 " (cutoff:3.500A) Proline residue: c 136 - end of helix No H-bonds generated for 'chain 'c' and resid 131 through 136' Processing helix chain 'c' and resid 207 through 215 removed outlier: 3.836A pdb=" N ALA c 211 " --> pdb=" O LYS c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 221 through 226 removed outlier: 3.955A pdb=" N MET c 225 " --> pdb=" O ARG c 221 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASN c 226 " --> pdb=" O GLY c 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 221 through 226' Processing helix chain 'c' and resid 260 through 268 removed outlier: 4.746A pdb=" N LYS c 265 " --> pdb=" O LYS c 261 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N PHE c 266 " --> pdb=" O ARG c 262 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE c 267 " --> pdb=" O THR c 263 " (cutoff:3.500A) removed outlier: 5.551A pdb=" N VAL c 268 " --> pdb=" O ASP c 264 " (cutoff:3.500A) Processing helix chain 'd' and resid 56 through 61 removed outlier: 5.281A pdb=" N THR d 61 " --> pdb=" O ALA d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 62 through 72 Processing helix chain 'd' and resid 98 through 103 removed outlier: 4.293A pdb=" N ALA d 102 " --> pdb=" O VAL d 98 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N ASP d 103 " --> pdb=" O GLU d 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 98 through 103' Processing helix chain 'd' and resid 120 through 125 Processing helix chain 'd' and resid 39 through 44 Processing helix chain 'e' and resid 15 through 20 Processing helix chain 'e' and resid 24 through 40 removed outlier: 3.640A pdb=" N ARG e 40 " --> pdb=" O ALA e 36 " (cutoff:3.500A) Processing helix chain 'e' and resid 48 through 53 removed outlier: 6.474A pdb=" N THR e 53 " --> pdb=" O ARG e 49 " (cutoff:3.500A) Processing helix chain 'e' and resid 97 through 116 Processing helix chain 'e' and resid 130 through 142 Processing helix chain 'e' and resid 154 through 163 removed outlier: 4.541A pdb=" N ASN e 163 " --> pdb=" O LEU e 159 " (cutoff:3.500A) Processing helix chain 'e' and resid 176 through 183 removed outlier: 3.614A pdb=" N ILE e 181 " --> pdb=" O PRO e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 189 through 201 Processing helix chain 'f' and resid 2 through 21 removed outlier: 4.661A pdb=" N VAL f 13 " --> pdb=" O LYS f 9 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N LYS f 14 " --> pdb=" O ASP f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 46 through 62 removed outlier: 4.025A pdb=" N LEU f 50 " --> pdb=" O ASP f 46 " (cutoff:3.500A) Processing helix chain 'f' and resid 93 through 111 removed outlier: 4.562A pdb=" N VAL f 108 " --> pdb=" O ILE f 104 " (cutoff:3.500A) Proline residue: f 109 - end of helix Processing helix chain 'f' and resid 162 through 174 removed outlier: 3.754A pdb=" N PHE f 173 " --> pdb=" O LEU f 169 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP f 174 " --> pdb=" O LEU f 170 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 45 removed outlier: 3.869A pdb=" N ALA f 45 " --> pdb=" O GLU f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 134 through 139 Proline residue: f 139 - end of helix Processing helix chain 'g' and resid 2 through 8 Proline residue: g 8 - end of helix Processing helix chain 'g' and resid 60 through 81 removed outlier: 3.606A pdb=" N THR g 80 " --> pdb=" O VAL g 76 " (cutoff:3.500A) Processing helix chain 'g' and resid 137 through 153 removed outlier: 3.546A pdb=" N TYR g 151 " --> pdb=" O ASP g 147 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ARG g 152 " --> pdb=" O LEU g 148 " (cutoff:3.500A) Processing helix chain 'h' and resid 22 through 28 Processing helix chain 'h' and resid 29 through 34 Processing helix chain 'i' and resid 24 through 38 removed outlier: 3.800A pdb=" N GLU i 31 " --> pdb=" O ARG i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 88 through 96 Processing helix chain 'i' and resid 97 through 110 removed outlier: 4.185A pdb=" N ILE i 101 " --> pdb=" O PRO i 97 " (cutoff:3.500A) Proline residue: i 110 - end of helix Processing helix chain 'i' and resid 112 through 122 removed outlier: 3.847A pdb=" N LYS i 121 " --> pdb=" O ALA i 117 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU i 122 " --> pdb=" O MET i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 67 through 72 removed outlier: 4.413A pdb=" N LYS i 72 " --> pdb=" O ASN i 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 67 through 72' Processing helix chain 'j' and resid 104 through 109 removed outlier: 4.619A pdb=" N ARG j 108 " --> pdb=" O THR j 104 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N SER j 109 " --> pdb=" O ARG j 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 104 through 109' Processing helix chain 'j' and resid 112 through 119 Processing helix chain 'k' and resid 37 through 42 removed outlier: 3.842A pdb=" N ARG k 41 " --> pdb=" O GLY k 37 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N SER k 42 " --> pdb=" O GLN k 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 37 through 42' Processing helix chain 'k' and resid 56 through 62 Proline residue: k 62 - end of helix Processing helix chain 'k' and resid 68 through 75 removed outlier: 3.804A pdb=" N ALA k 72 " --> pdb=" O SER k 68 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N ILE k 73 " --> pdb=" O ARG k 69 " (cutoff:3.500A) removed outlier: 5.402A pdb=" N ALA k 75 " --> pdb=" O ALA k 71 " (cutoff:3.500A) Processing helix chain 'k' and resid 78 through 85 removed outlier: 3.728A pdb=" N LEU k 82 " --> pdb=" O ARG k 78 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ALA k 83 " --> pdb=" O LEU k 79 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LYS k 84 " --> pdb=" O SER k 80 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL k 85 " --> pdb=" O ASP k 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 78 through 85' Processing helix chain 'k' and resid 91 through 99 Processing helix chain 'k' and resid 128 through 139 Processing helix chain 'l' and resid 42 through 58 Processing helix chain 'l' and resid 109 through 125 removed outlier: 4.102A pdb=" N LYS l 123 " --> pdb=" O LEU l 119 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU l 124 " --> pdb=" O ALA l 120 " (cutoff:3.500A) Proline residue: l 125 - end of helix Processing helix chain 'm' and resid 13 through 32 Processing helix chain 'm' and resid 38 through 58 removed outlier: 4.182A pdb=" N ARG m 46 " --> pdb=" O LYS m 42 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL m 47 " --> pdb=" O GLU m 43 " (cutoff:3.500A) Proline residue: m 50 - end of helix removed outlier: 4.362A pdb=" N THR m 57 " --> pdb=" O THR m 53 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N ASP m 58 " --> pdb=" O LEU m 54 " (cutoff:3.500A) Processing helix chain 'm' and resid 59 through 71 removed outlier: 3.937A pdb=" N THR m 70 " --> pdb=" O ALA m 66 " (cutoff:3.500A) Processing helix chain 'm' and resid 72 through 88 removed outlier: 4.877A pdb=" N GLY m 84 " --> pdb=" O PHE m 80 " (cutoff:3.500A) Proline residue: m 85 - end of helix Processing helix chain 'n' and resid 2 through 22 removed outlier: 4.446A pdb=" N ALA n 6 " --> pdb=" O ASP n 2 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ARG n 13 " --> pdb=" O ARG n 9 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 55 through 63 removed outlier: 5.041A pdb=" N GLN n 61 " --> pdb=" O ALA n 57 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU n 62 " --> pdb=" O ILE n 58 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LYS n 63 " --> pdb=" O ALA n 59 " (cutoff:3.500A) Processing helix chain 'n' and resid 67 through 86 Processing helix chain 'n' and resid 101 through 114 Processing helix chain 'o' and resid 2 through 13 removed outlier: 4.048A pdb=" N GLN o 12 " --> pdb=" O LEU o 8 " (cutoff:3.500A) Processing helix chain 'o' and resid 97 through 104 removed outlier: 4.397A pdb=" N ARG o 101 " --> pdb=" O LEU o 97 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLU o 102 " --> pdb=" O TYR o 98 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ARG o 103 " --> pdb=" O TYR o 99 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 97 through 104' Processing helix chain 'p' and resid 6 through 22 removed outlier: 3.590A pdb=" N LYS p 22 " --> pdb=" O LEU p 18 " (cutoff:3.500A) Processing helix chain 'p' and resid 26 through 31 removed outlier: 3.661A pdb=" N ARG p 30 " --> pdb=" O GLY p 26 " (cutoff:3.500A) Processing helix chain 'p' and resid 32 through 37 removed outlier: 3.602A pdb=" N GLN p 37 " --> pdb=" O ARG p 33 " (cutoff:3.500A) Processing helix chain 'p' and resid 39 through 73 removed outlier: 3.866A pdb=" N ARG p 51 " --> pdb=" O TYR p 47 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ARG p 55 " --> pdb=" O ARG p 51 " (cutoff:3.500A) Processing helix chain 'p' and resid 75 through 87 Processing helix chain 'p' and resid 91 through 102 Processing helix chain 'p' and resid 103 through 118 Processing helix chain 'r' and resid 13 through 25 removed outlier: 3.801A pdb=" N VAL r 20 " --> pdb=" O LYS r 16 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE r 24 " --> pdb=" O VAL r 20 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 40 removed outlier: 5.659A pdb=" N ASN r 40 " --> pdb=" O LEU r 36 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 61 removed outlier: 3.605A pdb=" N VAL r 45 " --> pdb=" O LYS r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 70 removed outlier: 3.629A pdb=" N LEU r 69 " --> pdb=" O ASP r 65 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N LYS r 70 " --> pdb=" O ILE r 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 65 through 70' Processing helix chain 's' and resid 3 through 11 removed outlier: 3.667A pdb=" N LYS s 9 " --> pdb=" O GLU s 5 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N LEU s 11 " --> pdb=" O LEU s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 17 through 27 Processing helix chain 's' and resid 39 through 50 Processing helix chain 't' and resid 66 through 71 removed outlier: 3.795A pdb=" N VAL t 70 " --> pdb=" O GLN t 66 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ALA t 71 " --> pdb=" O VAL t 67 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 66 through 71' Processing helix chain 'u' and resid 13 through 24 Processing helix chain 'u' and resid 43 through 53 removed outlier: 4.349A pdb=" N LYS u 53 " --> pdb=" O ASN u 49 " (cutoff:3.500A) Processing helix chain 'u' and resid 54 through 59 removed outlier: 3.885A pdb=" N SER u 58 " --> pdb=" O ALA u 54 " (cutoff:3.500A) Processing helix chain 'w' and resid 52 through 63 Processing helix chain 'w' and resid 64 through 75 Processing helix chain 'x' and resid 2 through 10 removed outlier: 3.563A pdb=" N GLU x 8 " --> pdb=" O LYS x 4 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LYS x 9 " --> pdb=" O GLU x 5 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N SER x 10 " --> pdb=" O LEU x 6 " (cutoff:3.500A) Processing helix chain 'x' and resid 11 through 35 Processing helix chain 'x' and resid 39 through 62 removed outlier: 4.552A pdb=" N LEU x 43 " --> pdb=" O GLN x 39 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N LYS x 44 " --> pdb=" O SER x 40 " (cutoff:3.500A) Processing helix chain 'y' and resid 17 through 28 Processing helix chain 'y' and resid 41 through 52 Processing helix chain 'z' and resid 9 through 19 removed outlier: 4.752A pdb=" N HIS z 19 " --> pdb=" O MET z 15 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 19 through 24 removed outlier: 5.916A pdb=" N HIS 0 19 " --> pdb=" O SER 0 13 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE 0 48 " --> pdb=" O SER 0 14 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU 0 34 " --> pdb=" O GLU 0 51 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 22 through 25 removed outlier: 5.673A pdb=" N PHE 2 22 " --> pdb=" O VAL 2 50 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '3' and resid 14 through 19 Processing sheet with id= 4, first strand: chain '4' and resid 11 through 15 Processing sheet with id= 5, first strand: chain 'B' and resid 15 through 18 removed outlier: 5.480A pdb=" N HIS B 15 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.869A pdb=" N HIS B 39 " --> pdb=" O GLY B 17 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 89 through 93 Processing sheet with id= 7, first strand: chain 'C' and resid 54 through 59 removed outlier: 3.812A pdb=" N ARG C 54 " --> pdb=" O HIS C 69 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 164 through 170 removed outlier: 5.945A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 141 through 145 removed outlier: 3.716A pdb=" N ASP D 141 " --> pdb=" O PHE D 182 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET D 178 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU D 179 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 12 through 16 removed outlier: 6.727A pdb=" N LEU E 36 " --> pdb=" O ILE E 16 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 83 through 88 removed outlier: 7.642A pdb=" N HIS E 83 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ALA E 99 " --> pdb=" O ASN E 122 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N ASN E 122 " --> pdb=" O ALA E 99 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 33 through 40 Processing sheet with id= 13, first strand: chain 'F' and resid 38 through 42 removed outlier: 5.862A pdb=" N TYR F 59 " --> pdb=" O TRP F 42 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N HIS F 3 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ARG F 86 " --> pdb=" O MET F 9 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'F' and resid 43 through 46 Processing sheet with id= 15, first strand: chain 'G' and resid 72 through 79 removed outlier: 6.359A pdb=" N THR G 72 " --> pdb=" O VAL G 91 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'H' and resid 23 through 29 removed outlier: 6.261A pdb=" N ALA H 23 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP H 48 " --> pdb=" O THR H 62 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.613A pdb=" N CYS H 127 " --> pdb=" O VAL H 103 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL H 103 " --> pdb=" O ILE H 126 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'I' and resid 5 through 11 Processing sheet with id= 19, first strand: chain 'I' and resid 26 through 30 removed outlier: 3.578A pdb=" N LYS I 27 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 39 through 42 removed outlier: 4.759A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 44 through 52 Processing sheet with id= 22, first strand: chain 'K' and resid 42 through 45 removed outlier: 7.101A pdb=" N VAL K 84 " --> pdb=" O THR K 108 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 29 through 33 removed outlier: 5.211A pdb=" N LEU L 81 " --> pdb=" O VAL L 98 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 36 through 41 removed outlier: 5.253A pdb=" N LYS L 51 " --> pdb=" O ILE L 67 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'P' and resid 4 through 10 removed outlier: 5.132A pdb=" N GLY P 49 " --> pdb=" O ASN P 40 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'Q' and resid 7 through 11 removed outlier: 6.682A pdb=" N GLU Q 60 " --> pdb=" O VAL Q 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Q' and resid 19 through 30 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'S' and resid 30 through 34 Processing sheet with id= 29, first strand: chain 'c' and resid 2 through 6 removed outlier: 5.545A pdb=" N VAL c 16 " --> pdb=" O CYS c 6 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'c' and resid 80 through 83 removed outlier: 3.535A pdb=" N ARG c 80 " --> pdb=" O LEU c 93 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU c 93 " --> pdb=" O GLU c 79 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N ILE c 74 " --> pdb=" O SER c 118 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N SER c 118 " --> pdb=" O ILE c 74 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N ASP c 114 " --> pdb=" O VAL c 78 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N GLY c 127 " --> pdb=" O GLN c 115 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N GLN c 117 " --> pdb=" O GLY c 127 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'c' and resid 138 through 142 removed outlier: 4.053A pdb=" N SER c 139 " --> pdb=" O ILE c 164 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N THR c 173 " --> pdb=" O VAL c 165 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU c 180 " --> pdb=" O LEU c 176 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'c' and resid 90 through 96 removed outlier: 5.466A pdb=" N ASN c 90 " --> pdb=" O ALA c 106 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU c 100 " --> pdb=" O TYR c 96 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'd' and resid 3 through 6 removed outlier: 3.976A pdb=" N GLU d 168 " --> pdb=" O SER d 113 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'd' and resid 10 through 16 removed outlier: 3.636A pdb=" N GLY d 10 " --> pdb=" O VAL d 26 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL d 20 " --> pdb=" O THR d 16 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'd' and resid 79 through 84 removed outlier: 5.849A pdb=" N ARG d 46 " --> pdb=" O LEU d 84 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN d 49 " --> pdb=" O THR d 35 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLN d 94 " --> pdb=" O VAL d 34 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 105 through 108 removed outlier: 6.562A pdb=" N LYS d 105 " --> pdb=" O VAL d 177 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'e' and resid 1 through 6 removed outlier: 4.227A pdb=" N SER e 10 " --> pdb=" O LEU e 5 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 117 through 120 removed outlier: 5.753A pdb=" N ARG e 117 " --> pdb=" O ASP e 184 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'f' and resid 65 through 69 removed outlier: 3.522A pdb=" N GLY f 86 " --> pdb=" O THR f 68 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N GLY f 39 " --> pdb=" O GLY f 151 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLY f 151 " --> pdb=" O GLY f 39 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 72 through 75 removed outlier: 6.702A pdb=" N LYS f 72 " --> pdb=" O GLN f 81 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N GLN f 81 " --> pdb=" O LYS f 72 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'g' and resid 15 through 20 removed outlier: 6.051A pdb=" N GLN g 22 " --> pdb=" O LEU g 37 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N GLY g 31 " --> pdb=" O GLY g 28 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'g' and resid 41 through 46 removed outlier: 4.450A pdb=" N ALA g 46 " --> pdb=" O THR g 49 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'g' and resid 94 through 99 removed outlier: 7.081A pdb=" N ASN g 101 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'g' and resid 121 through 125 removed outlier: 5.872A pdb=" N THR g 129 " --> pdb=" O LEU g 89 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'h' and resid 1 through 5 removed outlier: 4.606A pdb=" N ASP h 17 " --> pdb=" O LEU h 5 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'i' and resid 52 through 57 removed outlier: 4.785A pdb=" N ASP i 19 " --> pdb=" O LEU i 140 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'i' and resid 74 through 78 removed outlier: 7.345A pdb=" N GLY i 83 " --> pdb=" O THR i 78 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'j' and resid 56 through 60 removed outlier: 4.553A pdb=" N ASP j 56 " --> pdb=" O ILE j 43 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N LYS j 40 " --> pdb=" O ILE j 22 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR j 6 " --> pdb=" O CYS j 21 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N ASN j 82 " --> pdb=" O MET j 7 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'l' and resid 37 through 40 No H-bonds generated for sheet with id= 49 Processing sheet with id= 50, first strand: chain 'l' and resid 62 through 65 removed outlier: 3.553A pdb=" N TYR l 103 " --> pdb=" O LEU l 33 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU l 33 " --> pdb=" O LEU l 102 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N LYS l 100 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'l' and resid 30 through 36 removed outlier: 7.748A pdb=" N SER l 30 " --> pdb=" O LYS l 133 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LYS l 127 " --> pdb=" O VAL l 36 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'm' and resid 33 through 37 removed outlier: 5.637A pdb=" N ALA m 108 " --> pdb=" O PHE m 102 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N PHE m 102 " --> pdb=" O ALA m 108 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N MET m 110 " --> pdb=" O CYS m 100 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'n' and resid 49 through 52 removed outlier: 3.570A pdb=" N VAL n 49 " --> pdb=" O VAL n 39 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'o' and resid 38 through 45 removed outlier: 6.400A pdb=" N THR o 25 " --> pdb=" O LYS o 87 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER o 83 " --> pdb=" O LYS o 29 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'o' and resid 49 through 52 removed outlier: 3.676A pdb=" N ALA o 49 " --> pdb=" O THR o 60 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N SER o 57 " --> pdb=" O THR o 76 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'q' and resid 11 through 15 removed outlier: 3.581A pdb=" N MET q 40 " --> pdb=" O VAL q 4 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N LEU q 39 " --> pdb=" O GLY q 50 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N GLU q 46 " --> pdb=" O ASN q 43 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'q' and resid 18 through 23 removed outlier: 4.122A pdb=" N GLN q 18 " --> pdb=" O ILE q 98 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP q 95 " --> pdb=" O VAL q 64 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LYS q 60 " --> pdb=" O THR q 99 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLU q 31 " --> pdb=" O VAL q 63 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'q' and resid 57 through 60 Processing sheet with id= 59, first strand: chain 'q' and resid 65 through 68 Processing sheet with id= 60, first strand: chain 'q' and resid 71 through 78 removed outlier: 4.131A pdb=" N TYR q 83 " --> pdb=" O ARG q 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'r' and resid 2 through 8 Processing sheet with id= 62, first strand: chain 's' and resid 28 through 33 removed outlier: 6.207A pdb=" N ASN s 28 " --> pdb=" O LEU s 87 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LYS s 66 " --> pdb=" O ARG s 77 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N ASP s 79 " --> pdb=" O LYS s 64 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N LYS s 64 " --> pdb=" O ASP s 79 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS s 81 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL s 62 " --> pdb=" O LYS s 81 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA s 83 " --> pdb=" O THR s 60 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR s 60 " --> pdb=" O ALA s 83 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL s 85 " --> pdb=" O VAL s 58 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VAL s 58 " --> pdb=" O VAL s 85 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 40 through 45 removed outlier: 4.660A pdb=" N ASN t 40 " --> pdb=" O ALA t 63 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 't' and resid 82 through 86 removed outlier: 5.111A pdb=" N ARG t 82 " --> pdb=" O LYS t 97 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ARG t 94 " --> pdb=" O ILE t 103 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLU t 101 " --> pdb=" O PHE t 96 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'u' and resid 69 through 72 removed outlier: 6.831A pdb=" N ALA u 39 " --> pdb=" O ARG u 9 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE u 89 " --> pdb=" O PRO u 27 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'v' and resid 51 through 54 removed outlier: 4.264A pdb=" N THR v 58 " --> pdb=" O GLY v 54 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 65 through 71 Processing sheet with id= 68, first strand: chain 'w' and resid 11 through 19 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'w' and resid 34 through 41 Processing sheet with id= 70, first strand: chain 'y' and resid 33 through 39 removed outlier: 4.376A pdb=" N HIS y 34 " --> pdb=" O GLN y 9 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET y 54 " --> pdb=" O THR y 10 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'z' and resid 29 through 32 removed outlier: 4.574A pdb=" N GLU z 36 " --> pdb=" O ASP z 31 " (cutoff:3.500A) 1943 hydrogen bonds defined for protein. 5718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3919 hydrogen bonds 6106 hydrogen bond angles 0 basepair planarities 1559 basepair parallelities 2302 stacking parallelities Total time for adding SS restraints: 226.57 Time building geometry restraints manager: 65.96 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.42: 79127 1.42 - 1.71: 72631 1.71 - 1.99: 264 1.99 - 2.28: 0 2.28 - 2.56: 1 Bond restraints: 152023 Sorted by residual: bond pdb=" C ARG l 81 " pdb=" N MET l 82 " ideal model delta sigma weight residual 1.330 2.562 -1.232 1.38e-02 5.25e+03 7.98e+03 bond pdb=" C5 U a2449 " pdb=" C6 U a2449 " ideal model delta sigma weight residual 1.337 1.496 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C10 T8B A1689 " pdb=" C11 T8B A1689 " ideal model delta sigma weight residual 1.511 1.380 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" CG PRO F 101 " pdb=" CD PRO F 101 " ideal model delta sigma weight residual 1.503 1.284 0.219 3.40e-02 8.65e+02 4.13e+01 bond pdb=" C14 T8B A1689 " pdb=" C15 T8B A1689 " ideal model delta sigma weight residual 1.566 1.448 0.118 2.00e-02 2.50e+03 3.45e+01 ... (remaining 152018 not shown) Histogram of bond angle deviations from ideal: 87.50 - 97.97: 8 97.97 - 108.44: 47175 108.44 - 118.91: 105328 118.91 - 129.39: 71384 129.39 - 139.86: 3502 Bond angle restraints: 227397 Sorted by residual: angle pdb=" O ARG l 81 " pdb=" C ARG l 81 " pdb=" N MET l 82 " ideal model delta sigma weight residual 122.36 99.62 22.74 1.34e+00 5.57e-01 2.88e+02 angle pdb=" CA ARG l 81 " pdb=" C ARG l 81 " pdb=" N MET l 82 " ideal model delta sigma weight residual 115.58 91.07 24.51 1.55e+00 4.16e-01 2.50e+02 angle pdb=" C ARG l 81 " pdb=" N MET l 82 " pdb=" CA MET l 82 " ideal model delta sigma weight residual 121.45 96.04 25.41 2.14e+00 2.18e-01 1.41e+02 angle pdb=" C1' 2MA a2503 " pdb=" N9 2MA a2503 " pdb=" C8 2MA a2503 " ideal model delta sigma weight residual 106.32 138.25 -31.93 3.00e+00 1.11e-01 1.13e+02 angle pdb=" N PRO F 101 " pdb=" CD PRO F 101 " pdb=" CG PRO F 101 " ideal model delta sigma weight residual 103.20 87.50 15.70 1.50e+00 4.44e-01 1.10e+02 ... (remaining 227392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 85479 35.91 - 71.83: 10571 71.83 - 107.74: 1172 107.74 - 143.66: 21 143.66 - 179.57: 10 Dihedral angle restraints: 97253 sinusoidal: 81343 harmonic: 15910 Sorted by residual: dihedral pdb=" O4' U a1915 " pdb=" C1' U a1915 " pdb=" N1 U a1915 " pdb=" C2 U a1915 " ideal model delta sinusoidal sigma weight residual -160.00 -0.94 -159.06 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U A 365 " pdb=" C1' U A 365 " pdb=" N1 U A 365 " pdb=" C2 U A 365 " ideal model delta sinusoidal sigma weight residual 200.00 57.30 142.70 1 1.50e+01 4.44e-03 7.66e+01 dihedral pdb=" O4' U a1779 " pdb=" C1' U a1779 " pdb=" N1 U a1779 " pdb=" C2 U a1779 " ideal model delta sinusoidal sigma weight residual 200.00 60.91 139.09 1 1.50e+01 4.44e-03 7.49e+01 ... (remaining 97250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 25901 0.078 - 0.156: 2841 0.156 - 0.233: 181 0.233 - 0.311: 21 0.311 - 0.389: 3 Chirality restraints: 28947 Sorted by residual: chirality pdb=" C1* PSU A 516 " pdb=" O4* PSU A 516 " pdb=" C2* PSU A 516 " pdb=" C5 PSU A 516 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" C1* PSU a2580 " pdb=" O4* PSU a2580 " pdb=" C2* PSU a2580 " pdb=" C5 PSU a2580 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA ASP K 119 " pdb=" N ASP K 119 " pdb=" C ASP K 119 " pdb=" CB ASP K 119 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.53e+00 ... (remaining 28944 not shown) Planarity restraints: 12175 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1516 " -0.075 2.00e-02 2.50e+03 6.21e-01 8.68e+03 pdb=" C4' 2MG A1516 " -0.461 2.00e-02 2.50e+03 pdb=" O4' 2MG A1516 " -0.693 2.00e-02 2.50e+03 pdb=" C3' 2MG A1516 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG A1516 " 0.657 2.00e-02 2.50e+03 pdb=" C2' 2MG A1516 " 0.177 2.00e-02 2.50e+03 pdb=" O2' 2MG A1516 " -0.972 2.00e-02 2.50e+03 pdb=" C1' 2MG A1516 " -0.208 2.00e-02 2.50e+03 pdb=" N9 2MG A1516 " 0.986 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC A1407 " 0.064 2.00e-02 2.50e+03 6.00e-01 8.11e+03 pdb=" C4' 5MC A1407 " 0.447 2.00e-02 2.50e+03 pdb=" O4' 5MC A1407 " 0.629 2.00e-02 2.50e+03 pdb=" C3' 5MC A1407 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 5MC A1407 " -0.638 2.00e-02 2.50e+03 pdb=" C2' 5MC A1407 " -0.173 2.00e-02 2.50e+03 pdb=" O2' 5MC A1407 " 0.970 2.00e-02 2.50e+03 pdb=" C1' 5MC A1407 " 0.223 2.00e-02 2.50e+03 pdb=" N1 5MC A1407 " -0.935 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG A1207 " 0.052 2.00e-02 2.50e+03 5.97e-01 8.02e+03 pdb=" C4' 2MG A1207 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG A1207 " 0.684 2.00e-02 2.50e+03 pdb=" C3' 2MG A1207 " -0.603 2.00e-02 2.50e+03 pdb=" O3' 2MG A1207 " -0.606 2.00e-02 2.50e+03 pdb=" C2' 2MG A1207 " -0.205 2.00e-02 2.50e+03 pdb=" O2' 2MG A1207 " 0.946 2.00e-02 2.50e+03 pdb=" C1' 2MG A1207 " 0.210 2.00e-02 2.50e+03 pdb=" N9 2MG A1207 " -0.914 2.00e-02 2.50e+03 ... (remaining 12172 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 389 2.37 - 3.01: 70145 3.01 - 3.64: 265233 3.64 - 4.27: 430485 4.27 - 4.90: 572919 Nonbonded interactions: 1339171 Sorted by model distance: nonbonded pdb=" OP2 G a 578 " pdb="MG MG a6105 " model vdw 1.743 2.170 nonbonded pdb=" OP1 C a1914 " pdb="MG MG a6207 " model vdw 1.743 2.170 nonbonded pdb=" OP1 G A1094 " pdb="MG MG A1621 " model vdw 1.746 2.170 nonbonded pdb=" OP1 U a 567 " pdb="MG MG a6010 " model vdw 1.781 2.170 nonbonded pdb=" OP2 A a1156 " pdb="MG MG a6031 " model vdw 1.784 2.170 ... (remaining 1339166 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.130 Extract box with map and model: 31.510 Check model and map are aligned: 1.510 Set scattering table: 0.950 Process input model: 531.790 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.310 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:11.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 589.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 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 : 0.008 1.232 152023 Z= 0.516 Angle : 0.940 31.930 227397 Z= 0.467 Chirality : 0.049 0.389 28947 Planarity : 0.019 0.621 12175 Dihedral : 23.136 179.569 86991 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 1.25 % Allowed : 17.92 % Favored : 80.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.33 (0.11), residues: 5482 helix: 0.92 (0.12), residues: 1856 sheet: -0.12 (0.15), residues: 1141 loop : 0.00 (0.12), residues: 2485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP c 248 HIS 0.013 0.003 HIS w 34 PHE 0.028 0.003 PHE R 10 TYR 0.026 0.003 TYR r 38 ARG 0.011 0.001 ARG c 221 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10964 Ramachandran restraints generated. 5482 Oldfield, 0 Emsley, 5482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10964 Ramachandran restraints generated. 5482 Oldfield, 0 Emsley, 5482 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 961 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 904 time to evaluate : 6.141 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 3 36 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.8118 (ttt-90) REVERT: F 44 ARG cc_start: 0.6733 (mtp-110) cc_final: 0.6440 (mtt-85) REVERT: H 96 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8722 (ttp) REVERT: h 1 MET cc_start: 0.7159 (ttm) cc_final: 0.6806 (ttt) outliers start: 57 outliers final: 46 residues processed: 942 average time/residue: 2.4303 time to fit residues: 3129.1438 Evaluate side-chains 944 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 896 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 23 SER Chi-restraints excluded: chain D residue 119 SER Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 189 SER Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 40 GLU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 10 LYS Chi-restraints excluded: chain L residue 15 LYS Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 272 SER Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 827 optimal weight: 1.9990 chunk 742 optimal weight: 0.1980 chunk 412 optimal weight: 30.0000 chunk 253 optimal weight: 9.9990 chunk 501 optimal weight: 30.0000 chunk 396 optimal weight: 5.9990 chunk 768 optimal weight: 9.9990 chunk 297 optimal weight: 5.9990 chunk 467 optimal weight: 10.0000 chunk 571 optimal weight: 10.0000 chunk 889 optimal weight: 1.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS B 177 ASN D 36 GLN D 40 GLN D 116 GLN E 61 GLN E 73 ASN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN d 185 ASN g 101 ASN g 116 GLN i 128 ASN k 93 ASN s 28 ASN t 46 GLN w 20 HIS x 27 ASN x 39 GLN x 45 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.0591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 152023 Z= 0.213 Angle : 0.678 16.366 227397 Z= 0.365 Chirality : 0.038 0.372 28947 Planarity : 0.006 0.144 12175 Dihedral : 23.143 178.670 76042 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.19 % Favored : 97.70 % Rotamer: Outliers : 2.29 % Allowed : 16.30 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.79 (0.11), residues: 5484 helix: 1.52 (0.12), residues: 1878 sheet: -0.03 (0.15), residues: 1126 loop : 0.15 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.007 0.001 HIS w 34 PHE 0.024 0.002 PHE R 10 TYR 0.019 0.002 TYR r 38 ARG 0.005 0.001 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1036 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 931 time to evaluate : 5.860 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5864 (ptt90) REVERT: B 115 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6829 (mmtm) REVERT: E 23 LYS cc_start: 0.8896 (OUTLIER) cc_final: 0.8183 (pttt) REVERT: F 44 ARG cc_start: 0.6562 (mtp-110) cc_final: 0.6356 (mtt-85) REVERT: F 102 MET cc_start: 0.7803 (mpm) cc_final: 0.7221 (mpm) REVERT: G 76 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7438 (mtpt) REVERT: H 89 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7607 (ptpt) REVERT: H 90 ASP cc_start: 0.7995 (OUTLIER) cc_final: 0.7692 (p0) REVERT: Q 40 ARG cc_start: 0.7919 (OUTLIER) cc_final: 0.7461 (mmm160) REVERT: c 23 GLU cc_start: 0.7799 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: c 217 ARG cc_start: 0.9078 (OUTLIER) cc_final: 0.8789 (mtm110) REVERT: c 242 LYS cc_start: 0.8727 (mttt) cc_final: 0.8499 (mtmt) REVERT: e 88 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.8368 (mmp80) REVERT: g 101 ASN cc_start: 0.6852 (OUTLIER) cc_final: 0.6591 (p0) REVERT: h 1 MET cc_start: 0.7143 (ttm) cc_final: 0.6820 (ttt) REVERT: w 45 ARG cc_start: 0.7954 (OUTLIER) cc_final: 0.7048 (ptt-90) outliers start: 105 outliers final: 41 residues processed: 997 average time/residue: 2.4328 time to fit residues: 3325.1641 Evaluate side-chains 954 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 901 time to evaluate : 5.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain c residue 23 GLU Chi-restraints excluded: chain c residue 217 ARG Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 101 ASN Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain u residue 92 VAL Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 494 optimal weight: 10.0000 chunk 276 optimal weight: 20.0000 chunk 740 optimal weight: 10.0000 chunk 606 optimal weight: 9.9990 chunk 245 optimal weight: 6.9990 chunk 891 optimal weight: 7.9990 chunk 963 optimal weight: 0.9980 chunk 794 optimal weight: 10.0000 chunk 884 optimal weight: 9.9990 chunk 303 optimal weight: 7.9990 chunk 715 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS D 36 GLN D 40 GLN D 116 GLN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN g 101 ASN i 128 ASN i 138 GLN k 93 ASN t 46 GLN x 27 ASN x 39 GLN x 58 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.0373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 152023 Z= 0.350 Angle : 0.817 23.367 227397 Z= 0.422 Chirality : 0.044 0.375 28947 Planarity : 0.008 0.161 12175 Dihedral : 23.175 179.798 75992 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 2.49 % Allowed : 15.69 % Favored : 81.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.64 (0.11), residues: 5484 helix: 1.36 (0.12), residues: 1881 sheet: -0.08 (0.15), residues: 1121 loop : 0.08 (0.12), residues: 2482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.009 0.002 HIS w 34 PHE 0.027 0.003 PHE R 10 TYR 0.023 0.003 TYR D 76 ARG 0.007 0.001 ARG f 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1026 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 912 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6437 (OUTLIER) cc_final: 0.5948 (ptt90) REVERT: E 23 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8218 (pttt) REVERT: F 44 ARG cc_start: 0.6625 (mtp-110) cc_final: 0.6403 (mtt-85) REVERT: F 102 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.7378 (mpm) REVERT: G 76 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7417 (mtpt) REVERT: H 90 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7700 (p0) REVERT: H 96 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8730 (ttp) REVERT: I 4 ASN cc_start: 0.4420 (OUTLIER) cc_final: 0.4113 (m-40) REVERT: J 5 ARG cc_start: 0.5252 (OUTLIER) cc_final: 0.3985 (tmm160) REVERT: Q 40 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7477 (mmm160) REVERT: U 18 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7584 (mtp85) REVERT: e 88 ARG cc_start: 0.8688 (OUTLIER) cc_final: 0.8417 (mmp80) REVERT: f 174 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.6021 (m-30) REVERT: w 45 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7133 (ptt-90) outliers start: 114 outliers final: 59 residues processed: 970 average time/residue: 2.4499 time to fit residues: 3255.2666 Evaluate side-chains 971 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 899 time to evaluate : 5.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 179 GLU Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain J residue 5 ARG Chi-restraints excluded: chain J residue 40 ILE Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 35 GLU Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 880 optimal weight: 6.9990 chunk 670 optimal weight: 9.9990 chunk 462 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 425 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 chunk 894 optimal weight: 0.9990 chunk 947 optimal weight: 8.9990 chunk 467 optimal weight: 10.0000 chunk 848 optimal weight: 9.9990 chunk 255 optimal weight: 0.5980 overall best weight: 5.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS D 36 GLN D 40 GLN D 116 GLN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN g 104 ASN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN t 46 GLN x 27 ASN x 39 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 152023 Z= 0.317 Angle : 0.782 21.898 227397 Z= 0.408 Chirality : 0.042 0.377 28947 Planarity : 0.007 0.157 12175 Dihedral : 23.165 179.985 75992 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 2.60 % Allowed : 15.73 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.66 (0.11), residues: 5484 helix: 1.38 (0.12), residues: 1885 sheet: -0.07 (0.15), residues: 1120 loop : 0.09 (0.12), residues: 2479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP c 248 HIS 0.009 0.002 HIS w 34 PHE 0.030 0.002 PHE R 10 TYR 0.022 0.002 TYR r 38 ARG 0.008 0.001 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1034 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 915 time to evaluate : 6.010 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 5 ILE cc_start: 0.7997 (OUTLIER) cc_final: 0.7717 (pp) REVERT: 4 59 ARG cc_start: 0.6429 (OUTLIER) cc_final: 0.5920 (ptt90) REVERT: E 23 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8212 (pttt) REVERT: F 44 ARG cc_start: 0.6604 (mtp-110) cc_final: 0.6404 (mtt-85) REVERT: F 102 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.7345 (mpm) REVERT: G 76 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7409 (mtpt) REVERT: H 89 LYS cc_start: 0.8042 (OUTLIER) cc_final: 0.7641 (ptpt) REVERT: H 90 ASP cc_start: 0.8009 (OUTLIER) cc_final: 0.7691 (p0) REVERT: H 96 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8730 (ttp) REVERT: I 4 ASN cc_start: 0.4439 (OUTLIER) cc_final: 0.4130 (m-40) REVERT: Q 40 ARG cc_start: 0.7932 (OUTLIER) cc_final: 0.7468 (mmm160) REVERT: U 18 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.7580 (mtp85) REVERT: d 1 MET cc_start: 0.6624 (OUTLIER) cc_final: 0.4669 (tmt) REVERT: e 1 MET cc_start: 0.6994 (OUTLIER) cc_final: 0.6718 (ttt) REVERT: e 88 ARG cc_start: 0.8684 (OUTLIER) cc_final: 0.8415 (mmp80) REVERT: f 174 ASP cc_start: 0.6232 (OUTLIER) cc_final: 0.6020 (m-30) REVERT: t 24 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8309 (ttpm) REVERT: w 45 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7103 (ptt-90) outliers start: 119 outliers final: 62 residues processed: 982 average time/residue: 2.4813 time to fit residues: 3341.6592 Evaluate side-chains 967 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 888 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 5 ILE Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 1 MET Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 14 SER Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain h residue 41 LYS Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 788 optimal weight: 0.4980 chunk 537 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 705 optimal weight: 2.9990 chunk 390 optimal weight: 4.9990 chunk 808 optimal weight: 0.6980 chunk 654 optimal weight: 9.9990 chunk 1 optimal weight: 9.9990 chunk 483 optimal weight: 10.0000 chunk 850 optimal weight: 7.9990 chunk 239 optimal weight: 20.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS D 36 GLN D 40 GLN D 116 GLN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN c 37 ASN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN t 46 GLN x 27 ASN x 39 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 152023 Z= 0.213 Angle : 0.677 17.850 227397 Z= 0.366 Chirality : 0.038 0.370 28947 Planarity : 0.006 0.149 12175 Dihedral : 23.142 178.663 75989 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.39 % Rotamer: Outliers : 2.34 % Allowed : 16.24 % Favored : 81.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.83 (0.11), residues: 5484 helix: 1.58 (0.12), residues: 1880 sheet: -0.03 (0.15), residues: 1123 loop : 0.15 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 201 HIS 0.006 0.001 HIS c 230 PHE 0.024 0.002 PHE R 10 TYR 0.020 0.002 TYR r 38 ARG 0.009 0.000 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1009 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 902 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.6010 (ptt90) REVERT: E 14 LYS cc_start: 0.8877 (mtpp) cc_final: 0.8628 (mttt) REVERT: E 23 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8101 (pttp) REVERT: F 102 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.7330 (mpm) REVERT: G 76 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7428 (mtpt) REVERT: H 90 ASP cc_start: 0.7997 (OUTLIER) cc_final: 0.7680 (p0) REVERT: H 96 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8752 (ttp) REVERT: Q 40 ARG cc_start: 0.7926 (OUTLIER) cc_final: 0.7453 (mmm160) REVERT: U 18 ARG cc_start: 0.7838 (OUTLIER) cc_final: 0.7603 (mtp85) REVERT: d 1 MET cc_start: 0.6639 (OUTLIER) cc_final: 0.4713 (tmt) REVERT: e 1 MET cc_start: 0.6949 (ttm) cc_final: 0.6712 (ttt) REVERT: e 88 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8386 (mmp80) REVERT: e 162 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8081 (mtm180) REVERT: f 174 ASP cc_start: 0.6207 (OUTLIER) cc_final: 0.5989 (m-30) REVERT: h 1 MET cc_start: 0.7064 (ttm) cc_final: 0.6754 (ptm) REVERT: t 24 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8292 (ttpm) REVERT: w 45 ARG cc_start: 0.7971 (OUTLIER) cc_final: 0.7051 (ptt-90) outliers start: 107 outliers final: 61 residues processed: 959 average time/residue: 2.4823 time to fit residues: 3255.4108 Evaluate side-chains 971 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 896 time to evaluate : 5.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain l residue 110 GLU Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 318 optimal weight: 5.9990 chunk 853 optimal weight: 9.9990 chunk 187 optimal weight: 0.0370 chunk 556 optimal weight: 20.0000 chunk 233 optimal weight: 2.9990 chunk 948 optimal weight: 20.0000 chunk 787 optimal weight: 7.9990 chunk 439 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 313 optimal weight: 20.0000 chunk 497 optimal weight: 9.9990 overall best weight: 5.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS D 36 GLN D 40 GLN D 116 GLN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN c 37 ASN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN i 138 GLN k 93 ASN x 27 ASN x 39 GLN x 58 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 152023 Z= 0.313 Angle : 0.777 21.770 227397 Z= 0.406 Chirality : 0.042 0.370 28947 Planarity : 0.007 0.157 12175 Dihedral : 23.141 179.985 75989 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 2.29 % Allowed : 16.30 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.73 (0.11), residues: 5484 helix: 1.47 (0.12), residues: 1886 sheet: -0.06 (0.15), residues: 1118 loop : 0.11 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP c 248 HIS 0.008 0.002 HIS c 230 PHE 0.025 0.002 PHE R 10 TYR 0.023 0.002 TYR r 38 ARG 0.008 0.001 ARG G 4 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1013 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 908 time to evaluate : 5.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6438 (OUTLIER) cc_final: 0.5905 (ptt90) REVERT: B 115 LYS cc_start: 0.7271 (OUTLIER) cc_final: 0.6828 (mmtm) REVERT: E 23 LYS cc_start: 0.8920 (OUTLIER) cc_final: 0.8213 (pttt) REVERT: F 102 MET cc_start: 0.7850 (OUTLIER) cc_final: 0.7316 (mpm) REVERT: G 76 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7392 (mtpt) REVERT: H 89 LYS cc_start: 0.8039 (OUTLIER) cc_final: 0.7631 (ptpt) REVERT: H 90 ASP cc_start: 0.8005 (OUTLIER) cc_final: 0.7683 (p0) REVERT: H 96 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8721 (ttp) REVERT: I 4 ASN cc_start: 0.4412 (OUTLIER) cc_final: 0.4138 (m-40) REVERT: Q 40 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7470 (mmm160) REVERT: U 18 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7620 (mtp85) REVERT: d 1 MET cc_start: 0.6644 (OUTLIER) cc_final: 0.4677 (tmt) REVERT: e 88 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8407 (mmp80) REVERT: e 162 ARG cc_start: 0.9045 (OUTLIER) cc_final: 0.7228 (mtm-85) REVERT: f 174 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.6016 (m-30) REVERT: h 1 MET cc_start: 0.7193 (ttm) cc_final: 0.6745 (ptm) REVERT: t 24 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8307 (ttpm) REVERT: w 45 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7136 (ptt-90) outliers start: 105 outliers final: 64 residues processed: 965 average time/residue: 2.5221 time to fit residues: 3334.8914 Evaluate side-chains 984 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 903 time to evaluate : 5.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 143 LYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 24 SER Chi-restraints excluded: chain f residue 158 THR Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 111 LYS Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 914 optimal weight: 2.9990 chunk 106 optimal weight: 10.0000 chunk 540 optimal weight: 10.0000 chunk 692 optimal weight: 10.0000 chunk 536 optimal weight: 10.0000 chunk 798 optimal weight: 5.9990 chunk 529 optimal weight: 10.0000 chunk 944 optimal weight: 6.9990 chunk 591 optimal weight: 10.0000 chunk 575 optimal weight: 10.0000 chunk 436 optimal weight: 10.0000 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 29 GLN 2 43 HIS ** B 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 170 HIS D 36 GLN D 40 GLN D 116 GLN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN c 37 ASN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN t 46 GLN x 27 ASN x 39 GLN x 58 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8753 moved from start: 0.0392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.097 152023 Z= 0.399 Angle : 0.871 24.268 227397 Z= 0.445 Chirality : 0.046 0.380 28947 Planarity : 0.008 0.170 12175 Dihedral : 23.173 179.522 75989 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.68 % Favored : 97.21 % Rotamer: Outliers : 2.47 % Allowed : 16.13 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.56 (0.11), residues: 5484 helix: 1.27 (0.12), residues: 1884 sheet: -0.11 (0.15), residues: 1120 loop : 0.04 (0.12), residues: 2480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP c 248 HIS 0.010 0.002 HIS c 230 PHE 0.028 0.003 PHE R 10 TYR 0.025 0.003 TYR r 38 ARG 0.009 0.001 ARG f 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 911 time to evaluate : 5.947 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.5822 (ptt90) REVERT: B 115 LYS cc_start: 0.7277 (OUTLIER) cc_final: 0.6877 (mmtm) REVERT: D 154 ARG cc_start: 0.7729 (OUTLIER) cc_final: 0.6086 (ptp-170) REVERT: E 23 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8195 (pttt) REVERT: F 102 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7373 (mpm) REVERT: G 76 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7391 (mtpt) REVERT: H 89 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7690 (ptpt) REVERT: H 90 ASP cc_start: 0.8020 (OUTLIER) cc_final: 0.7705 (p0) REVERT: H 96 MET cc_start: 0.9025 (OUTLIER) cc_final: 0.8700 (ttp) REVERT: I 4 ASN cc_start: 0.4480 (OUTLIER) cc_final: 0.4199 (m-40) REVERT: Q 40 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7496 (mmm160) REVERT: U 18 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7572 (mtp85) REVERT: d 1 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.4770 (tmt) REVERT: e 88 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8398 (mmp80) REVERT: e 162 ARG cc_start: 0.9063 (OUTLIER) cc_final: 0.8037 (mtm180) REVERT: f 174 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6063 (m-30) REVERT: h 1 MET cc_start: 0.7186 (ttm) cc_final: 0.6720 (ptm) REVERT: t 24 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (ttpm) REVERT: w 45 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7192 (ptt-90) outliers start: 113 outliers final: 62 residues processed: 977 average time/residue: 2.5231 time to fit residues: 3377.0417 Evaluate side-chains 979 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 899 time to evaluate : 5.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 18 VAL Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain S residue 71 LEU Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 49 THR Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 584 optimal weight: 6.9990 chunk 377 optimal weight: 3.9990 chunk 564 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 chunk 182 optimal weight: 9.9990 chunk 600 optimal weight: 6.9990 chunk 643 optimal weight: 5.9990 chunk 467 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 742 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN B 170 HIS D 36 GLN D 40 GLN D 116 GLN E 73 ASN E 146 ASN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN c 37 ASN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN t 46 GLN x 27 ASN x 39 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.0493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 152023 Z= 0.321 Angle : 0.783 21.925 227397 Z= 0.409 Chirality : 0.043 0.375 28947 Planarity : 0.007 0.157 12175 Dihedral : 23.159 179.950 75988 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.59 % Favored : 97.30 % Rotamer: Outliers : 2.12 % Allowed : 16.56 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.64 (0.11), residues: 5484 helix: 1.36 (0.12), residues: 1885 sheet: -0.10 (0.15), residues: 1118 loop : 0.08 (0.12), residues: 2481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.008 0.002 HIS c 230 PHE 0.026 0.002 PHE R 10 TYR 0.023 0.003 TYR r 38 ARG 0.009 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1001 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 904 time to evaluate : 5.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6426 (OUTLIER) cc_final: 0.5944 (ptt90) REVERT: B 115 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6836 (mmtm) REVERT: C 88 ARG cc_start: 0.7163 (OUTLIER) cc_final: 0.6649 (tmm160) REVERT: D 154 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6056 (ptp-170) REVERT: E 23 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8210 (pttt) REVERT: F 102 MET cc_start: 0.7840 (OUTLIER) cc_final: 0.7410 (mpm) REVERT: G 76 LYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7391 (mtpt) REVERT: H 89 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7652 (ptpt) REVERT: H 90 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7697 (p0) REVERT: H 96 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8737 (ttp) REVERT: I 4 ASN cc_start: 0.4445 (OUTLIER) cc_final: 0.4169 (m-40) REVERT: Q 40 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7496 (mmm160) REVERT: U 18 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7578 (mtp85) REVERT: d 1 MET cc_start: 0.6692 (OUTLIER) cc_final: 0.4725 (tmt) REVERT: e 88 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.8398 (mmp80) REVERT: e 162 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8024 (mtm180) REVERT: f 174 ASP cc_start: 0.6309 (OUTLIER) cc_final: 0.6071 (m-30) REVERT: h 1 MET cc_start: 0.7182 (ttm) cc_final: 0.6710 (ptm) REVERT: t 24 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8304 (ttpm) REVERT: w 45 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7122 (ptt-90) outliers start: 97 outliers final: 58 residues processed: 960 average time/residue: 2.5237 time to fit residues: 3304.8406 Evaluate side-chains 977 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 900 time to evaluate : 5.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain U residue 18 ARG Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 6 LYS Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain i residue 12 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 859 optimal weight: 9.9990 chunk 904 optimal weight: 10.0000 chunk 825 optimal weight: 0.1980 chunk 880 optimal weight: 0.0570 chunk 529 optimal weight: 10.0000 chunk 383 optimal weight: 9.9990 chunk 691 optimal weight: 20.0000 chunk 270 optimal weight: 10.0000 chunk 795 optimal weight: 20.0000 chunk 832 optimal weight: 0.6980 chunk 877 optimal weight: 10.0000 overall best weight: 4.1902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN B 170 HIS D 36 GLN D 40 GLN D 116 GLN E 146 ASN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN t 46 GLN x 27 ASN x 39 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 152023 Z= 0.262 Angle : 0.725 20.906 227397 Z= 0.386 Chirality : 0.040 0.367 28947 Planarity : 0.007 0.154 12175 Dihedral : 23.155 179.419 75987 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.63 % Favored : 97.26 % Rotamer: Outliers : 1.92 % Allowed : 16.83 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.71 (0.11), residues: 5484 helix: 1.45 (0.12), residues: 1886 sheet: -0.08 (0.15), residues: 1125 loop : 0.11 (0.12), residues: 2473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 201 HIS 0.007 0.001 HIS c 230 PHE 0.025 0.002 PHE R 10 TYR 0.024 0.002 TYR D 135 ARG 0.009 0.001 ARG C 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 986 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 898 time to evaluate : 6.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6419 (OUTLIER) cc_final: 0.5945 (ptt90) REVERT: B 115 LYS cc_start: 0.7265 (OUTLIER) cc_final: 0.6823 (mmtm) REVERT: D 154 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.6036 (ptp-170) REVERT: D 167 LYS cc_start: 0.6943 (OUTLIER) cc_final: 0.6677 (mptt) REVERT: E 23 LYS cc_start: 0.8885 (OUTLIER) cc_final: 0.8158 (pttt) REVERT: F 102 MET cc_start: 0.7836 (OUTLIER) cc_final: 0.7354 (mpm) REVERT: G 76 LYS cc_start: 0.7681 (OUTLIER) cc_final: 0.7390 (mtpt) REVERT: H 89 LYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7634 (ptpt) REVERT: H 90 ASP cc_start: 0.8007 (OUTLIER) cc_final: 0.7690 (p0) REVERT: H 96 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8752 (ttp) REVERT: I 4 ASN cc_start: 0.4429 (OUTLIER) cc_final: 0.4177 (m110) REVERT: Q 40 ARG cc_start: 0.7929 (OUTLIER) cc_final: 0.7484 (mmm160) REVERT: d 1 MET cc_start: 0.6679 (OUTLIER) cc_final: 0.4722 (tmt) REVERT: e 88 ARG cc_start: 0.8689 (OUTLIER) cc_final: 0.8406 (mmp80) REVERT: e 162 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.7160 (mtm-85) REVERT: f 174 ASP cc_start: 0.6297 (OUTLIER) cc_final: 0.6069 (m-30) REVERT: h 1 MET cc_start: 0.7174 (ttm) cc_final: 0.6696 (ptm) REVERT: t 24 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8296 (ttpm) REVERT: w 45 ARG cc_start: 0.7975 (OUTLIER) cc_final: 0.7117 (ptt-90) outliers start: 88 outliers final: 56 residues processed: 946 average time/residue: 2.5381 time to fit residues: 3277.5035 Evaluate side-chains 963 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 889 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain F residue 102 MET Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 91 GLU Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain e residue 162 ARG Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain n residue 83 LEU Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain x residue 60 LYS Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 578 optimal weight: 10.0000 chunk 930 optimal weight: 10.0000 chunk 568 optimal weight: 10.0000 chunk 441 optimal weight: 30.0000 chunk 647 optimal weight: 7.9990 chunk 976 optimal weight: 10.0000 chunk 898 optimal weight: 9.9990 chunk 777 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 600 optimal weight: 9.9990 chunk 476 optimal weight: 10.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN B 170 HIS D 36 GLN D 40 GLN D 116 GLN E 73 ASN E 146 ASN F 17 GLN F 46 GLN F 55 HIS G 68 ASN G 142 HIS L 77 HIS O 35 GLN c 37 ASN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN x 27 ASN x 39 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.0392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.117 152023 Z= 0.511 Angle : 0.988 25.195 227397 Z= 0.493 Chirality : 0.051 0.392 28947 Planarity : 0.009 0.184 12175 Dihedral : 23.192 179.061 75984 Min Nonbonded Distance : 1.732 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 1.92 % Allowed : 16.96 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.39 (0.11), residues: 5484 helix: 1.07 (0.11), residues: 1885 sheet: -0.17 (0.15), residues: 1124 loop : -0.02 (0.12), residues: 2475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP c 248 HIS 0.010 0.003 HIS o 77 PHE 0.030 0.004 PHE R 10 TYR 0.027 0.004 TYR r 38 ARG 0.012 0.001 ARG f 167 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10968 Ramachandran restraints generated. 5484 Oldfield, 0 Emsley, 5484 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 988 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 900 time to evaluate : 6.065 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 4 59 ARG cc_start: 0.6433 (OUTLIER) cc_final: 0.5956 (ptt90) REVERT: B 115 LYS cc_start: 0.7255 (OUTLIER) cc_final: 0.6852 (mmtm) REVERT: C 88 ARG cc_start: 0.7126 (OUTLIER) cc_final: 0.6528 (tmm160) REVERT: D 154 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6096 (ptp-170) REVERT: D 167 LYS cc_start: 0.6930 (OUTLIER) cc_final: 0.6719 (mptt) REVERT: E 23 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8203 (pttt) REVERT: F 102 MET cc_start: 0.7848 (mpm) cc_final: 0.7256 (mpm) REVERT: G 76 LYS cc_start: 0.7721 (OUTLIER) cc_final: 0.7358 (mtpt) REVERT: H 89 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7714 (ptpt) REVERT: H 90 ASP cc_start: 0.8028 (OUTLIER) cc_final: 0.7733 (p0) REVERT: H 96 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8719 (ttp) REVERT: I 4 ASN cc_start: 0.4487 (OUTLIER) cc_final: 0.4195 (m-40) REVERT: Q 40 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7557 (mmm160) REVERT: U 21 ARG cc_start: 0.7059 (mmm160) cc_final: 0.6788 (mmp80) REVERT: d 1 MET cc_start: 0.6707 (OUTLIER) cc_final: 0.4873 (tmt) REVERT: e 88 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8104 (mmp80) REVERT: f 174 ASP cc_start: 0.6307 (OUTLIER) cc_final: 0.6076 (m-30) REVERT: t 24 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8319 (ttpm) REVERT: w 45 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7245 (ptt-90) outliers start: 88 outliers final: 57 residues processed: 948 average time/residue: 2.5368 time to fit residues: 3274.3647 Evaluate side-chains 961 residues out of total 4577 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 887 time to evaluate : 5.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 4 residue 59 ARG Chi-restraints excluded: chain 4 residue 66 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 115 LYS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 211 THR Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 88 ARG Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 206 GLU Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 154 ARG Chi-restraints excluded: chain D residue 156 LYS Chi-restraints excluded: chain D residue 163 GLU Chi-restraints excluded: chain D residue 167 LYS Chi-restraints excluded: chain E residue 23 LYS Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 100 SER Chi-restraints excluded: chain G residue 76 LYS Chi-restraints excluded: chain G residue 83 SER Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain H residue 76 GLN Chi-restraints excluded: chain H residue 89 LYS Chi-restraints excluded: chain H residue 90 ASP Chi-restraints excluded: chain H residue 96 MET Chi-restraints excluded: chain I residue 4 ASN Chi-restraints excluded: chain I residue 46 MET Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 129 VAL Chi-restraints excluded: chain L residue 86 ARG Chi-restraints excluded: chain N residue 11 VAL Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain O residue 75 VAL Chi-restraints excluded: chain O residue 79 THR Chi-restraints excluded: chain O residue 80 GLN Chi-restraints excluded: chain Q residue 17 MET Chi-restraints excluded: chain Q residue 40 ARG Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain R residue 14 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain R residue 66 SER Chi-restraints excluded: chain c residue 162 VAL Chi-restraints excluded: chain c residue 182 ARG Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 95 SER Chi-restraints excluded: chain e residue 88 ARG Chi-restraints excluded: chain e residue 127 GLU Chi-restraints excluded: chain f residue 174 ASP Chi-restraints excluded: chain g residue 10 VAL Chi-restraints excluded: chain g residue 16 ASP Chi-restraints excluded: chain g residue 17 VAL Chi-restraints excluded: chain g residue 43 VAL Chi-restraints excluded: chain g residue 51 THR Chi-restraints excluded: chain g residue 92 VAL Chi-restraints excluded: chain g residue 168 VAL Chi-restraints excluded: chain h residue 35 LYS Chi-restraints excluded: chain j residue 76 VAL Chi-restraints excluded: chain j residue 114 LYS Chi-restraints excluded: chain k residue 129 LYS Chi-restraints excluded: chain n residue 49 VAL Chi-restraints excluded: chain o residue 85 SER Chi-restraints excluded: chain t residue 15 THR Chi-restraints excluded: chain t residue 24 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain w residue 45 ARG Chi-restraints excluded: chain y residue 4 THR Chi-restraints excluded: chain z residue 23 THR Chi-restraints excluded: chain z residue 57 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 980 random chunks: chunk 617 optimal weight: 10.0000 chunk 828 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 716 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 216 optimal weight: 10.0000 chunk 778 optimal weight: 10.0000 chunk 325 optimal weight: 9.9990 chunk 799 optimal weight: 0.0980 chunk 98 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 4.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 29 GLN B 170 HIS D 36 GLN D 40 GLN D 116 GLN E 73 ASN E 146 ASN F 17 GLN F 46 GLN F 55 HIS G 142 HIS L 77 HIS O 35 GLN d 185 ASN ** e 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 81 GLN ** g 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 128 ASN k 93 ASN t 46 GLN x 27 ASN x 39 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.117653 restraints weight = 111691.417| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 0.39 r_work: 0.3103 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work: 0.2890 rms_B_bonded: 3.85 restraints_weight: 0.1250 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.0566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 152023 Z= 0.286 Angle : 0.760 20.436 227397 Z= 0.399 Chirality : 0.041 0.371 28947 Planarity : 0.007 0.156 12175 Dihedral : 23.140 179.915 75984 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.57 % Favored : 97.32 % Rotamer: Outliers : 1.68 % Allowed : 17.20 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: 0.65 (0.11), residues: 5484 helix: 1.38 (0.12), residues: 1886 sheet: -0.09 (0.15), residues: 1120 loop : 0.07 (0.12), residues: 2478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP c 248 HIS 0.008 0.002 HIS c 230 PHE 0.025 0.002 PHE R 10 TYR 0.023 0.002 TYR D 135 ARG 0.012 0.001 ARG C 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50098.16 seconds wall clock time: 867 minutes 16.75 seconds (52036.75 seconds total)