Starting phenix.real_space_refine on Mon Mar 18 00:48:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryg_24739/03_2024/7ryg_24739_updated.pdb" } resolution = 2.38 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= 0.003 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 95 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Zn 1 6.06 5 P 4406 5.49 5 Mg 4 5.21 5 S 142 5.16 5 C 69095 2.51 5 N 25581 2.21 5 O 38341 1.98 5 F 9 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "0 ASP 3": "OD1" <-> "OD2" Residue "0 GLU 47": "OE1" <-> "OE2" Residue "2 ASP 53": "OD1" <-> "OD2" Residue "2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 35": "OE1" <-> "OE2" Residue "C ASP 72": "OD1" <-> "OD2" Residue "C GLU 100": "OE1" <-> "OE2" Residue "C ASP 114": "OD1" <-> "OD2" Residue "C ASP 121": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "D GLU 42": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D GLU 58": "OE1" <-> "OE2" Residue "D GLU 94": "OE1" <-> "OE2" Residue "D GLU 179": "OE1" <-> "OE2" Residue "D ASP 203": "OD1" <-> "OD2" Residue "E GLU 21": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E GLU 196": "OE1" <-> "OE2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ASP 10": "OD1" <-> "OD2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ASP 51": "OD1" <-> "OD2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F ASP 101": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F ASP 147": "OD1" <-> "OD2" Residue "F ASP 163": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G PHE 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 124": "OE1" <-> "OE2" Residue "H PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 31": "OE1" <-> "OE2" Residue "I ASP 71": "OD1" <-> "OD2" Residue "I GLU 79": "OE1" <-> "OE2" Residue "I GLU 86": "OE1" <-> "OE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 12": "OD1" <-> "OD2" Residue "J GLU 45": "OE1" <-> "OE2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J ASP 80": "OD1" <-> "OD2" Residue "J ASP 81": "OD1" <-> "OD2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 78": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L GLU 91": "OE1" <-> "OE2" Residue "M GLU 22": "OE1" <-> "OE2" Residue "M GLU 49": "OE1" <-> "OE2" Residue "M GLU 114": "OE1" <-> "OE2" Residue "N PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ASP 19": "OD1" <-> "OD2" Residue "O GLU 22": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "P PHE 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ASP 81": "OD1" <-> "OD2" Residue "P ASP 97": "OD1" <-> "OD2" Residue "Q GLU 23": "OE1" <-> "OE2" Residue "Q ASP 37": "OD1" <-> "OD2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R GLU 59": "OE1" <-> "OE2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R ASP 94": "OD1" <-> "OD2" Residue "S GLU 4": "OE1" <-> "OE2" Residue "S GLU 41": "OE1" <-> "OE2" Residue "S GLU 47": "OE1" <-> "OE2" Residue "T GLU 35": "OE1" <-> "OE2" Residue "T GLU 99": "OE1" <-> "OE2" Residue "U PHE 4": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 27": "OE1" <-> "OE2" Residue "U GLU 50": "OE1" <-> "OE2" Residue "V TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V ASP 64": "OD1" <-> "OD2" Residue "V GLU 70": "OE1" <-> "OE2" Residue "V TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ASP 19": "OD1" <-> "OD2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Z GLU 24": "OE1" <-> "OE2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ASP 206": "OD1" <-> "OD2" Residue "c GLU 41": "OE1" <-> "OE2" Residue "c ASP 83": "OD1" <-> "OD2" Residue "c GLU 85": "OE1" <-> "OE2" Residue "c GLU 90": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c GLU 152": "OE1" <-> "OE2" Residue "c GLU 161": "OE1" <-> "OE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "e ASP 18": "OD1" <-> "OD2" Residue "e GLU 54": "OE1" <-> "OE2" Residue "e GLU 64": "OE1" <-> "OE2" Residue "e GLU 100": "OE1" <-> "OE2" Residue "e GLU 162": "OE1" <-> "OE2" Residue "f GLU 5": "OE1" <-> "OE2" Residue "f GLU 23": "OE1" <-> "OE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 123": "OE1" <-> "OE2" Residue "g GLU 146": "OE1" <-> "OE2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "h GLU 50": "OE1" <-> "OE2" Residue "h ASP 114": "OD1" <-> "OD2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "i TYR 5": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 40": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i GLU 57": "OE1" <-> "OE2" Residue "i TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 90": "OE1" <-> "OE2" Residue "j GLU 24": "OE1" <-> "OE2" Residue "j GLU 66": "OE1" <-> "OE2" Residue "j TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ASP 75": "OD1" <-> "OD2" Residue "k ASP 75": "OD1" <-> "OD2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "o GLU 10": "OE1" <-> "OE2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "o ASP 68": "OD1" <-> "OD2" Residue "p PHE 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "t ASP 59": "OD1" <-> "OD2" Residue "u TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 44": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 137579 Number of models: 1 Model: "" Number of chains: 55 Chain: "0" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 427 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "1" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 363 Classifications: {'peptide': 44} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "2" Number of atoms: 509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 509 Classifications: {'peptide': 63} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 61} Chain: "3" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 295 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "A" Number of atoms: 57610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2685, 57610 Classifications: {'RNA': 2685} Modifications used: {'rna2p': 3, 'rna2p_pur': 257, 'rna2p_pyr': 142, 'rna3p': 9, 'rna3p_pur': 1281, 'rna3p_pyr': 993} Link IDs: {'rna2p': 401, 'rna3p': 2283} Chain breaks: 5 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 5 Chain: "B" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 2450 Classifications: {'RNA': 115} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 56, 'rna3p_pyr': 47} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2111 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 16, 'TRANS': 255} Chain: "D" Number of atoms: 1572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1572 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 205} Chain: "E" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1516 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 193} Chain: "F" Number of atoms: 1370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1370 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 6, 'TRANS': 167} Chain: "G" Number of atoms: 1318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1318 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "H" Number of atoms: 458 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 458 Classifications: {'peptide': 60} Link IDs: {'PTRANS': 1, 'TRANS': 58} Chain: "I" Number of atoms: 1125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1125 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 133} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 946 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "K" Number of atoms: 1071 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1071 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 3, 'TRANS': 140} Chain: "L" Number of atoms: 1087 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1087 Classifications: {'peptide': 137} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 130} Chain: "M" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 942 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 857 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 112} Chain: "O" Number of atoms: 913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 913 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 5, 'TRANS': 110} Chain: "P" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 934 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 807 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 826 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain: "S" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 1, 'TRANS': 89} Chain: "T" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 766 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "U" Number of atoms: 760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 760 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "V" Number of atoms: 581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 581 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "W" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 632 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 486 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Chain: "Y" Number of atoms: 463 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 463 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 56} Chain: "Z" Number of atoms: 447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 447 Classifications: {'peptide': 54} Link IDs: {'TRANS': 53} Chain: "a" Number of atoms: 32782 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1528, 32782 Classifications: {'RNA': 1528} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 106, 'rna2p_pyr': 84, 'rna3p': 8, 'rna3p_pur': 757, 'rna3p_pyr': 572} Link IDs: {'rna2p': 190, 'rna3p': 1337} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 6 Chain: "b" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1769 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "c" Number of atoms: 1690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1690 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain: "d" Number of atoms: 1631 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1631 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 200} Chain: "e" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1129 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 4, 'TRANS': 150} Chain: "f" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 867 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 2, 'TRANS': 101} Chain: "g" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 6, 'TRANS': 129} Chain breaks: 1 Chain: "h" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 125} Chain: "i" Number of atoms: 991 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 991 Classifications: {'peptide': 126} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain: "j" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 94} Chain: "k" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 862 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "l" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 945 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 115} Chain: "m" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 903 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "n" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 792 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "o" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 705 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 644 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 3, 'TRANS': 78} Chain: "q" Number of atoms: 621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 621 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 2, 'TRANS': 76} Chain: "r" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "s" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 646 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "t" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 663 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "u" Number of atoms: 473 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 473 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 2, 'TRANS': 54} Chain: "v" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1636 Classifications: {'RNA': 77} Modifications used: {'5*END': 1, 'rna2p': 2, 'rna2p_pur': 5, 'rna2p_pyr': 3, 'rna3p': 2, 'rna3p_pur': 34, 'rna3p_pyr': 31} Link IDs: {'rna2p': 9, 'rna3p': 67} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 2 Chain: "w" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 65 Classifications: {'RNA': 3} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 2} 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: "a" Number of atoms: 127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 127 Unusual residues: {' MG': 4, '80P': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1382 SG CYS 3 11 179.539 123.440 137.460 1.00 26.30 S ATOM 1398 SG CYS 3 14 178.748 125.235 140.717 1.00 25.14 S ATOM 1503 SG CYS 3 27 180.168 127.215 137.795 1.00 25.68 S Time building chain proxies: 52.45, per 1000 atoms: 0.38 Number of scatterers: 137579 At special positions: 0 Unit cell: (227.601, 251.559, 278.784, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 1 29.99 S 142 16.00 P 4406 15.00 Mg 4 11.99 F 9 9.00 O 38341 8.00 N 25581 7.00 C 69095 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: 54.86 Conformation dependent library (CDL) restraints added in 7.0 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 14 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 11 " Number of angles added : 3 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10090 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: 171 helices and 65 sheets defined 39.5% alpha, 19.2% beta 1380 base pairs and 2135 stacking pairs defined. Time for finding SS restraints: 67.27 Creating SS restraints... Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.085A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.435A 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: 3.671A pdb=" N ARG 2 13 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 36 through 45 removed outlier: 3.721A pdb=" N ARG 2 44 " --> pdb=" O ILE 2 40 " (cutoff:3.500A) removed outlier: 5.630A pdb=" N GLY 2 45 " --> pdb=" O ARG 2 41 " (cutoff:3.500A) Processing helix chain '2' and resid 50 through 62 removed outlier: 4.299A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N SER 2 56 " --> pdb=" O SER 2 52 " (cutoff:3.500A) Proline residue: 2 62 - end of helix Processing helix chain 'C' and resid 10 through 15 removed outlier: 5.003A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.748A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.538A 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: 3.855A pdb=" N MET 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: 3.857A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.122A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.631A 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: 4.592A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ILE C 268 " --> pdb=" O THR C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 57 through 62 removed outlier: 3.611A pdb=" N VAL D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 57 through 62' Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 86 through 91 removed outlier: 3.508A pdb=" N GLU D 91 " --> pdb=" O GLU D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 123 through 129 removed outlier: 4.230A pdb=" N TRP D 128 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 19 Processing helix chain 'E' and resid 23 through 39 removed outlier: 4.020A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 removed outlier: 3.672A pdb=" N LEU E 133 " --> pdb=" O LYS E 129 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 162 removed outlier: 4.487A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 182 removed outlier: 3.750A pdb=" N PHE E 182 " --> pdb=" O SER E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'F' and resid 5 through 21 removed outlier: 4.250A pdb=" N ASN F 9 " --> pdb=" O LYS F 5 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.374A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.960A pdb=" N GLY F 62 " --> pdb=" O GLN F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.847A pdb=" N ILE 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 Processing helix chain 'G' and resid 2 through 8 Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 58 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.724A pdb=" N TYR G 151 " --> pdb=" O GLU G 147 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ARG G 152 " --> pdb=" O ILE 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 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.297A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.889A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 3.644A pdb=" N MET I 108 " --> pdb=" O ALA I 104 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 122 removed outlier: 4.168A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N MET I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 118 Processing helix chain 'K' and resid 39 through 44 removed outlier: 3.739A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N LYS K 44 " --> pdb=" O GLN K 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 39 through 44' Processing helix chain 'K' and resid 58 through 64 removed outlier: 3.650A pdb=" N LEU K 63 " --> pdb=" O ILE K 59 " (cutoff:3.500A) Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 70 through 77 removed outlier: 4.045A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 4.259A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N GLU K 88 " --> pdb=" O LEU K 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 80 through 88' Processing helix chain 'K' and resid 93 through 101 Processing helix chain 'K' and resid 130 through 141 Processing helix chain 'L' and resid 43 through 59 Processing helix chain 'L' and resid 110 through 126 removed outlier: 3.720A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Proline residue: L 126 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 56 removed outlier: 3.759A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.900A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.697A 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 3 through 23 removed outlier: 4.347A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N THR N 15 " --> pdb=" O ARG N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 66 through 85 Processing helix chain 'N' and resid 100 through 113 Processing helix chain 'O' and resid 5 through 16 removed outlier: 4.118A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.689A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N SER O 107 " --> pdb=" O LEU O 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 100 through 107' Processing helix chain 'P' and resid 6 through 22 Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.752A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 removed outlier: 3.672A pdb=" N GLN P 37 " --> pdb=" O ARG P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 4.081A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.004A 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: 3.839A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 4.052A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.977A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N LYS R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 2 through 10 removed outlier: 3.648A pdb=" N GLN S 8 " --> pdb=" O GLU S 4 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N LEU S 10 " --> pdb=" O ILE S 6 " (cutoff:3.500A) Processing helix chain 'S' and resid 16 through 26 Processing helix chain 'S' and resid 38 through 50 Processing helix chain 'T' and resid 64 through 69 removed outlier: 4.229A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N ALA T 69 " --> pdb=" O ILE T 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 64 through 69' Processing helix chain 'U' and resid 12 through 17 removed outlier: 5.098A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.997A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASN 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: 3.671A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N LYS X 9 " --> pdb=" O ASP X 5 " (cutoff:3.500A) removed outlier: 5.586A 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 40 through 61 removed outlier: 4.066A pdb=" N GLN X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 27 Processing helix chain 'Y' and resid 40 through 51 removed outlier: 3.630A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 18 Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.868A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 3.933A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.974A pdb=" N THR b 48 " --> pdb=" O ASN b 44 " (cutoff:3.500A) Proline residue: b 50 - end of helix Processing helix chain 'b' and resid 75 through 90 removed outlier: 5.000A pdb=" N ASN b 80 " --> pdb=" O ARG b 76 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ILE b 81 " --> pdb=" O ALA b 77 " (cutoff:3.500A) Processing helix chain 'b' and resid 105 through 126 removed outlier: 3.818A pdb=" N LEU b 109 " --> pdb=" O ASN b 105 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 5.226A pdb=" N THR b 132 " --> pdb=" O PHE b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 133 through 150 Processing helix chain 'b' and resid 167 through 172 Processing helix chain 'b' and resid 173 through 182 Processing helix chain 'b' and resid 208 through 228 removed outlier: 4.924A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N GLU b 228 " --> pdb=" O LEU b 224 " (cutoff:3.500A) Processing helix chain 'c' and resid 6 through 12 removed outlier: 3.753A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 3.663A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 Processing helix chain 'c' and resid 81 through 96 removed outlier: 4.284A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.227A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 5.600A 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 'c' and resid 210 through 215 Processing helix chain 'd' and resid 7 through 16 removed outlier: 4.346A pdb=" N LEU d 11 " --> pdb=" O PRO d 7 " (cutoff:3.500A) Processing helix chain 'd' and resid 27 through 33 Processing helix chain 'd' and resid 51 through 68 removed outlier: 3.559A pdb=" N LYS d 60 " --> pdb=" O GLN d 56 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.020A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.907A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 Processing helix chain 'd' and resid 112 through 123 Processing helix chain 'd' and resid 148 through 153 removed outlier: 5.080A pdb=" N GLN d 153 " --> pdb=" O GLU d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 4.150A pdb=" N GLY d 168 " --> pdb=" O ALA d 164 " (cutoff:3.500A) Processing helix chain 'd' and resid 189 through 194 Proline residue: d 194 - end of helix Processing helix chain 'd' and resid 198 through 208 removed outlier: 4.566A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.284A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.671A pdb=" N VAL e 113 " --> pdb=" O ALA e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 131 through 146 Processing helix chain 'e' and resid 148 through 157 Processing helix chain 'e' and resid 159 through 164 Processing helix chain 'f' and resid 11 through 19 removed outlier: 4.373A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 5.329A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 removed outlier: 4.026A pdb=" N ALA f 32 " --> pdb=" O GLN f 28 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP f 33 " --> pdb=" O ILE f 29 " (cutoff:3.500A) 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 54 removed outlier: 3.621A pdb=" N ALA g 39 " --> pdb=" O LYS g 35 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 Processing helix chain 'g' and resid 92 through 112 removed outlier: 4.066A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR g 97 " --> pdb=" O PRO g 93 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA g 98 " --> pdb=" O SER g 94 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N SER 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 148 removed outlier: 4.172A pdb=" N ALA g 147 " --> pdb=" O ARG g 143 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ASN g 148 " --> pdb=" O MET g 144 " (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 113 through 121 Processing helix chain 'i' and resid 32 through 37 Processing helix chain 'i' and resid 39 through 54 Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 89 Processing helix chain 'i' and resid 90 through 100 Proline residue: i 94 - end of helix Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.682A pdb=" N VAL j 84 " --> pdb=" O THR j 80 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.606A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLY k 50 " --> pdb=" O SER k 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 45 through 50' Processing helix chain 'k' and resid 53 through 59 removed outlier: 4.782A pdb=" N SER k 57 " --> pdb=" O GLY k 53 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N THR k 58 " --> pdb=" O SER k 54 " (cutoff:3.500A) Proline residue: k 59 - end of helix No H-bonds generated for 'chain 'k' and resid 53 through 59' Processing helix chain 'k' and resid 60 through 77 removed outlier: 4.059A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.478A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.195A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 Processing helix chain 'm' and resid 49 through 64 removed outlier: 3.708A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL m 63 " --> pdb=" O GLU m 59 " (cutoff:3.500A) Proline residue: m 64 - end of helix Processing helix chain 'm' and resid 66 through 84 removed outlier: 3.634A pdb=" N GLY m 84 " --> pdb=" O LEU m 80 " (cutoff:3.500A) 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: 3.689A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.656A pdb=" N GLN n 90 " --> pdb=" O ASP n 86 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY n 91 " --> pdb=" O THR n 87 " (cutoff:3.500A) 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 removed outlier: 3.874A pdb=" N ARG o 8 " --> pdb=" O THR o 4 " (cutoff:3.500A) Processing helix chain 'o' and resid 24 through 43 removed outlier: 4.196A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.557A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.178A 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 71 through 82 Processing helix chain 'p' and resid 86 through 100 Processing helix chain 'r' and resid 25 through 34 removed outlier: 3.772A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 4.842A 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 removed outlier: 4.193A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.476A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.422A 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 42 Processing helix chain 't' and resid 43 through 65 Proline residue: t 56 - end of helix Processing helix chain 't' and resid 68 through 87 removed outlier: 3.575A pdb=" N LEU t 86 " --> pdb=" O GLN t 82 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA t 87 " --> pdb=" O VAL t 83 " (cutoff:3.500A) Processing helix chain 'u' and resid 11 through 27 Processing helix chain 'u' and resid 28 through 38 removed outlier: 3.610A pdb=" N VAL u 32 " --> pdb=" O VAL u 28 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 removed outlier: 3.505A pdb=" N LYS u 46 " --> pdb=" O THR u 42 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '0' and resid 15 through 20 removed outlier: 6.147A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N MET 0 30 " --> pdb=" O GLU 0 47 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '2' and resid 21 through 24 No H-bonds generated for sheet with id= 2 Processing sheet with id= 3, first strand: chain '3' and resid 1 through 4 removed outlier: 6.332A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N SER 3 13 " --> pdb=" O SER 3 28 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 3 through 6 removed outlier: 5.338A pdb=" N VAL C 16 " --> pdb=" O CYS C 6 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'C' and resid 80 through 83 removed outlier: 3.910A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLY C 127 " --> pdb=" O LYS C 115 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLN C 117 " --> pdb=" O GLY C 127 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 138 through 142 removed outlier: 3.868A pdb=" N SER C 139 " --> pdb=" O LEU C 164 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.311A pdb=" N HIS C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.117A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 13.660A pdb=" N GLY D 201 " --> pdb=" O LYS D 117 " (cutoff:3.500A) removed outlier: 11.874A pdb=" N LYS D 117 " --> pdb=" O GLY D 201 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 80 through 84 removed outlier: 6.729A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 11, first strand: chain 'D' and resid 25 through 29 No H-bonds generated for sheet with id= 11 Processing sheet with id= 12, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.489A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 41 through 45 removed outlier: 4.632A pdb=" N GLY E 41 " --> pdb=" O GLN E 89 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N ARG E 43 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ARG E 87 " --> pdb=" O ARG E 43 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS E 45 " --> pdb=" O ALA E 85 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N ALA E 85 " --> pdb=" O HIS E 45 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.732A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASP E 167 " --> pdb=" O ALA E 145 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 65 through 69 removed outlier: 3.722A pdb=" N VAL F 66 " --> pdb=" O LYS F 88 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS F 88 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 17, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 18, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 19, first strand: chain 'G' and resid 121 through 125 removed outlier: 5.563A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'H' and resid 16 through 20 removed outlier: 4.342A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 14 through 19 Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.392A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.254A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N ILE J 86 " --> pdb=" O ALA J 11 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN J 59 " --> pdb=" O LEU J 87 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'K' and resid 122 through 125 Processing sheet with id= 25, first strand: chain 'L' and resid 39 through 42 Processing sheet with id= 26, first strand: chain 'L' and resid 63 through 67 removed outlier: 5.931A pdb=" N LEU L 103 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 37 removed outlier: 6.145A pdb=" N ALA M 108 " --> pdb=" O PHE M 102 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N PHE M 102 " --> pdb=" O ALA M 108 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N MET M 110 " --> pdb=" O ALA M 100 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.647A pdb=" N ALA N 50 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 41 through 47 removed outlier: 6.592A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 52 through 56 removed outlier: 3.977A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N ARG O 56 " --> pdb=" O ASN O 59 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.127A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.109A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 69 removed outlier: 3.725A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 removed outlier: 4.881A pdb=" N THR R 100 " --> pdb=" O GLY R 79 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.440A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 38 through 44 removed outlier: 5.318A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 80 through 85 removed outlier: 7.132A pdb=" N ARG T 80 " --> pdb=" O LYS T 95 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 4 through 7 Processing sheet with id= 40, first strand: chain 'U' and resid 41 through 46 removed outlier: 3.577A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ARG U 97 " --> pdb=" O TYR U 35 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N HIS U 92 " --> pdb=" O GLN U 82 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.255A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 43, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.576A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 34 through 41 Processing sheet with id= 45, first strand: chain 'Y' and resid 32 through 38 removed outlier: 4.355A pdb=" N HIS Y 33 " --> pdb=" O GLN Y 8 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'b' and resid 69 through 73 Processing sheet with id= 47, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.744A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.529A pdb=" N GLY c 148 " --> pdb=" O PHE c 203 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'd' and resid 142 through 147 removed outlier: 3.800A pdb=" N ASP d 143 " --> pdb=" O PHE d 184 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU d 180 " --> pdb=" O VAL d 147 " (cutoff:3.500A) removed outlier: 8.835A pdb=" N TRP d 172 " --> pdb=" O LYS d 185 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 11 through 15 removed outlier: 6.575A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.999A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'e' and resid 32 through 39 Processing sheet with id= 53, first strand: chain 'f' and resid 38 through 42 removed outlier: 6.438A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'f' and resid 43 through 47 removed outlier: 4.053A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N TYR f 59 " --> pdb=" O GLY f 43 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.103A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.555A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.667A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 42 through 52 removed outlier: 5.630A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 28 through 34 removed outlier: 7.376A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 29 through 34 removed outlier: 4.364A pdb=" N SER l 78 " --> pdb=" O CYS l 34 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 35 through 41 removed outlier: 4.813A pdb=" N LYS l 51 " --> pdb=" O ILE l 67 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'p' and resid 22 through 28 removed outlier: 3.655A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'q' and resid 8 through 12 removed outlier: 6.876A pdb=" N THR q 61 " --> pdb=" O VAL q 77 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 20 through 31 No H-bonds generated for sheet with id= 64 Processing sheet with id= 65, first strand: chain 's' and resid 30 through 34 removed outlier: 4.636A pdb=" N LEU s 47 " --> pdb=" O VAL s 62 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N ASN s 56 " --> pdb=" O ASN s 53 " (cutoff:3.500A) 1891 hydrogen bonds defined for protein. 5586 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3466 hydrogen bonds 5500 hydrogen bond angles 0 basepair planarities 1380 basepair parallelities 2135 stacking parallelities Total time for adding SS restraints: 199.40 Time building geometry restraints manager: 59.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 12641 1.31 - 1.43: 66708 1.43 - 1.56: 61034 1.56 - 1.69: 8841 1.69 - 1.82: 253 Bond restraints: 149477 Sorted by residual: bond pdb=" C4 5MU v 55 " pdb=" C5 5MU v 55 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.11e+02 bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.802 1.450 0.352 2.00e-02 2.50e+03 3.11e+02 bond pdb=" C11 80P a1602 " pdb=" C12 80P a1602 " ideal model delta sigma weight residual 1.240 1.554 -0.314 2.00e-02 2.50e+03 2.47e+02 bond pdb=" C11 80P a1603 " pdb=" C12 80P a1603 " ideal model delta sigma weight residual 1.240 1.546 -0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C08 80P a1602 " pdb=" C09 80P a1602 " ideal model delta sigma weight residual 1.332 1.631 -0.299 2.00e-02 2.50e+03 2.23e+02 ... (remaining 149472 not shown) Histogram of bond angle deviations from ideal: 99.20 - 108.56: 48961 108.56 - 117.92: 91902 117.92 - 127.27: 73057 127.27 - 136.63: 9737 136.63 - 145.99: 4 Bond angle restraints: 223661 Sorted by residual: angle pdb=" C11 80P a1601 " pdb=" C12 80P a1601 " pdb=" C13 80P a1601 " ideal model delta sigma weight residual 142.25 116.69 25.56 3.00e+00 1.11e-01 7.26e+01 angle pdb=" C11 80P a1603 " pdb=" C12 80P a1603 " pdb=" C13 80P a1603 " ideal model delta sigma weight residual 142.25 116.97 25.28 3.00e+00 1.11e-01 7.10e+01 angle pdb=" C11 80P a1602 " pdb=" C12 80P a1602 " pdb=" C13 80P a1602 " ideal model delta sigma weight residual 142.25 117.24 25.01 3.00e+00 1.11e-01 6.95e+01 angle pdb=" C13 80P a1601 " pdb=" C12 80P a1601 " pdb=" C17 80P a1601 " ideal model delta sigma weight residual 101.90 123.63 -21.73 3.00e+00 1.11e-01 5.25e+01 angle pdb=" C13 80P a1603 " pdb=" C12 80P a1603 " pdb=" C17 80P a1603 " ideal model delta sigma weight residual 101.90 123.19 -21.29 3.00e+00 1.11e-01 5.04e+01 ... (remaining 223656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 84398 35.97 - 71.95: 9802 71.95 - 107.92: 1146 107.92 - 143.89: 35 143.89 - 179.87: 72 Dihedral angle restraints: 95453 sinusoidal: 79787 harmonic: 15666 Sorted by residual: dihedral pdb=" O4' U a1378 " pdb=" C1' U a1378 " pdb=" N1 U a1378 " pdb=" C2 U a1378 " ideal model delta sinusoidal sigma weight residual -160.00 10.16 -170.16 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C A 912 " pdb=" C1' C A 912 " pdb=" N1 C A 912 " pdb=" C2 C A 912 " ideal model delta sinusoidal sigma weight residual 200.00 30.09 169.91 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' C a 516 " pdb=" C1' C a 516 " pdb=" N1 C a 516 " pdb=" C2 C a 516 " ideal model delta sinusoidal sigma weight residual 200.00 30.94 169.06 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 95450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.133: 28564 1.133 - 2.265: 0 2.265 - 3.398: 0 3.398 - 4.531: 0 4.531 - 5.664: 3 Chirality restraints: 28567 Sorted by residual: chirality pdb=" C08 80P a1602 " pdb=" C07 80P a1602 " pdb=" C09 80P a1602 " pdb=" C21 80P a1602 " both_signs ideal model delta sigma weight residual False 2.49 -3.18 5.66 2.00e-01 2.50e+01 8.02e+02 chirality pdb=" C08 80P a1603 " pdb=" C07 80P a1603 " pdb=" C09 80P a1603 " pdb=" C21 80P a1603 " both_signs ideal model delta sigma weight residual False 2.49 -3.15 5.64 2.00e-01 2.50e+01 7.94e+02 chirality pdb=" C08 80P a1601 " pdb=" C07 80P a1601 " pdb=" C09 80P a1601 " pdb=" C21 80P a1601 " both_signs ideal model delta sigma weight residual False 2.49 -3.06 5.54 2.00e-01 2.50e+01 7.68e+02 ... (remaining 28564 not shown) Planarity restraints: 11978 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.058 2.00e-02 2.50e+03 6.17e-01 8.58e+03 pdb=" C4' 7MG A2065 " 0.458 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.736 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.628 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.198 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.947 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.197 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.979 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " -0.046 2.00e-02 2.50e+03 6.05e-01 8.25e+03 pdb=" C4' 7MG a 524 " -0.452 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " -0.723 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " 0.608 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " 0.208 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " -0.931 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " -0.204 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.055 2.00e-02 2.50e+03 5.90e-01 7.84e+03 pdb=" C4' 2MG a1204 " 0.437 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.624 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.620 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.962 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.221 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.897 2.00e-02 2.50e+03 ... (remaining 11975 not shown) Histogram of nonbonded interaction distances: 1.80 - 2.42: 292 2.42 - 3.04: 74272 3.04 - 3.66: 242227 3.66 - 4.28: 384316 4.28 - 4.90: 518435 Nonbonded interactions: 1219542 Sorted by model distance: nonbonded pdb=" O2' G A 799 " pdb=" OP1 A A 800 " model vdw 1.799 2.440 nonbonded pdb=" O37 80P a1603 " pdb="MG MG a1606 " model vdw 1.831 2.170 nonbonded pdb=" O2' A A1923 " pdb=" O5' A A1924 " model vdw 1.890 2.440 nonbonded pdb=" OP2 U a 423 " pdb=" O2' G a 424 " model vdw 1.916 2.440 nonbonded pdb=" O2' U A 533 " pdb=" OD2 ASP P 49 " model vdw 1.925 2.440 ... (remaining 1219537 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: 7.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.600 Construct map_model_manager: 0.080 Extract box with map and model: 29.650 Check model and map are aligned: 1.450 Set scattering table: 0.950 Process input model: 488.210 Find NCS groups from input model: 2.670 Set up NCS constraints: 0.330 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:10.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 541.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 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 : 0.006 0.353 149477 Z= 0.357 Angle : 0.612 25.555 223661 Z= 0.311 Chirality : 0.067 5.664 28567 Planarity : 0.017 0.617 11978 Dihedral : 23.286 179.867 85363 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.64 % Favored : 97.24 % Rotamer: Outliers : 2.32 % Allowed : 24.97 % Favored : 72.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.11), residues: 5407 helix: 2.18 (0.12), residues: 1862 sheet: 0.68 (0.16), residues: 1027 loop : -0.25 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP c 201 HIS 0.017 0.001 HIS f 94 PHE 0.018 0.001 PHE o 43 TYR 0.017 0.001 TYR T 94 ARG 0.016 0.001 ARG F 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1193 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1089 time to evaluate : 5.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 0 6 ARG cc_start: 0.7618 (OUTLIER) cc_final: 0.6990 (mtp180) REVERT: 2 59 ARG cc_start: 0.7986 (mtp180) cc_final: 0.7731 (mtp180) REVERT: 3 36 ARG cc_start: 0.6895 (ttp-170) cc_final: 0.6628 (ttt180) REVERT: C 10 SER cc_start: 0.7882 (m) cc_final: 0.7596 (m) REVERT: F 81 ASP cc_start: 0.5582 (OUTLIER) cc_final: 0.5344 (m-30) REVERT: I 37 ARG cc_start: 0.8447 (ttt180) cc_final: 0.8188 (ttt180) REVERT: L 41 ARG cc_start: 0.8004 (mtt180) cc_final: 0.7639 (mtp85) REVERT: P 56 GLN cc_start: 0.8152 (mt0) cc_final: 0.7921 (mt0) REVERT: Z 38 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7611 (ttm-80) REVERT: d 72 ARG cc_start: 0.6041 (tmm160) cc_final: 0.5355 (ptt180) REVERT: g 26 PHE cc_start: 0.8170 (t80) cc_final: 0.7834 (t80) REVERT: i 70 ILE cc_start: 0.8083 (OUTLIER) cc_final: 0.7771 (mp) REVERT: l 114 ARG cc_start: 0.7452 (mtp-110) cc_final: 0.7212 (mtp-110) REVERT: n 90 GLN cc_start: 0.7389 (mt0) cc_final: 0.7137 (mt0) REVERT: p 19 MET cc_start: 0.8109 (pmm) cc_final: 0.7880 (ptp) outliers start: 104 outliers final: 87 residues processed: 1177 average time/residue: 2.2600 time to fit residues: 3678.2658 Evaluate side-chains 1141 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1051 time to evaluate : 5.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 2 residue 28 LYS Chi-restraints excluded: chain 2 residue 52 SER Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 124 ILE Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 119 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 86 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain U residue 57 SER Chi-restraints excluded: chain U residue 67 ILE Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 74 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 10 ASP Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 172 ARG Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain i residue 126 SER Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 47 GLU Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 67 GLU Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 96 VAL Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 29 THR Chi-restraints excluded: chain p residue 91 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 81 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 55 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 817 optimal weight: 5.9990 chunk 733 optimal weight: 30.0000 chunk 407 optimal weight: 6.9990 chunk 250 optimal weight: 7.9990 chunk 494 optimal weight: 0.3980 chunk 391 optimal weight: 5.9990 chunk 758 optimal weight: 1.9990 chunk 293 optimal weight: 6.9990 chunk 461 optimal weight: 0.0370 chunk 564 optimal weight: 9.9990 chunk 879 optimal weight: 0.9990 overall best weight: 1.8864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 29 GLN E 105 GLN I 63 GLN I 136 GLN O 9 GLN O 13 ASN O 32 GLN Q 86 GLN R 34 ASN S 58 ASN V 74 GLN W 36 HIS Z 4 GLN Z 5 GLN Z 25 ASN b 57 ASN b 105 ASN c 28 GLN c 100 GLN c 216 ASN d 138 GLN f 87 ASN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 29 HIS h 18 GLN h 53 GLN i 124 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 118 ASN m 14 HIS o 20 ASN o 28 GLN o 40 GLN o 62 GLN p 64 GLN q 31 GLN r 36 ASN r 61 GLN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 149477 Z= 0.270 Angle : 0.771 26.682 223661 Z= 0.395 Chirality : 0.046 2.433 28567 Planarity : 0.007 0.134 11978 Dihedral : 23.239 179.035 74807 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.66 % Favored : 97.24 % Rotamer: Outliers : 5.87 % Allowed : 22.65 % Favored : 71.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.11), residues: 5407 helix: 1.84 (0.12), residues: 1861 sheet: 0.59 (0.16), residues: 1029 loop : -0.35 (0.11), residues: 2517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP c 201 HIS 0.012 0.002 HIS j 15 PHE 0.023 0.002 PHE o 43 TYR 0.023 0.002 TYR n 73 ARG 0.013 0.001 ARG n 81 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1328 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 1065 time to evaluate : 5.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 59 ARG cc_start: 0.8098 (mtp180) cc_final: 0.7795 (mtp180) REVERT: C 223 MET cc_start: 0.7688 (mtp) cc_final: 0.7384 (mtp) REVERT: D 38 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7849 (mp) REVERT: E 24 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: I 37 ARG cc_start: 0.8555 (ttt180) cc_final: 0.8263 (ttt180) REVERT: I 109 LEU cc_start: 0.8140 (mt) cc_final: 0.7861 (mp) REVERT: L 14 LYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8436 (ttmm) REVERT: L 41 ARG cc_start: 0.8143 (mtt180) cc_final: 0.7795 (ttp-170) REVERT: P 56 GLN cc_start: 0.8250 (mt0) cc_final: 0.7973 (mt0) REVERT: P 84 LYS cc_start: 0.8199 (OUTLIER) cc_final: 0.6971 (ttmm) REVERT: Q 74 ILE cc_start: 0.8455 (OUTLIER) cc_final: 0.8123 (mp) REVERT: S 47 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7373 (mt-10) REVERT: U 91 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7580 (mtp) REVERT: V 77 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7066 (ptt180) REVERT: b 105 ASN cc_start: 0.4506 (OUTLIER) cc_final: 0.4265 (p0) REVERT: c 17 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7053 (mtt180) REVERT: d 72 ARG cc_start: 0.6290 (tmm160) cc_final: 0.5481 (ptt180) REVERT: d 113 ARG cc_start: 0.6481 (mtt90) cc_final: 0.6218 (mtm-85) REVERT: f 94 HIS cc_start: 0.5834 (OUTLIER) cc_final: 0.5068 (p90) REVERT: g 26 PHE cc_start: 0.8208 (t80) cc_final: 0.7884 (t80) REVERT: g 32 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7502 (mt0) REVERT: h 48 ASN cc_start: 0.7362 (t0) cc_final: 0.7008 (t0) REVERT: i 44 MET cc_start: 0.6969 (OUTLIER) cc_final: 0.6738 (mtt) REVERT: i 70 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7954 (mp) REVERT: j 99 GLN cc_start: 0.7523 (OUTLIER) cc_final: 0.7129 (mp10) REVERT: o 21 ASP cc_start: 0.7504 (t70) cc_final: 0.7244 (t70) REVERT: q 28 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.6697 (ptt90) REVERT: r 32 TYR cc_start: 0.6481 (m-80) cc_final: 0.6158 (m-80) REVERT: r 63 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6531 (ptp-170) REVERT: s 43 ASP cc_start: 0.6785 (OUTLIER) cc_final: 0.6548 (p0) outliers start: 263 outliers final: 147 residues processed: 1214 average time/residue: 2.2767 time to fit residues: 3843.5805 Evaluate side-chains 1204 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 1039 time to evaluate : 5.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 MET Chi-restraints excluded: chain 0 residue 32 ILE Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 52 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 67 VAL Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain H residue 58 GLU Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 118 MET Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 124 VAL Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 90 LYS Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 62 GLU Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 24 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain b residue 10 ASP Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 81 ILE Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 105 ASN Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 188 ILE Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 17 ARG Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 216 ASN Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 138 GLN Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 32 GLN Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain k residue 118 ASN Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 81 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 63 ARG Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 488 optimal weight: 0.7980 chunk 272 optimal weight: 8.9990 chunk 731 optimal weight: 4.9990 chunk 598 optimal weight: 3.9990 chunk 242 optimal weight: 7.9990 chunk 880 optimal weight: 9.9990 chunk 951 optimal weight: 0.9980 chunk 784 optimal weight: 0.9980 chunk 873 optimal weight: 30.0000 chunk 300 optimal weight: 6.9990 chunk 706 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 185 HIS E 96 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN K 101 ASN O 9 GLN O 13 ASN O 32 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN R 34 ASN S 58 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN b 57 ASN b 60 ASN b 105 ASN c 100 GLN c 139 GLN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN h 53 GLN i 124 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN o 20 ASN o 28 GLN o 37 ASN o 40 GLN p 64 GLN q 31 GLN r 61 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 149477 Z= 0.276 Angle : 0.766 24.615 223661 Z= 0.394 Chirality : 0.046 2.207 28567 Planarity : 0.007 0.136 11978 Dihedral : 23.202 179.944 74736 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.72 % Favored : 97.17 % Rotamer: Outliers : 6.23 % Allowed : 22.60 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.11), residues: 5407 helix: 1.66 (0.12), residues: 1850 sheet: 0.50 (0.16), residues: 1008 loop : -0.50 (0.11), residues: 2549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP c 201 HIS 0.012 0.002 HIS j 15 PHE 0.019 0.002 PHE o 43 TYR 0.020 0.002 TYR n 73 ARG 0.013 0.001 ARG c 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1326 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 279 poor density : 1047 time to evaluate : 5.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 59 ARG cc_start: 0.8163 (mtp180) cc_final: 0.7853 (mtp180) REVERT: C 18 LYS cc_start: 0.6515 (OUTLIER) cc_final: 0.6065 (mttp) REVERT: D 38 ILE cc_start: 0.8177 (OUTLIER) cc_final: 0.7762 (mp) REVERT: E 24 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7370 (tt0) REVERT: F 80 ARG cc_start: 0.4665 (OUTLIER) cc_final: 0.4434 (pmt-80) REVERT: F 130 MET cc_start: 0.3431 (OUTLIER) cc_final: 0.3155 (ttp) REVERT: I 84 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8414 (tp) REVERT: J 66 LYS cc_start: 0.8610 (OUTLIER) cc_final: 0.8320 (mtpp) REVERT: L 14 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: P 56 GLN cc_start: 0.8262 (mt0) cc_final: 0.7971 (mt0) REVERT: P 84 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.6987 (ttmm) REVERT: Q 74 ILE cc_start: 0.8423 (OUTLIER) cc_final: 0.8072 (mp) REVERT: S 20 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.6601 (mp10) REVERT: U 91 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: V 77 ARG cc_start: 0.7816 (OUTLIER) cc_final: 0.7211 (ptt180) REVERT: Z 38 ARG cc_start: 0.8145 (ttm-80) cc_final: 0.7844 (tmt90) REVERT: d 72 ARG cc_start: 0.6408 (ttm170) cc_final: 0.5715 (ptt180) REVERT: f 94 HIS cc_start: 0.5890 (OUTLIER) cc_final: 0.5173 (p90) REVERT: g 26 PHE cc_start: 0.8211 (t80) cc_final: 0.7892 (t80) REVERT: g 32 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7491 (mt0) REVERT: i 44 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6745 (mtt) REVERT: i 70 ILE cc_start: 0.8275 (OUTLIER) cc_final: 0.7971 (mp) REVERT: j 99 GLN cc_start: 0.7553 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: l 49 MET cc_start: 0.5559 (mmm) cc_final: 0.5319 (mmm) REVERT: o 21 ASP cc_start: 0.7499 (t70) cc_final: 0.7231 (t70) REVERT: q 28 ARG cc_start: 0.7880 (OUTLIER) cc_final: 0.6757 (ptt90) REVERT: r 32 TYR cc_start: 0.6467 (m-80) cc_final: 0.6143 (m-80) REVERT: r 63 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7247 (ptp-170) REVERT: s 43 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6556 (p0) outliers start: 279 outliers final: 167 residues processed: 1203 average time/residue: 2.2313 time to fit residues: 3714.3596 Evaluate side-chains 1221 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1033 time to evaluate : 5.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 MET Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain E residue 15 GLU Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 11 GLU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 80 ARG Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 24 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 25 VAL Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 42 TRP Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 32 GLN Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 81 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 63 ARG Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 870 optimal weight: 20.0000 chunk 662 optimal weight: 3.9990 chunk 457 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 420 optimal weight: 10.0000 chunk 591 optimal weight: 3.9990 chunk 883 optimal weight: 30.0000 chunk 935 optimal weight: 4.9990 chunk 461 optimal weight: 4.9990 chunk 837 optimal weight: 2.9990 chunk 252 optimal weight: 7.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 96 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 110 GLN K 18 HIS L 89 ASN O 9 GLN O 13 ASN O 32 GLN ** Q 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 58 ASN Z 4 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 139 GLN d 36 ASN e 120 HIS ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 148 ASN h 41 GLN h 42 GLN h 53 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN o 20 ASN o 28 GLN o 40 GLN p 64 GLN r 61 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.115 149477 Z= 0.553 Angle : 1.085 24.840 223661 Z= 0.531 Chirality : 0.060 2.434 28567 Planarity : 0.009 0.149 11978 Dihedral : 23.484 179.901 74720 Min Nonbonded Distance : 1.689 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.40 % Favored : 96.45 % Rotamer: Outliers : 7.33 % Allowed : 22.83 % Favored : 69.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.11), residues: 5407 helix: 0.82 (0.11), residues: 1839 sheet: 0.25 (0.16), residues: 1011 loop : -0.80 (0.11), residues: 2557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP c 201 HIS 0.017 0.003 HIS j 15 PHE 0.036 0.004 PHE s 16 TYR 0.032 0.004 TYR h 66 ARG 0.027 0.002 ARG o 53 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1391 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1063 time to evaluate : 5.735 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 2 24 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7347 (mttm) REVERT: C 18 LYS cc_start: 0.6618 (OUTLIER) cc_final: 0.6170 (mttp) REVERT: C 189 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7188 (mtp85) REVERT: D 38 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7824 (mp) REVERT: D 102 ASP cc_start: 0.7151 (OUTLIER) cc_final: 0.6882 (p0) REVERT: E 24 GLU cc_start: 0.8044 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: F 130 MET cc_start: 0.3353 (OUTLIER) cc_final: 0.3123 (ttp) REVERT: G 43 LEU cc_start: 0.6949 (OUTLIER) cc_final: 0.6655 (tp) REVERT: I 84 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8431 (tt) REVERT: J 66 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8409 (mtpp) REVERT: L 14 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8406 (ttmm) REVERT: P 56 GLN cc_start: 0.8325 (mt0) cc_final: 0.8048 (mt0) REVERT: P 84 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.6963 (ttmm) REVERT: Q 73 ARG cc_start: 0.8056 (OUTLIER) cc_final: 0.7753 (mtp180) REVERT: S 20 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6553 (mp10) REVERT: S 56 LYS cc_start: 0.8467 (OUTLIER) cc_final: 0.8084 (ttpt) REVERT: T 95 LYS cc_start: 0.7122 (OUTLIER) cc_final: 0.6909 (mmtt) REVERT: U 91 MET cc_start: 0.8327 (OUTLIER) cc_final: 0.7738 (mtp) REVERT: V 77 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.7391 (ptt180) REVERT: Z 38 ARG cc_start: 0.8147 (ttm-80) cc_final: 0.7878 (tmt90) REVERT: c 139 GLN cc_start: 0.6298 (mt0) cc_final: 0.5961 (mt0) REVERT: d 72 ARG cc_start: 0.6630 (OUTLIER) cc_final: 0.5870 (ptt180) REVERT: e 12 GLU cc_start: 0.5715 (OUTLIER) cc_final: 0.5457 (mt-10) REVERT: e 81 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7742 (mm110) REVERT: f 94 HIS cc_start: 0.6024 (OUTLIER) cc_final: 0.5458 (p90) REVERT: g 32 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7475 (mt0) REVERT: h 86 GLN cc_start: 0.7637 (OUTLIER) cc_final: 0.7414 (tt0) REVERT: i 44 MET cc_start: 0.7071 (OUTLIER) cc_final: 0.6773 (mtt) REVERT: i 70 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8237 (mt) REVERT: j 99 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7345 (mp10) REVERT: l 49 MET cc_start: 0.5655 (mmm) cc_final: 0.5282 (mmm) REVERT: n 85 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.7890 (tmt90) REVERT: q 28 ARG cc_start: 0.7910 (OUTLIER) cc_final: 0.6824 (ptt90) REVERT: r 32 TYR cc_start: 0.6525 (m-80) cc_final: 0.6231 (m-80) REVERT: r 54 GLN cc_start: 0.6216 (mm-40) cc_final: 0.6014 (mm-40) REVERT: s 43 ASP cc_start: 0.6857 (OUTLIER) cc_final: 0.6646 (p0) REVERT: u 45 ARG cc_start: 0.5278 (OUTLIER) cc_final: 0.5077 (mpp-170) outliers start: 328 outliers final: 219 residues processed: 1260 average time/residue: 2.2419 time to fit residues: 3915.0936 Evaluate side-chains 1295 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1045 time to evaluate : 5.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 MET Chi-restraints excluded: chain 0 residue 39 ILE Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 24 LYS Chi-restraints excluded: chain 2 residue 52 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 91 GLU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 140 LEU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 102 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 32 THR Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 40 LEU Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 56 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 8 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 24 GLN Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 144 GLU Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 76 VAL Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain c residue 201 TRP Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 61 LEU Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 32 GLN Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 135 ILE Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 86 GLN Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 32 THR Chi-restraints excluded: chain j residue 47 GLU Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 37 VAL Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain n residue 87 THR Chi-restraints excluded: chain o residue 53 ARG Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 14 VAL Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 45 LEU Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 81 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 63 ARG Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Chi-restraints excluded: chain u residue 45 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 779 optimal weight: 30.0000 chunk 531 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 696 optimal weight: 40.0000 chunk 386 optimal weight: 20.0000 chunk 798 optimal weight: 5.9990 chunk 646 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 477 optimal weight: 2.9990 chunk 839 optimal weight: 0.9980 chunk 236 optimal weight: 7.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 37 GLN E 96 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN L 89 ASN O 9 GLN O 13 ASN O 32 GLN Q 12 HIS Q 43 ASN S 58 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN b 60 ASN b 105 ASN c 100 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN h 98 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 90 GLN o 20 ASN o 28 GLN o 40 GLN p 64 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 149477 Z= 0.353 Angle : 0.852 24.908 223661 Z= 0.432 Chirality : 0.050 2.233 28567 Planarity : 0.007 0.138 11978 Dihedral : 23.266 179.991 74715 Min Nonbonded Distance : 1.698 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.83 % Favored : 97.06 % Rotamer: Outliers : 6.37 % Allowed : 24.23 % Favored : 69.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5407 helix: 1.11 (0.12), residues: 1859 sheet: 0.25 (0.15), residues: 1034 loop : -0.78 (0.11), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP c 201 HIS 0.014 0.002 HIS j 15 PHE 0.025 0.003 PHE s 16 TYR 0.022 0.003 TYR i 5 ARG 0.015 0.001 ARG n 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1334 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1049 time to evaluate : 5.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 36 ARG cc_start: 0.7097 (OUTLIER) cc_final: 0.6762 (ttp-170) REVERT: C 18 LYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6138 (mttp) REVERT: C 189 ARG cc_start: 0.7752 (OUTLIER) cc_final: 0.7239 (mtp85) REVERT: D 38 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7807 (mp) REVERT: D 102 ASP cc_start: 0.7100 (OUTLIER) cc_final: 0.6852 (p0) REVERT: E 24 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7380 (tt0) REVERT: F 130 MET cc_start: 0.3270 (OUTLIER) cc_final: 0.2967 (ttp) REVERT: G 84 GLU cc_start: 0.5699 (OUTLIER) cc_final: 0.5265 (pp20) REVERT: I 84 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8383 (tp) REVERT: J 66 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8335 (mtpp) REVERT: L 14 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8419 (ttmm) REVERT: L 89 ASN cc_start: 0.8094 (m-40) cc_final: 0.7659 (m110) REVERT: P 56 GLN cc_start: 0.8276 (mt0) cc_final: 0.7983 (mt0) REVERT: P 84 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.6968 (ttmm) REVERT: Q 73 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7735 (mtp180) REVERT: S 1 MET cc_start: 0.4288 (ttt) cc_final: 0.3986 (ttt) REVERT: S 20 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6598 (mp10) REVERT: T 3 LYS cc_start: 0.7224 (OUTLIER) cc_final: 0.6924 (tptp) REVERT: T 95 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6884 (mmtt) REVERT: U 91 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.7662 (mtp) REVERT: V 77 ARG cc_start: 0.7796 (OUTLIER) cc_final: 0.7311 (ptt180) REVERT: Z 38 ARG cc_start: 0.8087 (ttm-80) cc_final: 0.7836 (tmt90) REVERT: d 72 ARG cc_start: 0.6502 (tmm160) cc_final: 0.5778 (ptt180) REVERT: e 70 MET cc_start: 0.6444 (OUTLIER) cc_final: 0.5796 (ttm) REVERT: e 81 GLN cc_start: 0.8126 (OUTLIER) cc_final: 0.7701 (mm110) REVERT: f 93 GLU cc_start: 0.5730 (OUTLIER) cc_final: 0.5457 (mm-30) REVERT: f 94 HIS cc_start: 0.6090 (OUTLIER) cc_final: 0.5550 (p90) REVERT: g 26 PHE cc_start: 0.8225 (t80) cc_final: 0.7886 (t80) REVERT: g 32 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7450 (mt0) REVERT: i 44 MET cc_start: 0.7043 (OUTLIER) cc_final: 0.6814 (mtt) REVERT: i 70 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8056 (mt) REVERT: j 99 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7236 (mp10) REVERT: l 49 MET cc_start: 0.5655 (mmm) cc_final: 0.5317 (mmm) REVERT: q 28 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.6801 (ptt90) REVERT: r 32 TYR cc_start: 0.6469 (m-80) cc_final: 0.6166 (m-80) REVERT: r 54 GLN cc_start: 0.6183 (mm-40) cc_final: 0.5966 (mm-40) REVERT: s 43 ASP cc_start: 0.6812 (OUTLIER) cc_final: 0.6590 (p0) outliers start: 285 outliers final: 199 residues processed: 1209 average time/residue: 2.2820 time to fit residues: 3816.7728 Evaluate side-chains 1263 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1036 time to evaluate : 5.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 30 MET Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain E residue 189 VAL Chi-restraints excluded: chain E residue 197 VAL Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 66 LYS Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 35 LYS Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain Q residue 94 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 95 LYS Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 53 LYS Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 24 GLN Chi-restraints excluded: chain Y residue 47 ILE Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain b residue 214 LEU Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 149 ILE Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 90 GLU Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 93 GLU Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 32 GLN Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 44 MET Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 28 THR Chi-restraints excluded: chain j residue 47 GLU Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 45 ILE Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain q residue 81 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain r residue 63 ARG Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 314 optimal weight: 10.0000 chunk 842 optimal weight: 0.6980 chunk 184 optimal weight: 5.9990 chunk 549 optimal weight: 1.9990 chunk 230 optimal weight: 8.9990 chunk 936 optimal weight: 0.8980 chunk 777 optimal weight: 8.9990 chunk 433 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 309 optimal weight: 0.3980 chunk 491 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 53 HIS ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 13 ASN O 32 GLN Q 43 ASN Q 86 GLN U 16 GLN Z 4 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 139 GLN ** d 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 142 HIS h 41 GLN h 42 GLN i 35 GLN i 124 GLN ** j 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN o 37 ASN p 64 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.1455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 149477 Z= 0.171 Angle : 0.668 24.741 223661 Z= 0.349 Chirality : 0.042 2.027 28567 Planarity : 0.006 0.129 11978 Dihedral : 23.048 179.930 74709 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.77 % Favored : 97.13 % Rotamer: Outliers : 4.94 % Allowed : 25.51 % Favored : 69.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 5407 helix: 1.73 (0.12), residues: 1866 sheet: 0.42 (0.15), residues: 1057 loop : -0.59 (0.12), residues: 2484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP c 201 HIS 0.012 0.001 HIS f 94 PHE 0.013 0.001 PHE M 80 TYR 0.017 0.002 TYR N 98 ARG 0.012 0.001 ARG c 143 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1276 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1055 time to evaluate : 5.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 19 ARG cc_start: 0.8195 (mtt180) cc_final: 0.7614 (mtt180) REVERT: C 5 LYS cc_start: 0.6982 (tptp) cc_final: 0.6517 (tptp) REVERT: C 18 LYS cc_start: 0.6489 (OUTLIER) cc_final: 0.6057 (mttp) REVERT: C 223 MET cc_start: 0.7660 (OUTLIER) cc_final: 0.7424 (mtp) REVERT: D 95 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8485 (p) REVERT: D 102 ASP cc_start: 0.7038 (OUTLIER) cc_final: 0.6821 (p0) REVERT: F 130 MET cc_start: 0.3221 (OUTLIER) cc_final: 0.3020 (ttp) REVERT: K 4 ARG cc_start: 0.8301 (OUTLIER) cc_final: 0.7807 (mpt180) REVERT: L 14 LYS cc_start: 0.8862 (OUTLIER) cc_final: 0.8404 (ttmm) REVERT: L 89 ASN cc_start: 0.8183 (m-40) cc_final: 0.7951 (m110) REVERT: P 56 GLN cc_start: 0.8248 (mt0) cc_final: 0.7928 (mt0) REVERT: S 1 MET cc_start: 0.4159 (ttt) cc_final: 0.3838 (ttt) REVERT: S 20 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6613 (mp10) REVERT: T 3 LYS cc_start: 0.7085 (OUTLIER) cc_final: 0.6547 (tptp) REVERT: U 91 MET cc_start: 0.8264 (OUTLIER) cc_final: 0.7625 (mtp) REVERT: V 77 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.7173 (ptt180) REVERT: Z 38 ARG cc_start: 0.8038 (ttm-80) cc_final: 0.7779 (tmt90) REVERT: c 95 MET cc_start: 0.7658 (OUTLIER) cc_final: 0.6910 (mtm) REVERT: d 72 ARG cc_start: 0.6354 (ttm170) cc_final: 0.5732 (ptt180) REVERT: d 113 ARG cc_start: 0.6411 (mtt90) cc_final: 0.6050 (mtt180) REVERT: e 70 MET cc_start: 0.6165 (OUTLIER) cc_final: 0.5648 (ttm) REVERT: f 94 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5465 (p90) REVERT: g 26 PHE cc_start: 0.8193 (t80) cc_final: 0.7834 (t80) REVERT: i 70 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7806 (mp) REVERT: j 99 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7159 (mp10) REVERT: l 49 MET cc_start: 0.5844 (mmm) cc_final: 0.5469 (mmm) REVERT: q 7 ARG cc_start: 0.6496 (OUTLIER) cc_final: 0.6046 (mtt90) REVERT: q 28 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.6772 (ptt90) REVERT: r 32 TYR cc_start: 0.6452 (m-80) cc_final: 0.6109 (m-80) REVERT: r 63 ARG cc_start: 0.7497 (ptp-170) cc_final: 0.7224 (mtm180) REVERT: s 43 ASP cc_start: 0.6839 (OUTLIER) cc_final: 0.6613 (p0) outliers start: 221 outliers final: 129 residues processed: 1178 average time/residue: 2.3459 time to fit residues: 3816.2526 Evaluate side-chains 1186 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1038 time to evaluate : 5.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 26 MET Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 18 LYS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 130 MET Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain b residue 40 ILE Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 186 ILE Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 902 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 533 optimal weight: 7.9990 chunk 683 optimal weight: 30.0000 chunk 529 optimal weight: 3.9990 chunk 788 optimal weight: 0.8980 chunk 522 optimal weight: 0.0570 chunk 932 optimal weight: 1.9990 chunk 583 optimal weight: 4.9990 chunk 568 optimal weight: 10.0000 chunk 430 optimal weight: 0.8980 overall best weight: 1.3702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 9 GLN O 13 ASN O 32 GLN Q 43 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 100 GLN c 139 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN j 58 ASN o 20 ASN o 28 GLN p 64 GLN r 61 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 149477 Z= 0.208 Angle : 0.701 24.566 223661 Z= 0.364 Chirality : 0.043 2.115 28567 Planarity : 0.006 0.132 11978 Dihedral : 23.047 179.713 74693 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.79 % Favored : 97.10 % Rotamer: Outliers : 5.03 % Allowed : 26.02 % Favored : 68.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.11), residues: 5407 helix: 1.73 (0.12), residues: 1856 sheet: 0.37 (0.15), residues: 1056 loop : -0.56 (0.12), residues: 2495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP c 201 HIS 0.013 0.001 HIS f 94 PHE 0.017 0.002 PHE 0 45 TYR 0.019 0.002 TYR N 98 ARG 0.013 0.001 ARG c 143 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1246 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 225 poor density : 1021 time to evaluate : 5.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 10 LEU cc_start: 0.8709 (tp) cc_final: 0.8251 (tt) REVERT: C 5 LYS cc_start: 0.7010 (tptp) cc_final: 0.6542 (tptp) REVERT: C 223 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7336 (mtp) REVERT: C 266 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7751 (mmp) REVERT: D 38 ILE cc_start: 0.8251 (OUTLIER) cc_final: 0.7842 (mp) REVERT: L 14 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8394 (ttmm) REVERT: P 56 GLN cc_start: 0.8252 (mt0) cc_final: 0.7943 (mt0) REVERT: P 84 LYS cc_start: 0.8149 (OUTLIER) cc_final: 0.6975 (ttmm) REVERT: S 1 MET cc_start: 0.4035 (ttt) cc_final: 0.3711 (ttt) REVERT: S 20 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: T 3 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6799 (tptp) REVERT: U 47 GLU cc_start: 0.7182 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: U 91 MET cc_start: 0.8269 (OUTLIER) cc_final: 0.7608 (mtp) REVERT: V 77 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7240 (ptt180) REVERT: Z 38 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7776 (tmt90) REVERT: c 95 MET cc_start: 0.7702 (OUTLIER) cc_final: 0.6923 (mtm) REVERT: d 72 ARG cc_start: 0.6389 (ttm170) cc_final: 0.5749 (ptt180) REVERT: d 113 ARG cc_start: 0.6455 (mtt90) cc_final: 0.6127 (mtt90) REVERT: d 205 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5857 (tp) REVERT: e 70 MET cc_start: 0.6224 (OUTLIER) cc_final: 0.5573 (ttm) REVERT: f 94 HIS cc_start: 0.6111 (OUTLIER) cc_final: 0.5510 (p90) REVERT: g 26 PHE cc_start: 0.8203 (t80) cc_final: 0.7866 (t80) REVERT: i 70 ILE cc_start: 0.8224 (OUTLIER) cc_final: 0.7944 (mp) REVERT: j 99 GLN cc_start: 0.7543 (OUTLIER) cc_final: 0.7169 (mp10) REVERT: l 49 MET cc_start: 0.5787 (mmm) cc_final: 0.5421 (mmm) REVERT: q 7 ARG cc_start: 0.6541 (OUTLIER) cc_final: 0.6085 (mtt90) REVERT: q 28 ARG cc_start: 0.7866 (OUTLIER) cc_final: 0.6774 (ptt90) REVERT: r 32 TYR cc_start: 0.6480 (m-80) cc_final: 0.6129 (m-80) REVERT: r 63 ARG cc_start: 0.7553 (ptp-170) cc_final: 0.7296 (mtm180) REVERT: s 43 ASP cc_start: 0.6841 (OUTLIER) cc_final: 0.6625 (p0) outliers start: 225 outliers final: 157 residues processed: 1151 average time/residue: 2.2960 time to fit residues: 3661.3467 Evaluate side-chains 1193 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1017 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain S residue 86 LEU Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 8 MET Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain d residue 205 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain f residue 6 ILE Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 39 ILE Chi-restraints excluded: chain q residue 69 SER Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 577 optimal weight: 1.9990 chunk 372 optimal weight: 30.0000 chunk 557 optimal weight: 0.0980 chunk 281 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 180 optimal weight: 40.0000 chunk 593 optimal weight: 3.9990 chunk 635 optimal weight: 4.9990 chunk 461 optimal weight: 5.9990 chunk 86 optimal weight: 6.9990 chunk 733 optimal weight: 30.0000 overall best weight: 3.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS L 89 ASN N 99 HIS O 9 GLN O 13 ASN O 32 GLN Q 43 ASN S 58 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN b 60 ASN c 100 GLN c 139 GLN ** f 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 28 GLN o 37 ASN ** o 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 64 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.094 149477 Z= 0.455 Angle : 0.961 24.841 223661 Z= 0.476 Chirality : 0.054 2.369 28567 Planarity : 0.008 0.144 11978 Dihedral : 23.280 179.969 74691 Min Nonbonded Distance : 1.703 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.26 % Favored : 96.63 % Rotamer: Outliers : 5.70 % Allowed : 25.37 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.11), residues: 5407 helix: 1.10 (0.12), residues: 1847 sheet: 0.28 (0.16), residues: 1010 loop : -0.78 (0.11), residues: 2550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.004 TRP c 201 HIS 0.016 0.002 HIS j 15 PHE 0.030 0.003 PHE g 18 TYR 0.028 0.003 TYR h 66 ARG 0.015 0.001 ARG c 143 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1289 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1034 time to evaluate : 5.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 36 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6809 (ttp-170) REVERT: C 263 THR cc_start: 0.8351 (p) cc_final: 0.8090 (p) REVERT: D 38 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7758 (mp) REVERT: D 102 ASP cc_start: 0.7111 (OUTLIER) cc_final: 0.6870 (p0) REVERT: E 24 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: G 84 GLU cc_start: 0.5670 (OUTLIER) cc_final: 0.5273 (pp20) REVERT: L 14 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8413 (ttmm) REVERT: L 89 ASN cc_start: 0.8030 (m-40) cc_final: 0.7774 (m110) REVERT: P 56 GLN cc_start: 0.8304 (mt0) cc_final: 0.8007 (mt0) REVERT: P 84 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.6983 (ttmm) REVERT: S 1 MET cc_start: 0.4013 (ttt) cc_final: 0.3719 (ttt) REVERT: S 20 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.6599 (mp10) REVERT: T 3 LYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6804 (tptp) REVERT: U 91 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.7704 (mtp) REVERT: V 77 ARG cc_start: 0.7834 (OUTLIER) cc_final: 0.7429 (ptt180) REVERT: Z 38 ARG cc_start: 0.8115 (ttm-80) cc_final: 0.7760 (tmt90) REVERT: d 72 ARG cc_start: 0.6553 (OUTLIER) cc_final: 0.5847 (ptt180) REVERT: d 113 ARG cc_start: 0.6586 (mtt90) cc_final: 0.6221 (mtt90) REVERT: e 70 MET cc_start: 0.6448 (OUTLIER) cc_final: 0.5684 (ttm) REVERT: e 81 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7746 (mm110) REVERT: f 94 HIS cc_start: 0.6133 (OUTLIER) cc_final: 0.5532 (p90) REVERT: i 70 ILE cc_start: 0.8471 (OUTLIER) cc_final: 0.8166 (mt) REVERT: j 99 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7250 (mp10) REVERT: l 49 MET cc_start: 0.5838 (mmm) cc_final: 0.5494 (mmm) REVERT: q 7 ARG cc_start: 0.6548 (OUTLIER) cc_final: 0.6032 (mtt90) REVERT: q 28 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.6843 (ptt90) REVERT: r 32 TYR cc_start: 0.6511 (m-80) cc_final: 0.6186 (m-80) REVERT: r 63 ARG cc_start: 0.7647 (ptp-170) cc_final: 0.7258 (ptp-170) REVERT: s 43 ASP cc_start: 0.6840 (OUTLIER) cc_final: 0.6627 (p0) outliers start: 255 outliers final: 190 residues processed: 1180 average time/residue: 2.2970 time to fit residues: 3750.5592 Evaluate side-chains 1236 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 1026 time to evaluate : 5.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 16 VAL Chi-restraints excluded: chain 3 residue 36 ARG Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 134 LEU Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 15 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 34 LYS Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 26 SER Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain X residue 58 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 113 ILE Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 181 GLU Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 60 SER Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 118 LEU Chi-restraints excluded: chain g residue 135 ILE Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain j residue 100 ILE Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 79 LYS Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 47 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 59 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 848 optimal weight: 3.9990 chunk 893 optimal weight: 0.5980 chunk 815 optimal weight: 10.0000 chunk 869 optimal weight: 3.9990 chunk 523 optimal weight: 8.9990 chunk 378 optimal weight: 4.9990 chunk 682 optimal weight: 50.0000 chunk 266 optimal weight: 6.9990 chunk 785 optimal weight: 0.8980 chunk 822 optimal weight: 0.4980 chunk 866 optimal weight: 6.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 153 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 GLN K 18 HIS O 9 GLN O 13 ASN O 32 GLN Q 43 ASN S 58 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 100 GLN c 139 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN p 64 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 149477 Z= 0.282 Angle : 0.778 24.700 223661 Z= 0.399 Chirality : 0.046 2.195 28567 Planarity : 0.007 0.136 11978 Dihedral : 23.125 179.930 74691 Min Nonbonded Distance : 1.742 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 4.91 % Allowed : 26.40 % Favored : 68.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5407 helix: 1.36 (0.12), residues: 1850 sheet: 0.34 (0.16), residues: 1021 loop : -0.73 (0.11), residues: 2536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP c 201 HIS 0.015 0.002 HIS f 94 PHE 0.018 0.002 PHE D 121 TYR 0.020 0.002 TYR N 98 ARG 0.014 0.001 ARG c 143 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1029 time to evaluate : 5.881 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 10 LEU cc_start: 0.8704 (tp) cc_final: 0.8248 (tt) REVERT: 3 19 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7582 (mtt180) REVERT: C 157 SER cc_start: 0.7428 (t) cc_final: 0.7158 (p) REVERT: C 223 MET cc_start: 0.7677 (OUTLIER) cc_final: 0.7433 (mtp) REVERT: C 263 THR cc_start: 0.8349 (p) cc_final: 0.8098 (p) REVERT: D 38 ILE cc_start: 0.8276 (OUTLIER) cc_final: 0.7851 (mp) REVERT: G 84 GLU cc_start: 0.5556 (OUTLIER) cc_final: 0.5162 (pp20) REVERT: I 84 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8347 (tp) REVERT: L 14 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8402 (ttmm) REVERT: P 56 GLN cc_start: 0.8265 (mt0) cc_final: 0.7975 (mt0) REVERT: P 84 LYS cc_start: 0.8162 (OUTLIER) cc_final: 0.6965 (ttmm) REVERT: Q 73 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7736 (mtp180) REVERT: S 1 MET cc_start: 0.3945 (ttt) cc_final: 0.3648 (ttt) REVERT: S 20 GLN cc_start: 0.6995 (OUTLIER) cc_final: 0.6592 (mp10) REVERT: T 3 LYS cc_start: 0.7113 (OUTLIER) cc_final: 0.6631 (tptp) REVERT: U 47 GLU cc_start: 0.7267 (OUTLIER) cc_final: 0.6967 (mp0) REVERT: U 91 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7679 (mtp) REVERT: V 77 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7258 (ptt180) REVERT: Z 38 ARG cc_start: 0.8069 (ttm-80) cc_final: 0.7807 (tmt90) REVERT: d 72 ARG cc_start: 0.6442 (ttm170) cc_final: 0.5755 (ptt180) REVERT: d 113 ARG cc_start: 0.6499 (mtt90) cc_final: 0.6137 (mtt90) REVERT: d 205 LEU cc_start: 0.6188 (OUTLIER) cc_final: 0.5926 (tp) REVERT: e 12 GLU cc_start: 0.5691 (OUTLIER) cc_final: 0.5447 (mt-10) REVERT: e 70 MET cc_start: 0.6277 (OUTLIER) cc_final: 0.5621 (ttm) REVERT: f 94 HIS cc_start: 0.6149 (OUTLIER) cc_final: 0.5949 (p-80) REVERT: g 26 PHE cc_start: 0.8215 (t80) cc_final: 0.7876 (t80) REVERT: i 70 ILE cc_start: 0.8262 (OUTLIER) cc_final: 0.7975 (mt) REVERT: j 99 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7188 (mp10) REVERT: l 49 MET cc_start: 0.5820 (mmm) cc_final: 0.5480 (mmm) REVERT: m 47 GLU cc_start: 0.6724 (OUTLIER) cc_final: 0.6514 (pm20) REVERT: n 87 THR cc_start: 0.8655 (OUTLIER) cc_final: 0.8431 (t) REVERT: q 7 ARG cc_start: 0.6552 (OUTLIER) cc_final: 0.6111 (mtt90) REVERT: q 28 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6792 (ptt90) REVERT: r 32 TYR cc_start: 0.6464 (m-80) cc_final: 0.6133 (m-80) REVERT: s 43 ASP cc_start: 0.6793 (OUTLIER) cc_final: 0.6565 (p0) outliers start: 220 outliers final: 166 residues processed: 1158 average time/residue: 2.2763 time to fit residues: 3651.3067 Evaluate side-chains 1212 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1023 time to evaluate : 5.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 165 SER Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 116 SER Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 25 THR Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 47 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 28 LYS Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 90 GLU Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain d residue 205 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 47 GLU Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 87 THR Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 570 optimal weight: 4.9990 chunk 919 optimal weight: 3.9990 chunk 561 optimal weight: 1.9990 chunk 436 optimal weight: 0.6980 chunk 639 optimal weight: 3.9990 chunk 964 optimal weight: 4.9990 chunk 887 optimal weight: 10.0000 chunk 767 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 chunk 593 optimal weight: 3.9990 chunk 470 optimal weight: 6.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 153 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS N 39 GLN O 9 GLN O 13 ASN O 32 GLN Q 12 HIS Q 43 ASN S 58 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN c 139 GLN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 20 ASN o 28 GLN p 64 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.1807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 149477 Z= 0.320 Angle : 0.818 24.554 223661 Z= 0.416 Chirality : 0.048 2.254 28567 Planarity : 0.007 0.138 11978 Dihedral : 23.150 179.932 74684 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.13 % Favored : 96.78 % Rotamer: Outliers : 4.96 % Allowed : 26.54 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.11), residues: 5407 helix: 1.26 (0.12), residues: 1848 sheet: 0.29 (0.16), residues: 1024 loop : -0.75 (0.11), residues: 2535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP c 201 HIS 0.016 0.002 HIS f 94 PHE 0.019 0.002 PHE M 80 TYR 0.023 0.003 TYR N 98 ARG 0.013 0.001 ARG c 143 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10814 Ramachandran restraints generated. 5407 Oldfield, 0 Emsley, 5407 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1242 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1020 time to evaluate : 5.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 1 10 LEU cc_start: 0.8720 (tp) cc_final: 0.8282 (tt) REVERT: 3 19 ARG cc_start: 0.8178 (mtt180) cc_final: 0.7587 (mtt180) REVERT: C 157 SER cc_start: 0.7469 (t) cc_final: 0.7190 (p) REVERT: C 263 THR cc_start: 0.8347 (p) cc_final: 0.8096 (p) REVERT: D 38 ILE cc_start: 0.8192 (OUTLIER) cc_final: 0.7735 (mp) REVERT: D 102 ASP cc_start: 0.7081 (OUTLIER) cc_final: 0.6853 (p0) REVERT: E 24 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7404 (tt0) REVERT: G 84 GLU cc_start: 0.5586 (OUTLIER) cc_final: 0.5195 (pp20) REVERT: I 84 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8378 (tp) REVERT: L 14 LYS cc_start: 0.8870 (OUTLIER) cc_final: 0.8408 (ttmm) REVERT: P 56 GLN cc_start: 0.8277 (mt0) cc_final: 0.7986 (mt0) REVERT: P 84 LYS cc_start: 0.8166 (OUTLIER) cc_final: 0.6951 (ttmm) REVERT: Q 73 ARG cc_start: 0.8015 (OUTLIER) cc_final: 0.7747 (mtp180) REVERT: S 1 MET cc_start: 0.3970 (ttt) cc_final: 0.3673 (ttt) REVERT: S 20 GLN cc_start: 0.6996 (OUTLIER) cc_final: 0.6585 (mp10) REVERT: T 3 LYS cc_start: 0.7115 (OUTLIER) cc_final: 0.6651 (tptp) REVERT: U 91 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7664 (mtp) REVERT: V 77 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7319 (ptt180) REVERT: Z 38 ARG cc_start: 0.8082 (ttm-80) cc_final: 0.7810 (tmt90) REVERT: d 72 ARG cc_start: 0.6473 (OUTLIER) cc_final: 0.5764 (ptt180) REVERT: d 113 ARG cc_start: 0.6516 (mtt90) cc_final: 0.6165 (mtt90) REVERT: e 12 GLU cc_start: 0.5714 (OUTLIER) cc_final: 0.5459 (mt-10) REVERT: e 70 MET cc_start: 0.6305 (OUTLIER) cc_final: 0.5685 (ttm) REVERT: e 81 GLN cc_start: 0.8176 (OUTLIER) cc_final: 0.7747 (mm110) REVERT: f 94 HIS cc_start: 0.6164 (OUTLIER) cc_final: 0.5566 (p90) REVERT: g 26 PHE cc_start: 0.8223 (t80) cc_final: 0.7888 (t80) REVERT: i 70 ILE cc_start: 0.8325 (OUTLIER) cc_final: 0.8040 (mt) REVERT: j 99 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7207 (mp10) REVERT: l 49 MET cc_start: 0.5815 (mmm) cc_final: 0.5462 (mmm) REVERT: n 85 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8563 (tmt90) REVERT: q 7 ARG cc_start: 0.6550 (OUTLIER) cc_final: 0.6039 (mtt90) REVERT: q 28 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.6818 (ptt90) REVERT: r 32 TYR cc_start: 0.6477 (m-80) cc_final: 0.6134 (m-80) REVERT: r 63 ARG cc_start: 0.7616 (ptp-170) cc_final: 0.7258 (ptp-170) REVERT: s 43 ASP cc_start: 0.6798 (OUTLIER) cc_final: 0.6565 (p0) outliers start: 222 outliers final: 179 residues processed: 1156 average time/residue: 2.2921 time to fit residues: 3668.6628 Evaluate side-chains 1221 residues out of total 4477 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 1019 time to evaluate : 5.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 41 SER Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 2 LYS Chi-restraints excluded: chain 3 residue 37 GLN Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain C residue 223 MET Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 273 VAL Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 90 LEU Chi-restraints excluded: chain D residue 94 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 105 THR Chi-restraints excluded: chain E residue 24 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 37 ASN Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 59 LEU Chi-restraints excluded: chain F residue 60 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 81 ASP Chi-restraints excluded: chain F residue 98 GLU Chi-restraints excluded: chain F residue 150 ARG Chi-restraints excluded: chain F residue 154 ILE Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 49 LYS Chi-restraints excluded: chain G residue 84 GLU Chi-restraints excluded: chain G residue 98 VAL Chi-restraints excluded: chain G residue 173 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 57 GLN Chi-restraints excluded: chain I residue 84 LEU Chi-restraints excluded: chain I residue 87 THR Chi-restraints excluded: chain I residue 93 VAL Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain K residue 4 ARG Chi-restraints excluded: chain K residue 25 ILE Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 14 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 38 GLU Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 81 THR Chi-restraints excluded: chain M residue 113 VAL Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 37 TYR Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 102 ILE Chi-restraints excluded: chain O residue 55 ASN Chi-restraints excluded: chain P residue 22 LYS Chi-restraints excluded: chain P residue 74 LEU Chi-restraints excluded: chain P residue 84 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 19 THR Chi-restraints excluded: chain Q residue 53 VAL Chi-restraints excluded: chain Q residue 73 ARG Chi-restraints excluded: chain R residue 4 THR Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 24 ILE Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 25 THR Chi-restraints excluded: chain S residue 35 ILE Chi-restraints excluded: chain S residue 47 GLU Chi-restraints excluded: chain S residue 55 VAL Chi-restraints excluded: chain T residue 3 LYS Chi-restraints excluded: chain T residue 58 THR Chi-restraints excluded: chain T residue 86 ILE Chi-restraints excluded: chain U residue 27 GLU Chi-restraints excluded: chain U residue 62 GLU Chi-restraints excluded: chain U residue 64 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 73 VAL Chi-restraints excluded: chain U residue 75 ASN Chi-restraints excluded: chain U residue 91 MET Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 31 VAL Chi-restraints excluded: chain V residue 67 VAL Chi-restraints excluded: chain V residue 77 ARG Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain Y residue 4 ILE Chi-restraints excluded: chain Y residue 49 LYS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 52 GLN Chi-restraints excluded: chain b residue 54 ASP Chi-restraints excluded: chain b residue 57 ASN Chi-restraints excluded: chain b residue 62 LEU Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 95 ASP Chi-restraints excluded: chain b residue 115 ARG Chi-restraints excluded: chain b residue 141 ARG Chi-restraints excluded: chain b residue 150 LEU Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 173 ILE Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 190 ASP Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 27 LYS Chi-restraints excluded: chain c residue 46 LYS Chi-restraints excluded: chain c residue 49 ASN Chi-restraints excluded: chain c residue 51 MET Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 94 ILE Chi-restraints excluded: chain c residue 122 SER Chi-restraints excluded: chain c residue 129 MET Chi-restraints excluded: chain c residue 142 MET Chi-restraints excluded: chain c residue 154 SER Chi-restraints excluded: chain d residue 72 ARG Chi-restraints excluded: chain d residue 75 SER Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain d residue 124 SER Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 192 ASP Chi-restraints excluded: chain d residue 204 GLU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 18 ASP Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 70 MET Chi-restraints excluded: chain e residue 71 ILE Chi-restraints excluded: chain e residue 81 GLN Chi-restraints excluded: chain e residue 130 THR Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 54 ILE Chi-restraints excluded: chain f residue 60 ILE Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 94 HIS Chi-restraints excluded: chain g residue 12 ILE Chi-restraints excluded: chain g residue 22 THR Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 74 GLU Chi-restraints excluded: chain g residue 97 THR Chi-restraints excluded: chain g residue 146 GLU Chi-restraints excluded: chain h residue 21 LYS Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 58 SER Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 64 THR Chi-restraints excluded: chain i residue 70 ILE Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 18 ILE Chi-restraints excluded: chain j residue 48 ARG Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 19 VAL Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain l residue 8 ILE Chi-restraints excluded: chain l residue 52 VAL Chi-restraints excluded: chain l residue 63 VAL Chi-restraints excluded: chain l residue 82 ILE Chi-restraints excluded: chain l residue 97 THR Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 101 SER Chi-restraints excluded: chain l residue 109 ASP Chi-restraints excluded: chain m residue 11 ASP Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 85 CYS Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain n residue 85 ARG Chi-restraints excluded: chain n residue 87 THR Chi-restraints excluded: chain q residue 5 THR Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 9 LEU Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 28 ARG Chi-restraints excluded: chain q residue 75 THR Chi-restraints excluded: chain q residue 78 GLU Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 29 LEU Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain s residue 43 ASP Chi-restraints excluded: chain s residue 55 ARG Chi-restraints excluded: chain t residue 19 LYS Chi-restraints excluded: chain t residue 30 THR Chi-restraints excluded: chain t residue 33 LYS Chi-restraints excluded: chain t residue 34 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 968 random chunks: chunk 609 optimal weight: 3.9990 chunk 818 optimal weight: 6.9990 chunk 235 optimal weight: 6.9990 chunk 708 optimal weight: 1.9990 chunk 113 optimal weight: 6.9990 chunk 213 optimal weight: 7.9990 chunk 769 optimal weight: 0.6980 chunk 321 optimal weight: 0.0770 chunk 789 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 0 41 GLN C 153 GLN C 260 ASN ** F 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 18 HIS O 9 GLN O 13 ASN O 32 GLN Q 43 ASN S 58 ASN U 16 GLN Z 4 GLN Z 5 GLN Z 25 ASN ** Z 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 57 ASN ** f 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 42 GLN ** i 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN o 20 ASN o 28 GLN p 64 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.178562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.163623 restraints weight = 148885.952| |-----------------------------------------------------------------------------| r_work (start): 0.3906 rms_B_bonded: 0.41 r_work: 0.3728 rms_B_bonded: 1.58 restraints_weight: 0.5000 r_work: 0.3685 rms_B_bonded: 2.10 restraints_weight: 0.2500 r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 149477 Z= 0.252 Angle : 0.749 24.543 223661 Z= 0.386 Chirality : 0.045 2.163 28567 Planarity : 0.006 0.135 11978 Dihedral : 23.112 179.935 74684 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.89 % Favored : 97.02 % Rotamer: Outliers : 4.49 % Allowed : 27.09 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.11), residues: 5407 helix: 1.45 (0.12), residues: 1847 sheet: 0.34 (0.16), residues: 1023 loop : -0.71 (0.11), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP c 201 HIS 0.016 0.001 HIS f 94 PHE 0.017 0.002 PHE D 121 TYR 0.024 0.002 TYR N 98 ARG 0.013 0.001 ARG c 143 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48878.29 seconds wall clock time: 844 minutes 29.33 seconds (50669.33 seconds total)