Starting phenix.real_space_refine on Sun Mar 17 10:34:31 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ryh_24740/03_2024/7ryh_24740_updated.pdb" } resolution = 2.43 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= 0.045 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 4327 5.49 5 Mg 4 5.21 5 S 140 5.16 5 C 68301 2.51 5 N 25270 2.21 5 O 37777 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 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 31": "OE1" <-> "OE2" Residue "1 PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 TYR 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 17": "OE1" <-> "OE2" Residue "C TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "C GLU 79": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ASP 98": "OD1" <-> "OD2" Residue "C GLU 180": "OE1" <-> "OE2" Residue "D GLU 29": "OE1" <-> "OE2" Residue "D ASP 44": "OD1" <-> "OD2" Residue "D ASP 134": "OD1" <-> "OD2" Residue "D GLU 186": "OE1" <-> "OE2" Residue "E PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 24": "OE1" <-> "OE2" Residue "E ASP 90": "OD1" <-> "OD2" Residue "E ASP 115": "OD1" <-> "OD2" Residue "E GLU 121": "OE1" <-> "OE2" Residue "E ASP 139": "OD1" <-> "OD2" Residue "E GLU 154": "OE1" <-> "OE2" Residue "E ASP 175": "OD1" <-> "OD2" Residue "E GLU 198": "OE1" <-> "OE2" Residue "F ASP 46": "OD1" <-> "OD2" Residue "F ASP 113": "OD1" <-> "OD2" Residue "F GLU 140": "OE1" <-> "OE2" Residue "F ASP 144": "OD1" <-> "OD2" Residue "F ASP 153": "OD1" <-> "OD2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "H ASP 2": "OD1" <-> "OD2" Residue "H GLU 60": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "I GLU 60": "OE1" <-> "OE2" Residue "I TYR 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 90": "OE1" <-> "OE2" Residue "I GLU 99": "OE1" <-> "OE2" Residue "J GLU 5": "OE1" <-> "OE2" Residue "J ASP 9": "OD1" <-> "OD2" Residue "J ASP 56": "OD1" <-> "OD2" Residue "J PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 105": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 120": "OE1" <-> "OE2" Residue "K GLU 7": "OE1" <-> "OE2" Residue "K GLU 12": "OE1" <-> "OE2" Residue "K GLU 83": "OE1" <-> "OE2" Residue "K GLU 88": "OE1" <-> "OE2" Residue "K GLU 95": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "L GLU 48": "OE1" <-> "OE2" Residue "L PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 71": "OD1" <-> "OD2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "M ASP 58": "OD1" <-> "OD2" Residue "O GLU 12": "OE1" <-> "OE2" Residue "O PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 47": "OE1" <-> "OE2" Residue "O GLU 88": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "Q TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 22": "OD1" <-> "OD2" Residue "R ASP 68": "OD1" <-> "OD2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 53": "OE1" <-> "OE2" Residue "T GLU 60": "OE1" <-> "OE2" Residue "T TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 44": "OE1" <-> "OE2" Residue "V ASP 56": "OD1" <-> "OD2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W ASP 60": "OD1" <-> "OD2" Residue "Y GLU 36": "OE1" <-> "OE2" Residue "Z ASP 30": "OD1" <-> "OD2" Residue "Z PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 142": "OE1" <-> "OE2" Residue "b ASP 190": "OD1" <-> "OD2" Residue "b ASP 196": "OD1" <-> "OD2" Residue "b ASP 206": "OD1" <-> "OD2" Residue "b ASP 221": "OD1" <-> "OD2" Residue "c GLU 31": "OE1" <-> "OE2" Residue "c GLU 58": "OE1" <-> "OE2" Residue "c ASP 107": "OD1" <-> "OD2" Residue "c GLU 118": "OE1" <-> "OE2" Residue "c TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 190": "OE1" <-> "OE2" Residue "c TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 206": "OE1" <-> "OE2" Residue "d PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 80": "OE1" <-> "OE2" Residue "d ASP 101": "OD1" <-> "OD2" Residue "d GLU 174": "OE1" <-> "OE2" Residue "d ASP 192": "OD1" <-> "OD2" Residue "d GLU 196": "OE1" <-> "OE2" Residue "e GLU 12": "OE1" <-> "OE2" Residue "e ASP 18": "OD1" <-> "OD2" Residue "e PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 74": "OD1" <-> "OD2" Residue "e GLU 161": "OE1" <-> "OE2" Residue "f TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 18": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 60": "OE1" <-> "OE2" Residue "g PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 67": "OE1" <-> "OE2" Residue "g GLU 74": "OE1" <-> "OE2" Residue "g GLU 113": "OE1" <-> "OE2" Residue "h ASP 5": "OD1" <-> "OD2" Residue "h GLU 43": "OE1" <-> "OE2" Residue "i GLU 54": "OE1" <-> "OE2" Residue "i ASP 60": "OD1" <-> "OD2" Residue "i TYR 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 27": "OE1" <-> "OE2" Residue "j ASP 60": "OD1" <-> "OD2" Residue "l GLU 76": "OE1" <-> "OE2" Residue "m ASP 50": "OD1" <-> "OD2" Residue "m ASP 54": "OD1" <-> "OD2" Residue "m GLU 59": "OE1" <-> "OE2" Residue "m GLU 66": "OE1" <-> "OE2" Residue "m TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 10": "OE1" <-> "OE2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n GLU 26": "OE1" <-> "OE2" Residue "n ASP 38": "OD1" <-> "OD2" Residue "n TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "o ASP 21": "OD1" <-> "OD2" Residue "p ASP 41": "OD1" <-> "OD2" Residue "q ASP 16": "OD1" <-> "OD2" Residue "q GLU 27": "OE1" <-> "OE2" Residue "q ASP 49": "OD1" <-> "OD2" Residue "t GLU 49": "OE1" <-> "OE2" Residue "t ASP 63": "OD1" <-> "OD2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 135829 Number of models: 1 Model: "" Number of chains: 53 Chain: "0" Number of atoms: 400 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 400 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} 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': 255, 'rna2p_pyr': 140, 'rna3p': 9, 'rna3p_pur': 1283, 'rna3p_pyr': 995} Link IDs: {'rna2p': 397, 'rna3p': 2287} 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': 5, 'rna2p_pyr': 7, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 11, 'rna3p': 103} Chain: "C" Number of atoms: 2104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2104 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 16, 'TRANS': 254} 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: 1117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1117 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 132} 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: 614 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 614 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 2, 'TRANS': 75} 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: "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 1355 SG CYS 3 11 179.023 123.407 136.110 1.00 29.50 S ATOM 1371 SG CYS 3 14 178.359 125.296 139.330 1.00 28.52 S ATOM 1476 SG CYS 3 27 179.748 127.195 136.338 1.00 29.38 S Time building chain proxies: 50.94, per 1000 atoms: 0.38 Number of scatterers: 135829 At special positions: 0 Unit cell: (227.601, 250.47, 277.695, 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 140 16.00 P 4327 15.00 Mg 4 11.99 F 9 9.00 O 37777 8.00 N 25270 7.00 C 68301 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: 53.79 Conformation dependent library (CDL) restraints added in 6.6 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 11 " pdb="ZN ZN 3 101 " - pdb=" SG CYS 3 27 " Number of angles added : 3 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10078 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 39.6% alpha, 18.9% beta 1363 base pairs and 2088 stacking pairs defined. Time for finding SS restraints: 65.78 Creating SS restraints... Processing helix chain '0' and resid 22 through 27 Proline residue: 0 27 - end of helix Processing helix chain '1' and resid 8 through 16 Processing helix chain '1' and resid 17 through 25 removed outlier: 4.217A pdb=" N THR 1 24 " --> pdb=" O ALA 1 20 " (cutoff:3.500A) removed outlier: 5.440A 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 Processing helix chain '2' and resid 36 through 44 Processing helix chain '2' and resid 50 through 62 removed outlier: 4.101A pdb=" N ALA 2 55 " --> pdb=" O VAL 2 51 " (cutoff:3.500A) removed outlier: 5.131A 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: 5.284A pdb=" N PHE C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.756A pdb=" N VAL C 34 " --> pdb=" O TYR C 30 " (cutoff:3.500A) removed outlier: 5.506A 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: 3.788A 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: 4.092A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.157A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.516A 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: 4.683A pdb=" N THR C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.479A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 6.031A pdb=" N MET C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.542A 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: 5.015A pdb=" N THR D 62 " --> pdb=" O GLU D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 removed outlier: 3.772A pdb=" N ALA D 72 " --> pdb=" O HIS D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 92 removed outlier: 5.661A pdb=" N GLY D 92 " --> pdb=" O ALA D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 129 removed outlier: 4.258A pdb=" N TRP D 128 " --> pdb=" O GLY D 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 39 removed outlier: 3.666A pdb=" N GLY E 38 " --> pdb=" O TYR E 34 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ARG E 39 " --> pdb=" O LEU E 35 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 52 removed outlier: 6.359A pdb=" N SER E 52 " --> pdb=" O ARG E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 115 Processing helix chain 'E' and resid 129 through 141 Processing helix chain 'E' and resid 153 through 164 removed outlier: 4.546A pdb=" N ASN E 162 " --> pdb=" O LEU E 158 " (cutoff:3.500A) removed outlier: 4.652A pdb=" N LEU E 163 " --> pdb=" O ALA E 159 " (cutoff:3.500A) Proline residue: E 164 - end of helix Processing helix chain 'E' and resid 175 through 182 Processing helix chain 'E' and resid 188 through 199 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'F' and resid 5 through 21 removed outlier: 4.852A pdb=" N LYS F 13 " --> pdb=" O ASN F 9 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ALA F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.543A pdb=" N ASP F 46 " --> pdb=" O ALA F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 Processing helix chain 'F' and resid 93 through 111 removed outlier: 4.808A 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 removed outlier: 3.701A pdb=" N TRP G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N MET G 63 " --> pdb=" O LYS G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.882A pdb=" N ARG G 152 " --> pdb=" O ILE G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 29 Processing helix chain 'H' and resid 40 through 50 Processing helix chain 'H' and resid 51 through 59 removed outlier: 4.498A pdb=" N ALA H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 38 removed outlier: 3.835A 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: 3.774A 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: 3.569A pdb=" N LYS I 120 " --> pdb=" O TYR I 116 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.555A 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: 3.678A pdb=" N ARG K 43 " --> pdb=" O GLY K 39 " (cutoff:3.500A) removed outlier: 5.475A 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: 3.624A 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: 3.892A pdb=" N LEU K 74 " --> pdb=" O SER K 70 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS K 75 " --> pdb=" O GLN K 71 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N ALA K 77 " --> pdb=" O ALA K 73 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 88 removed outlier: 4.018A pdb=" N LEU K 84 " --> pdb=" O ARG K 80 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N LYS K 86 " --> pdb=" O SER K 82 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL K 87 " --> pdb=" O GLU K 83 " (cutoff:3.500A) removed outlier: 5.659A 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: 3.775A pdb=" N ALA L 123 " --> pdb=" O ALA L 119 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N LYS L 124 " --> pdb=" O LEU L 120 " (cutoff:3.500A) removed outlier: 3.942A 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 57 removed outlier: 3.716A pdb=" N ARG M 45 " --> pdb=" O ALA M 41 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.522A pdb=" N ASN M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.878A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 5.617A 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: 4.500A pdb=" N SER N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 4.563A 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: 3.786A pdb=" N SER O 14 " --> pdb=" O ALA O 10 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLN O 15 " --> pdb=" O ILE O 11 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU O 16 " --> pdb=" O GLU O 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 107 removed outlier: 4.683A pdb=" N ARG O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASP O 105 " --> pdb=" O TYR O 101 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU O 106 " --> pdb=" O TYR O 102 " (cutoff:3.500A) removed outlier: 5.592A 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 removed outlier: 3.772A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.739A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 32 through 37 Processing helix chain 'P' and resid 39 through 73 removed outlier: 4.042A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.948A 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: 3.894A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.187A 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: 4.169A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU R 46 " --> pdb=" O LYS R 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 4.049A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.984A 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: 4.447A 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: 4.156A pdb=" N VAL T 68 " --> pdb=" O HIS T 64 " (cutoff:3.500A) removed outlier: 5.385A 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: 3.605A pdb=" N GLN U 16 " --> pdb=" O ALA U 12 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N GLY U 17 " --> pdb=" O GLU U 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 12 through 17' Processing helix chain 'U' and resid 18 through 28 Processing helix chain 'U' and resid 47 through 58 removed outlier: 3.854A pdb=" N SER U 57 " --> pdb=" O LYS U 53 " (cutoff:3.500A) removed outlier: 5.367A 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: 5.152A 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: 4.109A 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: 3.661A pdb=" N MET Y 46 " --> pdb=" O SER Y 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 9 through 19 removed outlier: 5.010A pdb=" N HIS Z 19 " --> pdb=" O MET Z 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 7 through 15 removed outlier: 6.385A pdb=" N LEU b 11 " --> pdb=" O SER b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 29 through 34 removed outlier: 4.123A pdb=" N PHE b 34 " --> pdb=" O ARG b 30 " (cutoff:3.500A) Processing helix chain 'b' and resid 44 through 66 removed outlier: 3.989A 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 78 through 90 Processing helix chain 'b' and resid 107 through 126 removed outlier: 4.541A pdb=" N GLN b 111 " --> pdb=" O LYS b 107 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N SER b 112 " --> pdb=" O THR b 108 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLY b 126 " --> pdb=" O GLN b 122 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 132 removed outlier: 5.404A 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: 4.636A pdb=" N LYS b 227 " --> pdb=" O ILE b 223 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU b 228 " --> pdb=" O LEU b 224 " (cutoff:3.500A) Processing helix chain 'b' and resid 151 through 156 removed outlier: 4.098A pdb=" N ASN b 155 " --> pdb=" O GLY b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 101 through 106 removed outlier: 4.068A pdb=" N TRP b 106 " --> pdb=" O GLY b 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 101 through 106' Processing helix chain 'c' and resid 6 through 12 removed outlier: 4.139A pdb=" N ARG c 11 " --> pdb=" O PRO c 7 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 48 removed outlier: 4.110A pdb=" N LYS c 48 " --> pdb=" O THR c 44 " (cutoff:3.500A) Processing helix chain 'c' and resid 72 through 78 removed outlier: 4.192A pdb=" N VAL c 76 " --> pdb=" O ARG c 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 96 removed outlier: 3.647A pdb=" N GLU c 85 " --> pdb=" O GLY c 81 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLY c 96 " --> pdb=" O THR c 92 " (cutoff:3.500A) Processing helix chain 'c' and resid 108 through 113 removed outlier: 4.251A pdb=" N ASP c 112 " --> pdb=" O ARG c 108 " (cutoff:3.500A) removed outlier: 6.086A 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 removed outlier: 3.766A pdb=" N LYS c 126 " --> pdb=" O SER c 122 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N ARG c 127 " --> pdb=" O GLN c 123 " (cutoff:3.500A) 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: 4.422A 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: 4.075A pdb=" N LYS d 60 " --> pdb=" O GLN d 56 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS d 62 " --> pdb=" O ARG d 58 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL d 63 " --> pdb=" O GLU d 59 " (cutoff:3.500A) Processing helix chain 'd' and resid 70 through 85 removed outlier: 5.151A pdb=" N LYS d 85 " --> pdb=" O ALA d 81 " (cutoff:3.500A) Processing helix chain 'd' and resid 87 through 99 removed outlier: 3.581A pdb=" N SER d 98 " --> pdb=" O LYS d 94 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ARG d 99 " --> pdb=" O LEU d 95 " (cutoff:3.500A) Processing helix chain 'd' and resid 100 through 108 removed outlier: 3.773A pdb=" N GLY d 108 " --> pdb=" O VAL d 104 " (cutoff:3.500A) Processing helix chain 'd' and resid 112 through 123 removed outlier: 3.831A pdb=" N ARG d 123 " --> pdb=" O LEU d 119 " (cutoff:3.500A) Processing helix chain 'd' and resid 154 through 168 removed outlier: 3.961A 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: 4.128A pdb=" N ILE d 202 " --> pdb=" O ASN d 198 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LYS d 208 " --> pdb=" O GLU d 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 54 through 70 removed outlier: 4.227A pdb=" N MET e 70 " --> pdb=" O ALA e 66 " (cutoff:3.500A) Processing helix chain 'e' and resid 107 through 118 removed outlier: 3.587A 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: 4.585A pdb=" N ASP f 16 " --> pdb=" O PRO f 12 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N GLN f 17 " --> pdb=" O ASP f 13 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL f 18 " --> pdb=" O GLN f 14 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL f 19 " --> pdb=" O SER f 15 " (cutoff:3.500A) Processing helix chain 'f' and resid 20 through 33 removed outlier: 3.795A pdb=" N ALA f 32 " --> pdb=" O GLN f 28 " (cutoff:3.500A) Processing helix chain 'f' and resid 67 through 81 Processing helix chain 'g' and resid 20 through 31 removed outlier: 3.816A pdb=" N ALA g 24 " --> pdb=" O SER g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 55 removed outlier: 3.540A pdb=" N LYS g 55 " --> pdb=" O GLN g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 70 removed outlier: 3.521A pdb=" N GLU g 67 " --> pdb=" O GLU g 63 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N LYS g 68 " --> pdb=" O THR g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 111 removed outlier: 3.543A pdb=" N ARG g 96 " --> pdb=" O ARG g 92 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ALA g 109 " --> pdb=" O VAL g 105 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS g 110 " --> pdb=" O ASP g 106 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ARG g 111 " --> pdb=" O ALA g 107 " (cutoff:3.500A) Processing helix chain 'g' and resid 115 through 130 removed outlier: 3.538A pdb=" N ALA g 128 " --> pdb=" O LEU g 124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLU g 129 " --> pdb=" O LEU g 125 " (cutoff:3.500A) Processing helix chain 'g' and resid 132 through 148 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 removed outlier: 3.516A pdb=" N ARG i 43 " --> pdb=" O ARG i 39 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLN i 48 " --> pdb=" O MET i 44 " (cutoff:3.500A) Proline residue: i 49 - end of helix Processing helix chain 'i' and resid 69 through 90 Processing helix chain 'i' and resid 92 through 100 removed outlier: 3.534A pdb=" N GLY i 100 " --> pdb=" O LEU i 96 " (cutoff:3.500A) Processing helix chain 'j' and resid 14 through 33 Processing helix chain 'j' and resid 80 through 90 removed outlier: 3.839A pdb=" N ASP j 85 " --> pdb=" O ASP j 81 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N LEU j 87 " --> pdb=" O THR j 83 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET j 88 " --> pdb=" O VAL j 84 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LYS j 89 " --> pdb=" O ASP j 85 " (cutoff:3.500A) Processing helix chain 'k' and resid 45 through 50 removed outlier: 3.642A pdb=" N GLN k 49 " --> pdb=" O THR k 45 " (cutoff:3.500A) removed outlier: 3.905A 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 54 through 59 removed outlier: 4.558A 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 54 through 59' Processing helix chain 'k' and resid 60 through 77 removed outlier: 4.002A pdb=" N ASP k 75 " --> pdb=" O LYS k 71 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N TYR k 76 " --> pdb=" O ALA k 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 91 through 103 removed outlier: 4.237A pdb=" N VAL k 96 " --> pdb=" O ARG k 92 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLY k 100 " --> pdb=" O VAL k 96 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA k 101 " --> pdb=" O ARG k 97 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N GLY k 103 " --> pdb=" O LEU k 99 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 10 Processing helix chain 'l' and resid 113 through 118 removed outlier: 4.581A pdb=" N TYR l 117 " --> pdb=" O SER l 113 " (cutoff:3.500A) Processing helix chain 'm' and resid 14 through 22 removed outlier: 4.069A pdb=" N THR m 20 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N TYR m 21 " --> pdb=" O ILE m 17 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE m 22 " --> pdb=" O SER m 18 " (cutoff:3.500A) Processing helix chain 'm' and resid 26 through 38 removed outlier: 3.568A pdb=" N ALA m 36 " --> pdb=" O ASN m 32 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N VAL m 37 " --> pdb=" O ILE m 33 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLY m 38 " --> pdb=" O LEU m 34 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 49 removed outlier: 3.834A pdb=" N LEU m 48 " --> pdb=" O LYS m 44 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N ASP m 49 " --> pdb=" O ILE m 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 44 through 49' Processing helix chain 'm' and resid 50 through 64 removed outlier: 4.710A pdb=" N LYS m 62 " --> pdb=" O ALA m 58 " (cutoff:3.500A) removed outlier: 4.206A 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: 3.773A 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 33 removed outlier: 5.018A pdb=" N ALA n 22 " --> pdb=" O ALA n 18 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LYS n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA n 32 " --> pdb=" O LYS n 28 " (cutoff:3.500A) Processing helix chain 'n' and resid 37 through 51 removed outlier: 3.660A pdb=" N LEU n 51 " --> pdb=" O LYS n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 91 Processing helix chain 'o' and resid 4 through 16 Processing helix chain 'o' and resid 24 through 47 removed outlier: 4.398A pdb=" N GLY o 41 " --> pdb=" O ASN o 37 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N HIS o 42 " --> pdb=" O ASP o 38 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 74 removed outlier: 3.658A pdb=" N ARG o 53 " --> pdb=" O ASP o 49 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) removed outlier: 4.152A 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: 3.562A pdb=" N GLN r 31 " --> pdb=" O ASP r 27 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N THR r 34 " --> pdb=" O LYS r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 41 through 46 removed outlier: 3.776A pdb=" N THR r 45 " --> pdb=" O PRO r 41 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 66 Processing helix chain 's' and resid 12 through 26 removed outlier: 4.033A pdb=" N ASN s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 76 removed outlier: 4.661A pdb=" N PHE s 74 " --> pdb=" O LYS s 70 " (cutoff:3.500A) removed outlier: 4.461A 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 removed outlier: 3.613A pdb=" N LEU t 24 " --> pdb=" O HIS t 20 " (cutoff:3.500A) 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: 3.552A 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: 4.203A pdb=" N PHE u 37 " --> pdb=" O ARG u 33 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N TYR u 38 " --> pdb=" O LYS u 34 " (cutoff:3.500A) Processing helix chain 'u' and resid 40 through 64 removed outlier: 3.567A 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 21 removed outlier: 6.110A pdb=" N TYR 0 15 " --> pdb=" O SER 0 9 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N ILE 0 44 " --> pdb=" O SER 0 10 " (cutoff:3.500A) removed outlier: 6.380A 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 5 removed outlier: 6.569A pdb=" N HIS 3 33 " --> pdb=" O CYS 3 27 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N CYS 3 27 " --> pdb=" O HIS 3 33 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N ILE 3 23 " --> pdb=" O GLN 3 37 " (cutoff:3.500A) removed outlier: 8.782A 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: 5.025A 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: 3.945A pdb=" N ARG C 80 " --> pdb=" O LEU C 93 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N VAL C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N SER C 118 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'C' and resid 138 through 141 removed outlier: 6.545A pdb=" N ILE C 173 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.324A pdb=" N VAL D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N VAL D 27 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N GLY D 202 " --> pdb=" O LYS D 9 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N ASP D 203 " --> pdb=" O GLN D 115 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLN D 115 " --> pdb=" O ASP D 203 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU D 171 " --> pdb=" O SER D 116 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 37 through 41 removed outlier: 3.659A pdb=" N GLN D 37 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LEU D 41 " --> pdb=" O TYR D 46 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N TYR D 46 " --> pdb=" O LEU D 41 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N GLN D 50 " --> pdb=" O THR D 36 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N GLY D 97 " --> pdb=" O ILE D 35 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 182 through 185 Processing sheet with id= 10, first strand: chain 'D' and resid 25 through 30 removed outlier: 5.346A pdb=" N SER D 188 " --> pdb=" O VAL D 30 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 47 through 52 removed outlier: 4.819A pdb=" N GLN D 47 " --> pdb=" O VAL D 85 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'E' and resid 1 through 5 removed outlier: 4.467A pdb=" N SER E 9 " --> pdb=" O THR E 5 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 43 through 46 No H-bonds generated for sheet with id= 13 Processing sheet with id= 14, first strand: chain 'E' and resid 116 through 119 removed outlier: 3.827A pdb=" N LYS E 184 " --> pdb=" O ARG E 144 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 65 through 68 removed outlier: 6.314A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 6.670A 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 82 through 89 removed outlier: 6.036A pdb=" N LEU G 133 " --> pdb=" O ARG G 85 " (cutoff:3.500A) removed outlier: 5.368A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 20, first strand: chain 'H' and resid 18 through 21 removed outlier: 6.716A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 74 through 78 removed outlier: 4.284A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.142A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 39 through 42 Processing sheet with id= 24, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.321A pdb=" N LEU L 103 " --> pdb=" O ARG L 67 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR L 104 " --> pdb=" O ILE L 34 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE L 32 " --> pdb=" O ILE L 106 " (cutoff:3.500A) removed outlier: 7.883A pdb=" N SER L 31 " --> pdb=" O ARG L 134 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'M' and resid 33 through 37 removed outlier: 3.725A pdb=" N ALA M 108 " --> pdb=" O ARG M 103 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY M 101 " --> pdb=" O MET M 110 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'N' and resid 50 through 53 removed outlier: 3.715A pdb=" N VAL N 29 " --> pdb=" O ASP N 92 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'O' and resid 41 through 48 removed outlier: 6.788A pdb=" N THR O 28 " --> pdb=" O LYS O 90 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS O 86 " --> pdb=" O GLN O 32 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 52 through 55 removed outlier: 3.915A pdb=" N ALA O 52 " --> pdb=" O THR O 63 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N SER O 60 " --> pdb=" O THR O 79 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Q' and resid 11 through 15 removed outlier: 4.086A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 17 through 21 removed outlier: 4.054A pdb=" N GLU Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLU Q 95 " --> pdb=" O ILE Q 64 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N THR Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 32, first strand: chain 'Q' and resid 65 through 72 removed outlier: 3.786A pdb=" N GLY Q 65 " --> pdb=" O GLU Q 95 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLN Q 91 " --> pdb=" O HIS Q 69 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 34, first strand: chain 'S' and resid 28 through 32 removed outlier: 4.471A pdb=" N LYS S 65 " --> pdb=" O ARG S 76 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASP S 78 " --> pdb=" O LYS S 63 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LYS S 63 " --> pdb=" O ASP S 78 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N LYS S 80 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N ILE S 61 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ALA S 82 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR S 59 " --> pdb=" O ALA S 82 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL S 84 " --> pdb=" O VAL S 57 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N VAL S 57 " --> pdb=" O VAL S 84 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 38 through 42 removed outlier: 5.363A pdb=" N ASN T 38 " --> pdb=" O ALA T 61 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'T' and resid 82 through 85 Processing sheet with id= 37, first strand: chain 'U' and resid 73 through 76 removed outlier: 3.572A pdb=" N ALA U 93 " --> pdb=" O PRO U 31 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.302A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 40, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.326A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 34 through 40 Processing sheet with id= 42, first strand: chain 'Y' and resid 34 through 38 removed outlier: 7.188A pdb=" N MET Y 53 " --> pdb=" O THR Y 9 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 28 through 31 removed outlier: 4.088A pdb=" N GLU Z 35 " --> pdb=" O ASP Z 30 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 17 through 20 removed outlier: 5.474A pdb=" N HIS b 17 " --> pdb=" O ILE b 43 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N HIS b 41 " --> pdb=" O GLY b 19 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'b' and resid 92 through 95 Processing sheet with id= 46, first strand: chain 'c' and resid 54 through 59 removed outlier: 3.706A pdb=" N ASN c 54 " --> pdb=" O SER c 69 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 164 through 170 removed outlier: 3.615A pdb=" N GLY c 194 " --> pdb=" O THR c 191 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ASP c 181 " --> pdb=" O ARG c 204 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 143 through 146 Processing sheet with id= 49, first strand: chain 'e' and resid 10 through 15 removed outlier: 6.743A pdb=" N LEU e 35 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'e' and resid 83 through 87 removed outlier: 3.750A pdb=" N ALA e 98 " --> pdb=" O ASN e 121 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN e 121 " --> pdb=" O ALA e 98 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 31 through 40 removed outlier: 6.353A pdb=" N ARG e 44 " --> pdb=" O ASP e 40 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 38 through 42 removed outlier: 3.920A pdb=" N ARG f 38 " --> pdb=" O ASN f 63 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N TYR f 59 " --> pdb=" O TRP f 42 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N HIS f 3 " --> pdb=" O ARG f 92 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ARG f 86 " --> pdb=" O LEU f 9 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'f' and resid 43 through 47 removed outlier: 3.883A pdb=" N GLY f 43 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N TYR f 59 " --> pdb=" O GLY f 43 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N HIS f 55 " --> pdb=" O LEU f 47 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 23 through 29 removed outlier: 6.355A pdb=" N GLN h 23 " --> pdb=" O LEU h 64 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N SER h 58 " --> pdb=" O SER h 29 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN h 48 " --> pdb=" O THR h 63 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 75 through 78 removed outlier: 4.933A pdb=" N MET h 75 " --> pdb=" O SER h 131 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA h 128 " --> pdb=" O ILE h 104 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE h 104 " --> pdb=" O ILE h 127 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 3 through 9 removed outlier: 3.902A pdb=" N LYS i 25 " --> pdb=" O TYR i 59 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 42 through 52 removed outlier: 5.072A pdb=" N LYS j 71 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'k' and resid 29 through 35 removed outlier: 7.090A pdb=" N VAL k 83 " --> pdb=" O ASN k 107 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 82 through 87 removed outlier: 6.849A pdb=" N GLY k 87 " --> pdb=" O VAL k 112 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 29 through 32 removed outlier: 5.134A pdb=" N LEU l 81 " --> pdb=" O VAL l 98 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 36 through 41 removed outlier: 4.845A 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: 3.753A pdb=" N GLY p 55 " --> pdb=" O ILE p 37 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N LYS p 67 " --> pdb=" O ASN p 58 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'q' and resid 7 through 12 removed outlier: 5.984A pdb=" N ARG q 7 " --> pdb=" O GLU q 64 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU q 64 " --> pdb=" O ARG q 7 " (cutoff:3.500A) removed outlier: 6.907A 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 1849 hydrogen bonds defined for protein. 5451 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3424 hydrogen bonds 5418 hydrogen bond angles 0 basepair planarities 1363 basepair parallelities 2088 stacking parallelities Total time for adding SS restraints: 209.43 Time building geometry restraints manager: 58.56 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: 13350 1.31 - 1.44: 64936 1.44 - 1.56: 60309 1.56 - 1.69: 8681 1.69 - 1.82: 251 Bond restraints: 147527 Sorted by residual: bond pdb=" C4 5MU A1935 " pdb=" C5 5MU A1935 " ideal model delta sigma weight residual 1.802 1.449 0.353 2.00e-02 2.50e+03 3.12e+02 bond pdb=" C11 80P a1601 " pdb=" C12 80P a1601 " ideal model delta sigma weight residual 1.240 1.550 -0.310 2.00e-02 2.50e+03 2.40e+02 bond pdb=" C11 80P a1602 " pdb=" C12 80P a1602 " ideal model delta sigma weight residual 1.240 1.547 -0.307 2.00e-02 2.50e+03 2.36e+02 bond pdb=" C11 80P a1603 " pdb=" C12 80P a1603 " ideal model delta sigma weight residual 1.240 1.541 -0.301 2.00e-02 2.50e+03 2.27e+02 bond pdb=" C08 80P a1602 " pdb=" C09 80P a1602 " ideal model delta sigma weight residual 1.332 1.623 -0.291 2.00e-02 2.50e+03 2.12e+02 ... (remaining 147522 not shown) Histogram of bond angle deviations from ideal: 98.23 - 107.73: 31904 107.73 - 117.24: 102669 117.24 - 126.74: 73945 126.74 - 136.24: 12117 136.24 - 145.75: 4 Bond angle restraints: 220639 Sorted by residual: angle pdb=" C11 80P a1603 " pdb=" C12 80P a1603 " pdb=" C13 80P a1603 " ideal model delta sigma weight residual 142.25 116.18 26.07 3.00e+00 1.11e-01 7.55e+01 angle pdb=" C11 80P a1601 " pdb=" C12 80P a1601 " pdb=" C13 80P a1601 " ideal model delta sigma weight residual 142.25 116.72 25.53 3.00e+00 1.11e-01 7.24e+01 angle pdb=" C11 80P a1602 " pdb=" C12 80P a1602 " pdb=" C13 80P a1602 " ideal model delta sigma weight residual 142.25 116.97 25.28 3.00e+00 1.11e-01 7.10e+01 angle pdb=" C13 80P a1603 " pdb=" C12 80P a1603 " pdb=" C17 80P a1603 " ideal model delta sigma weight residual 101.90 123.62 -21.72 3.00e+00 1.11e-01 5.24e+01 angle pdb=" C13 80P a1601 " pdb=" C12 80P a1601 " pdb=" C17 80P a1601 " ideal model delta sigma weight residual 101.90 123.54 -21.64 3.00e+00 1.11e-01 5.20e+01 ... (remaining 220634 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 83297 36.00 - 71.99: 9683 71.99 - 107.99: 1108 107.99 - 143.99: 36 143.99 - 179.98: 72 Dihedral angle restraints: 94196 sinusoidal: 78548 harmonic: 15648 Sorted by residual: dihedral pdb=" O4' U A 503 " pdb=" C1' U A 503 " pdb=" N1 U A 503 " pdb=" C2 U A 503 " ideal model delta sinusoidal sigma weight residual 200.00 22.80 177.20 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' U a1378 " pdb=" C1' U a1378 " pdb=" N1 U a1378 " pdb=" C2 U a1378 " ideal model delta sinusoidal sigma weight residual 200.00 23.13 176.87 1 1.50e+01 4.44e-03 8.53e+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 27.76 172.24 1 1.50e+01 4.44e-03 8.49e+01 ... (remaining 94193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.121: 28169 1.121 - 2.242: 0 2.242 - 3.362: 0 3.362 - 4.483: 0 4.483 - 5.604: 3 Chirality restraints: 28172 Sorted by residual: 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 -3.12 5.60 2.00e-01 2.50e+01 7.85e+02 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 -3.12 5.60 2.00e-01 2.50e+01 7.85e+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 -3.10 5.59 2.00e-01 2.50e+01 7.80e+02 ... (remaining 28169 not shown) Planarity restraints: 11889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG A2065 " 0.053 2.00e-02 2.50e+03 6.11e-01 8.39e+03 pdb=" C4' 7MG A2065 " 0.453 2.00e-02 2.50e+03 pdb=" O4' 7MG A2065 " 0.716 2.00e-02 2.50e+03 pdb=" C3' 7MG A2065 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 7MG A2065 " -0.625 2.00e-02 2.50e+03 pdb=" C2' 7MG A2065 " -0.197 2.00e-02 2.50e+03 pdb=" O2' 7MG A2065 " 0.945 2.00e-02 2.50e+03 pdb=" C1' 7MG A2065 " 0.204 2.00e-02 2.50e+03 pdb=" N9 7MG A2065 " -0.960 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 7MG a 524 " -0.043 2.00e-02 2.50e+03 5.88e-01 7.78e+03 pdb=" C4' 7MG a 524 " -0.439 2.00e-02 2.50e+03 pdb=" O4' 7MG a 524 " -0.660 2.00e-02 2.50e+03 pdb=" C3' 7MG a 524 " 0.592 2.00e-02 2.50e+03 pdb=" O3' 7MG a 524 " 0.596 2.00e-02 2.50e+03 pdb=" C2' 7MG a 524 " 0.202 2.00e-02 2.50e+03 pdb=" O2' 7MG a 524 " -0.932 2.00e-02 2.50e+03 pdb=" C1' 7MG a 524 " -0.221 2.00e-02 2.50e+03 pdb=" N9 7MG a 524 " 0.905 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG a1204 " 0.053 2.00e-02 2.50e+03 5.72e-01 7.37e+03 pdb=" C4' 2MG a1204 " 0.421 2.00e-02 2.50e+03 pdb=" O4' 2MG a1204 " 0.589 2.00e-02 2.50e+03 pdb=" C3' 2MG a1204 " -0.599 2.00e-02 2.50e+03 pdb=" O3' 2MG a1204 " -0.585 2.00e-02 2.50e+03 pdb=" C2' 2MG a1204 " -0.194 2.00e-02 2.50e+03 pdb=" O2' 2MG a1204 " 0.940 2.00e-02 2.50e+03 pdb=" C1' 2MG a1204 " 0.236 2.00e-02 2.50e+03 pdb=" N9 2MG a1204 " -0.861 2.00e-02 2.50e+03 ... (remaining 11886 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.46: 375 2.46 - 3.07: 78850 3.07 - 3.68: 245195 3.68 - 4.29: 374517 4.29 - 4.90: 505773 Nonbonded interactions: 1204710 Sorted by model distance: nonbonded pdb=" OP1 A a1194 " pdb="MG MG a1605 " model vdw 1.844 2.170 nonbonded pdb=" O2' G a1402 " pdb=" O2' MA6 a1515 " model vdw 1.884 2.440 nonbonded pdb=" O2 C A1563 " pdb=" O2' A A1564 " model vdw 1.885 2.440 nonbonded pdb=" O2' G A 67 " pdb=" OP2 U A 69 " model vdw 1.886 2.440 nonbonded pdb=" NZ LYS G 86 " pdb=" OG SER G 165 " model vdw 1.914 2.520 ... (remaining 1204705 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: 7.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.590 Construct map_model_manager: 0.090 Extract box with map and model: 29.730 Check model and map are aligned: 1.430 Set scattering table: 0.930 Process input model: 496.730 Find NCS groups from input model: 2.680 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 551.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7155 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 : 0.005 0.353 147527 Z= 0.336 Angle : 0.614 26.070 220639 Z= 0.313 Chirality : 0.067 5.604 28172 Planarity : 0.015 0.611 11889 Dihedral : 23.265 179.981 84118 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.22 % Favored : 97.67 % Rotamer: Outliers : 2.55 % Allowed : 25.01 % Favored : 72.44 % 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: 1.17 (0.11), residues: 5401 helix: 2.09 (0.12), residues: 1838 sheet: 0.75 (0.16), residues: 1032 loop : -0.16 (0.12), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP s 34 HIS 0.005 0.001 HIS 2 30 PHE 0.026 0.001 PHE F 99 TYR 0.013 0.001 TYR 2 63 ARG 0.016 0.001 ARG b 88 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1025 time to evaluate : 5.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 3 23 ILE cc_start: 0.7786 (mm) cc_final: 0.7470 (mm) REVERT: C 67 PHE cc_start: 0.8327 (m-80) cc_final: 0.8015 (m-80) REVERT: C 189 ARG cc_start: 0.7915 (OUTLIER) cc_final: 0.7608 (mtt90) REVERT: E 129 LYS cc_start: 0.8336 (mmtm) cc_final: 0.8133 (mptm) REVERT: I 63 GLN cc_start: 0.8084 (mm-40) cc_final: 0.7733 (mm-40) REVERT: L 82 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7842 (mtm-85) REVERT: V 15 ASP cc_start: 0.7946 (t0) cc_final: 0.7615 (t70) REVERT: V 55 ARG cc_start: 0.8415 (ptm-80) cc_final: 0.8206 (ptm-80) outliers start: 114 outliers final: 92 residues processed: 1130 average time/residue: 2.1867 time to fit residues: 3433.6054 Evaluate side-chains 1071 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 978 time to evaluate : 5.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 3 ASP Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain C residue 71 LYS Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 166 VAL Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 54 VAL Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU 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 K residue 29 VAL Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 107 ASP Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain c residue 216 ASN Chi-restraints excluded: chain d residue 32 THR Chi-restraints excluded: chain d residue 101 ASP Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 119 ARG Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 24 GLU Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain m residue 59 GLU Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 86 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 58 VAL Chi-restraints excluded: chain s residue 63 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 810 optimal weight: 8.9990 chunk 727 optimal weight: 6.9990 chunk 403 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 490 optimal weight: 5.9990 chunk 388 optimal weight: 9.9990 chunk 752 optimal weight: 8.9990 chunk 291 optimal weight: 10.0000 chunk 457 optimal weight: 6.9990 chunk 560 optimal weight: 6.9990 chunk 871 optimal weight: 40.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 HIS C 142 HIS C 163 GLN C 185 HIS D 47 GLN E 105 GLN E 114 GLN F 17 GLN G 139 GLN J 110 GLN O 9 GLN O 13 ASN P 56 GLN P 71 GLN ** P 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 6 GLN R 37 ASN S 58 ASN T 38 ASN U 82 GLN W 34 HIS Y 19 HIS Y 48 ASN Z 4 GLN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 140 ASN c 213 GLN d 122 HIS e 120 HIS e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 58 HIS h 42 GLN h 48 ASN ** h 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 29 GLN l 112 GLN m 12 ASN o 40 GLN q 31 GLN s 56 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.014 0.167 147527 Z= 0.858 Angle : 1.414 25.516 220639 Z= 0.664 Chirality : 0.075 2.529 28172 Planarity : 0.011 0.158 11889 Dihedral : 23.796 179.845 73583 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.22 % Allowed : 2.89 % Favored : 96.89 % Rotamer: Outliers : 8.61 % Allowed : 21.25 % Favored : 70.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.11), residues: 5401 helix: 0.48 (0.12), residues: 1841 sheet: 0.16 (0.15), residues: 1023 loop : -0.76 (0.11), residues: 2537 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP s 34 HIS 0.024 0.004 HIS c 18 PHE 0.055 0.005 PHE s 10 TYR 0.036 0.005 TYR P 32 ARG 0.033 0.002 ARG i 111 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1362 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 977 time to evaluate : 5.651 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: 1 13 LYS cc_start: 0.8356 (OUTLIER) cc_final: 0.7996 (mptm) REVERT: C 67 PHE cc_start: 0.8470 (m-80) cc_final: 0.8099 (m-80) REVERT: C 167 ARG cc_start: 0.7130 (tmm-80) cc_final: 0.6928 (ttm110) REVERT: D 160 LYS cc_start: 0.8535 (OUTLIER) cc_final: 0.8272 (mttm) REVERT: F 17 GLN cc_start: 0.5231 (OUTLIER) cc_final: 0.4572 (tp40) REVERT: F 26 MET cc_start: 0.7663 (OUTLIER) cc_final: 0.6408 (mmm) REVERT: F 47 LYS cc_start: 0.5278 (OUTLIER) cc_final: 0.4564 (mtmm) REVERT: F 142 ASP cc_start: 0.3514 (OUTLIER) cc_final: 0.3196 (t0) REVERT: I 34 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7974 (ttt-90) REVERT: L 137 MET cc_start: 0.7772 (OUTLIER) cc_final: 0.7501 (ttp) REVERT: M 23 ASN cc_start: 0.8740 (OUTLIER) cc_final: 0.8288 (m-40) REVERT: O 28 THR cc_start: 0.8311 (t) cc_final: 0.7960 (m) REVERT: O 113 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8177 (mt) REVERT: P 85 LYS cc_start: 0.8352 (OUTLIER) cc_final: 0.7981 (mttt) REVERT: T 65 ILE cc_start: 0.8183 (tt) cc_final: 0.7928 (tt) REVERT: W 72 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6663 (mpt-90) REVERT: Y 10 LYS cc_start: 0.8774 (OUTLIER) cc_final: 0.7514 (mttt) REVERT: d 10 LYS cc_start: 0.4685 (mptt) cc_final: 0.3871 (mptt) REVERT: e 158 LYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7142 (mttp) REVERT: g 32 GLN cc_start: 0.7922 (OUTLIER) cc_final: 0.7642 (mt0) REVERT: g 61 PHE cc_start: 0.6003 (t80) cc_final: 0.5782 (t80) REVERT: h 88 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7525 (mmt90) REVERT: h 111 ILE cc_start: 0.8500 (OUTLIER) cc_final: 0.8276 (mm) REVERT: j 67 ILE cc_start: 0.8585 (OUTLIER) cc_final: 0.8220 (tt) REVERT: m 41 GLU cc_start: 0.6500 (mt-10) cc_final: 0.6129 (mp0) REVERT: m 59 GLU cc_start: 0.7026 (mp0) cc_final: 0.6773 (mp0) REVERT: m 110 LYS cc_start: 0.8133 (OUTLIER) cc_final: 0.7882 (mtmt) REVERT: n 19 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7797 (ttmt) REVERT: o 54 ARG cc_start: 0.8453 (OUTLIER) cc_final: 0.7648 (mtp85) REVERT: o 77 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.5196 (mtm-85) REVERT: t 16 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7162 (mtpm) outliers start: 385 outliers final: 244 residues processed: 1216 average time/residue: 2.1614 time to fit residues: 3652.4162 Evaluate side-chains 1219 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 952 time to evaluate : 5.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 9 SER Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 13 LYS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 3 residue 6 SER Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 175 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 198 GLN Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 140 SER Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 17 GLN Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain H residue 53 GLU Chi-restraints excluded: chain I residue 34 ARG Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 56 ASP Chi-restraints excluded: chain K residue 72 ILE Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 143 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain L residue 131 ILE Chi-restraints excluded: chain L residue 137 MET Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 59 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain O residue 113 ILE Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 77 SER Chi-restraints excluded: chain P residue 85 LYS Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 33 VAL Chi-restraints excluded: chain S residue 38 THR Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain S residue 72 THR Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 56 ILE Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 78 ILE Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain W residue 78 ILE Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain Y residue 3 THR Chi-restraints excluded: chain Y residue 10 LYS Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain b residue 23 ARG Chi-restraints excluded: chain b residue 34 PHE Chi-restraints excluded: chain b residue 85 GLN Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 185 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 61 SER Chi-restraints excluded: chain c residue 66 VAL Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 153 VAL Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 93 LEU Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 19 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 11 GLU Chi-restraints excluded: chain g residue 17 LYS Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 32 GLN Chi-restraints excluded: chain g residue 38 ILE Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 94 SER Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 77 LYS Chi-restraints excluded: chain h residue 88 ARG Chi-restraints excluded: chain h residue 92 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 111 ILE Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 53 LEU Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 91 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain j residue 6 ILE Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 78 LEU Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain k residue 112 VAL Chi-restraints excluded: chain k residue 115 ILE Chi-restraints excluded: chain l residue 14 THR Chi-restraints excluded: chain l residue 55 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 111 ASN Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 33 ILE Chi-restraints excluded: chain m residue 42 THR Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 110 LYS Chi-restraints excluded: chain m residue 113 ARG Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 19 LYS Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 54 ARG Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 77 ARG Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 19 ASP Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain r residue 38 LYS Chi-restraints excluded: chain r residue 55 LEU Chi-restraints excluded: chain r residue 66 SER Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 32 LYS Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 61 ILE Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 37 SER Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 53 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 484 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 725 optimal weight: 2.9990 chunk 593 optimal weight: 0.5980 chunk 240 optimal weight: 0.6980 chunk 873 optimal weight: 40.0000 chunk 943 optimal weight: 2.9990 chunk 777 optimal weight: 20.0000 chunk 866 optimal weight: 0.6980 chunk 297 optimal weight: 4.9990 chunk 700 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS E 96 ASN E 105 GLN E 114 GLN I 136 GLN O 9 GLN O 13 ASN O 78 GLN P 101 HIS S 58 ASN W 36 HIS Y 48 ASN Z 4 GLN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 100 GLN c 123 GLN d 138 GLN e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 GLN h 48 ASN i 98 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN s 56 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7197 moved from start: 0.1244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 147527 Z= 0.151 Angle : 0.664 24.472 220639 Z= 0.347 Chirality : 0.042 2.118 28172 Planarity : 0.005 0.124 11889 Dihedral : 23.167 179.899 73539 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.06 % Favored : 97.82 % Rotamer: Outliers : 4.81 % Allowed : 24.65 % Favored : 70.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.68 (0.11), residues: 5401 helix: 1.63 (0.12), residues: 1859 sheet: 0.59 (0.16), residues: 1036 loop : -0.47 (0.11), residues: 2506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP s 34 HIS 0.007 0.001 HIS s 57 PHE 0.015 0.002 PHE s 10 TYR 0.016 0.002 TYR d 67 ARG 0.008 0.001 ARG c 143 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1199 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 215 poor density : 984 time to evaluate : 5.684 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: 3 23 ILE cc_start: 0.7827 (mm) cc_final: 0.7519 (mm) REVERT: C 67 PHE cc_start: 0.8352 (m-80) cc_final: 0.8005 (m-80) REVERT: D 160 LYS cc_start: 0.8443 (OUTLIER) cc_final: 0.8236 (mttm) REVERT: F 142 ASP cc_start: 0.3710 (OUTLIER) cc_final: 0.3495 (t70) REVERT: J 86 ILE cc_start: 0.8489 (OUTLIER) cc_final: 0.8137 (mm) REVERT: J 116 SER cc_start: 0.8026 (p) cc_final: 0.7755 (p) REVERT: K 4 ARG cc_start: 0.8212 (mmt180) cc_final: 0.7908 (mmt180) REVERT: M 23 ASN cc_start: 0.8709 (OUTLIER) cc_final: 0.8206 (t0) REVERT: S 36 ASN cc_start: 0.8394 (m-40) cc_final: 0.8177 (m-40) REVERT: V 55 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.8201 (ptm-80) REVERT: c 16 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7397 (mttt) REVERT: g 31 MET cc_start: 0.8566 (ttp) cc_final: 0.8290 (ttp) REVERT: g 32 GLN cc_start: 0.7745 (OUTLIER) cc_final: 0.7431 (mt0) REVERT: i 125 PHE cc_start: 0.6849 (OUTLIER) cc_final: 0.6499 (t80) REVERT: k 34 THR cc_start: 0.5072 (OUTLIER) cc_final: 0.4808 (p) REVERT: n 15 LYS cc_start: 0.7674 (OUTLIER) cc_final: 0.7176 (tppt) outliers start: 215 outliers final: 110 residues processed: 1104 average time/residue: 2.2060 time to fit residues: 3368.9733 Evaluate side-chains 1074 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 955 time to evaluate : 5.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 163 GLN Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 132 LEU Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 115 GLU Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 11 LYS Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 73 GLN Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain f residue 70 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 63 GLU Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 15 LYS Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 81 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 862 optimal weight: 1.9990 chunk 656 optimal weight: 5.9990 chunk 453 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 416 optimal weight: 8.9990 chunk 586 optimal weight: 8.9990 chunk 876 optimal weight: 50.0000 chunk 927 optimal weight: 3.9990 chunk 457 optimal weight: 7.9990 chunk 830 optimal weight: 3.9990 chunk 250 optimal weight: 8.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS E 105 GLN O 9 GLN O 13 ASN P 56 GLN P 71 GLN P 101 HIS R 37 ASN Y 48 ASN b 96 HIS ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN d 138 GLN e 120 HIS e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN j 20 GLN k 21 HIS l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN s 56 ASN s 57 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.103 147527 Z= 0.455 Angle : 0.948 24.327 220639 Z= 0.469 Chirality : 0.054 2.255 28172 Planarity : 0.008 0.143 11889 Dihedral : 23.382 179.849 73483 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.78 % Favored : 97.07 % Rotamer: Outliers : 6.73 % Allowed : 23.89 % Favored : 69.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.11), residues: 5401 helix: 1.18 (0.12), residues: 1848 sheet: 0.34 (0.15), residues: 1034 loop : -0.67 (0.11), residues: 2519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP s 34 HIS 0.013 0.002 HIS c 18 PHE 0.042 0.003 PHE s 10 TYR 0.024 0.003 TYR c 168 ARG 0.017 0.001 ARG i 111 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1273 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 972 time to evaluate : 5.592 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: C 67 PHE cc_start: 0.8423 (m-80) cc_final: 0.8099 (m-80) REVERT: C 180 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7221 (tt0) REVERT: D 160 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8290 (mttm) REVERT: F 142 ASP cc_start: 0.3957 (OUTLIER) cc_final: 0.3276 (t70) REVERT: J 86 ILE cc_start: 0.8501 (OUTLIER) cc_final: 0.8128 (mm) REVERT: K 4 ARG cc_start: 0.8261 (mmt180) cc_final: 0.7863 (mmt180) REVERT: L 41 ARG cc_start: 0.8012 (OUTLIER) cc_final: 0.7275 (mtt180) REVERT: L 58 ILE cc_start: 0.7350 (OUTLIER) cc_final: 0.7137 (pt) REVERT: M 23 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8214 (t0) REVERT: O 28 THR cc_start: 0.8392 (t) cc_final: 0.8044 (m) REVERT: P 12 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7154 (ttm110) REVERT: V 55 ARG cc_start: 0.8464 (ptm-80) cc_final: 0.8223 (ptm-80) REVERT: W 72 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.6525 (mpt-90) REVERT: Y 14 HIS cc_start: 0.7144 (OUTLIER) cc_final: 0.6523 (p-80) REVERT: Y 17 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7557 (tmmt) REVERT: c 16 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7374 (mttt) REVERT: g 32 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7515 (mt0) REVERT: i 125 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.6548 (t80) REVERT: k 34 THR cc_start: 0.5124 (OUTLIER) cc_final: 0.4873 (p) REVERT: m 41 GLU cc_start: 0.6474 (mt-10) cc_final: 0.6133 (mp0) REVERT: t 16 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7092 (mtpm) outliers start: 301 outliers final: 195 residues processed: 1150 average time/residue: 2.2033 time to fit residues: 3518.0577 Evaluate side-chains 1173 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 211 poor density : 962 time to evaluate : 5.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 0 residue 44 ILE Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 142 ASP Chi-restraints excluded: chain F residue 145 LYS Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 43 LEU Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 30 MET Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Z residue 9 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain g residue 11 GLU Chi-restraints excluded: chain g residue 13 LEU 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 72 MET Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 92 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 61 ILE Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 35 THR Chi-restraints excluded: chain t residue 48 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 772 optimal weight: 0.9980 chunk 526 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 690 optimal weight: 0.6980 chunk 382 optimal weight: 30.0000 chunk 791 optimal weight: 7.9990 chunk 641 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 473 optimal weight: 20.0000 chunk 832 optimal weight: 1.9990 chunk 234 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS C 163 GLN E 105 GLN E 114 GLN G 143 GLN O 9 GLN O 13 ASN O 78 GLN P 56 GLN P 71 GLN P 101 HIS R 37 ASN S 58 ASN Y 48 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN j 20 GLN l 29 GLN l 46 ASN m 12 ASN m 52 GLN o 40 GLN q 31 GLN s 56 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.1542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 147527 Z= 0.279 Angle : 0.764 23.574 220639 Z= 0.391 Chirality : 0.047 2.251 28172 Planarity : 0.006 0.133 11889 Dihedral : 23.214 179.647 73480 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.43 % Favored : 97.41 % Rotamer: Outliers : 6.28 % Allowed : 24.71 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.41 (0.11), residues: 5401 helix: 1.45 (0.12), residues: 1849 sheet: 0.41 (0.15), residues: 1032 loop : -0.65 (0.11), residues: 2520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP s 34 HIS 0.009 0.001 HIS j 15 PHE 0.032 0.002 PHE s 10 TYR 0.023 0.002 TYR c 168 ARG 0.011 0.001 ARG m 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 987 time to evaluate : 5.682 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: C 67 PHE cc_start: 0.8387 (m-80) cc_final: 0.8023 (m-80) REVERT: C 177 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7187 (mmm160) REVERT: C 180 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7204 (tt0) REVERT: D 160 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8267 (mttm) REVERT: F 26 MET cc_start: 0.7496 (OUTLIER) cc_final: 0.6318 (mmm) REVERT: G 149 ARG cc_start: 0.7663 (OUTLIER) cc_final: 0.7175 (ttp80) REVERT: J 86 ILE cc_start: 0.8503 (OUTLIER) cc_final: 0.8133 (mm) REVERT: K 4 ARG cc_start: 0.8231 (mmt180) cc_final: 0.7869 (mmt180) REVERT: M 23 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8218 (t0) REVERT: N 93 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7427 (ptt90) REVERT: P 12 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7161 (ttm110) REVERT: V 55 ARG cc_start: 0.8470 (ptm-80) cc_final: 0.8230 (ptm-80) REVERT: W 72 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.6449 (mpt-90) REVERT: Y 14 HIS cc_start: 0.7113 (OUTLIER) cc_final: 0.6526 (p-80) REVERT: Y 17 LYS cc_start: 0.7714 (OUTLIER) cc_final: 0.7443 (tmmt) REVERT: c 16 LYS cc_start: 0.7820 (OUTLIER) cc_final: 0.7462 (mttt) REVERT: e 158 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7036 (mttp) REVERT: g 32 GLN cc_start: 0.7695 (OUTLIER) cc_final: 0.7406 (mt0) REVERT: i 125 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6544 (t80) REVERT: j 7 ARG cc_start: 0.7563 (OUTLIER) cc_final: 0.6867 (ttm170) REVERT: k 34 THR cc_start: 0.5254 (OUTLIER) cc_final: 0.5028 (p) REVERT: m 41 GLU cc_start: 0.6448 (mt-10) cc_final: 0.6092 (mp0) REVERT: m 107 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.7583 (mmp-170) REVERT: t 16 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7075 (mtpm) outliers start: 281 outliers final: 192 residues processed: 1150 average time/residue: 2.2273 time to fit residues: 3556.0044 Evaluate side-chains 1188 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 976 time to evaluate : 5.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain G residue 170 LEU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain b residue 29 MET Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 201 VAL Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 102 SER Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 132 VAL Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 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 63 GLU Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 92 LEU Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain r residue 55 LEU Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 35 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 312 optimal weight: 7.9990 chunk 835 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 544 optimal weight: 5.9990 chunk 229 optimal weight: 8.9990 chunk 928 optimal weight: 4.9990 chunk 771 optimal weight: 1.9990 chunk 430 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 487 optimal weight: 0.6980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS C 86 ASN C 163 GLN E 105 GLN O 9 GLN O 13 ASN P 56 GLN P 71 GLN P 101 HIS R 37 ASN T 47 ASN V 12 ASN Y 48 ASN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN d 138 GLN e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN j 20 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 147527 Z= 0.344 Angle : 0.834 23.387 220639 Z= 0.421 Chirality : 0.049 2.257 28172 Planarity : 0.007 0.138 11889 Dihedral : 23.261 179.620 73480 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.89 % Favored : 96.96 % Rotamer: Outliers : 6.84 % Allowed : 24.38 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 5401 helix: 1.34 (0.12), residues: 1850 sheet: 0.35 (0.15), residues: 1025 loop : -0.70 (0.11), residues: 2526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP s 34 HIS 0.010 0.002 HIS c 18 PHE 0.037 0.003 PHE s 10 TYR 0.026 0.003 TYR c 168 ARG 0.012 0.001 ARG i 111 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1280 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 306 poor density : 974 time to evaluate : 5.590 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: C 67 PHE cc_start: 0.8406 (m-80) cc_final: 0.8061 (m-80) REVERT: C 177 ARG cc_start: 0.7696 (OUTLIER) cc_final: 0.7269 (mmm160) REVERT: C 180 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: D 160 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8275 (mttm) REVERT: F 26 MET cc_start: 0.7476 (OUTLIER) cc_final: 0.6299 (mmm) REVERT: G 149 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7175 (ttp80) REVERT: J 86 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8129 (mm) REVERT: K 4 ARG cc_start: 0.8249 (mmt180) cc_final: 0.7861 (mmt180) REVERT: L 41 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7251 (mtt180) REVERT: L 58 ILE cc_start: 0.7197 (OUTLIER) cc_final: 0.6978 (pt) REVERT: M 23 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8218 (t0) REVERT: N 93 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7416 (ptt90) REVERT: O 28 THR cc_start: 0.8356 (t) cc_final: 0.7970 (m) REVERT: P 12 ARG cc_start: 0.7840 (OUTLIER) cc_final: 0.7165 (ttm110) REVERT: V 55 ARG cc_start: 0.8471 (ptm-80) cc_final: 0.8223 (ptm-80) REVERT: W 72 ARG cc_start: 0.7776 (OUTLIER) cc_final: 0.6463 (mpt-90) REVERT: Y 10 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.7528 (mttt) REVERT: Y 14 HIS cc_start: 0.7115 (OUTLIER) cc_final: 0.6514 (p-80) REVERT: Y 17 LYS cc_start: 0.7763 (OUTLIER) cc_final: 0.7502 (tmmt) REVERT: c 88 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.6202 (mt0) REVERT: e 158 LYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7067 (mttp) REVERT: g 32 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7484 (mt0) REVERT: g 137 LYS cc_start: 0.5128 (OUTLIER) cc_final: 0.4162 (ptmt) REVERT: i 125 PHE cc_start: 0.6889 (OUTLIER) cc_final: 0.6543 (t80) REVERT: j 7 ARG cc_start: 0.7581 (OUTLIER) cc_final: 0.6908 (ttm170) REVERT: k 34 THR cc_start: 0.5268 (OUTLIER) cc_final: 0.5065 (p) REVERT: t 16 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7101 (mtpm) outliers start: 306 outliers final: 226 residues processed: 1161 average time/residue: 2.2126 time to fit residues: 3565.3952 Evaluate side-chains 1212 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 963 time to evaluate : 5.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 29 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 10 LYS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain b residue 29 MET Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain g residue 13 LEU 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 65 THR Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 30 ARG Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 111 ASN Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 50 ASP Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 37 SER Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 35 THR Chi-restraints excluded: chain t residue 46 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 895 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 529 optimal weight: 9.9990 chunk 678 optimal weight: 20.0000 chunk 525 optimal weight: 4.9990 chunk 781 optimal weight: 2.9990 chunk 518 optimal weight: 9.9990 chunk 925 optimal weight: 2.9990 chunk 579 optimal weight: 6.9990 chunk 564 optimal weight: 7.9990 chunk 427 optimal weight: 0.6980 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS C 163 GLN E 114 GLN G 143 GLN J 110 GLN O 9 GLN O 13 ASN O 78 GLN P 56 GLN P 71 GLN P 101 HIS R 37 ASN S 58 ASN T 47 ASN V 12 ASN Y 48 ASN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN h 42 GLN h 86 GLN j 20 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 147527 Z= 0.348 Angle : 0.831 23.662 220639 Z= 0.419 Chirality : 0.049 2.247 28172 Planarity : 0.007 0.136 11889 Dihedral : 23.248 179.987 73477 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.63 % Favored : 97.20 % Rotamer: Outliers : 6.98 % Allowed : 24.47 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5401 helix: 1.33 (0.12), residues: 1850 sheet: 0.34 (0.15), residues: 1020 loop : -0.71 (0.11), residues: 2531 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP s 34 HIS 0.010 0.002 HIS j 15 PHE 0.037 0.003 PHE s 10 TYR 0.030 0.003 TYR c 168 ARG 0.012 0.001 ARG i 111 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1283 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 312 poor density : 971 time to evaluate : 5.671 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: 3 26 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6988 (pt) REVERT: C 67 PHE cc_start: 0.8408 (m-80) cc_final: 0.8065 (m-80) REVERT: C 177 ARG cc_start: 0.7688 (OUTLIER) cc_final: 0.7260 (mmm160) REVERT: C 180 GLU cc_start: 0.7566 (OUTLIER) cc_final: 0.7251 (tt0) REVERT: D 160 LYS cc_start: 0.8496 (OUTLIER) cc_final: 0.8273 (mttm) REVERT: F 26 MET cc_start: 0.7468 (OUTLIER) cc_final: 0.6399 (mmm) REVERT: G 149 ARG cc_start: 0.7680 (OUTLIER) cc_final: 0.7187 (ttp80) REVERT: J 86 ILE cc_start: 0.8502 (OUTLIER) cc_final: 0.8129 (mm) REVERT: K 4 ARG cc_start: 0.8247 (mmt180) cc_final: 0.7858 (mmt180) REVERT: L 41 ARG cc_start: 0.7985 (OUTLIER) cc_final: 0.7263 (mtt180) REVERT: L 58 ILE cc_start: 0.7186 (OUTLIER) cc_final: 0.6972 (pt) REVERT: M 23 ASN cc_start: 0.8729 (OUTLIER) cc_final: 0.8216 (t0) REVERT: N 93 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7390 (ptt90) REVERT: P 12 ARG cc_start: 0.7856 (OUTLIER) cc_final: 0.7179 (ttm110) REVERT: V 55 ARG cc_start: 0.8472 (ptm-80) cc_final: 0.8231 (ptm-80) REVERT: W 72 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6494 (mpt-90) REVERT: Y 10 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.7530 (mttt) REVERT: Y 14 HIS cc_start: 0.7116 (OUTLIER) cc_final: 0.6517 (p-80) REVERT: Y 17 LYS cc_start: 0.7758 (OUTLIER) cc_final: 0.7494 (tmmt) REVERT: e 158 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7063 (mttp) REVERT: g 32 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: g 137 LYS cc_start: 0.5202 (OUTLIER) cc_final: 0.4235 (ptmt) REVERT: i 58 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7297 (ptpp) REVERT: i 125 PHE cc_start: 0.6890 (OUTLIER) cc_final: 0.6544 (t80) REVERT: j 7 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.6933 (ttm170) REVERT: m 107 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7676 (mmp-170) REVERT: n 4 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7133 (mptt) REVERT: q 20 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7772 (mttm) REVERT: t 16 LYS cc_start: 0.7739 (OUTLIER) cc_final: 0.7088 (mtpm) outliers start: 312 outliers final: 247 residues processed: 1161 average time/residue: 2.2415 time to fit residues: 3622.5808 Evaluate side-chains 1232 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 959 time to evaluate : 5.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 1 residue 29 GLN Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 177 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 200 ASN Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 29 VAL Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 58 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain P residue 100 MET Chi-restraints excluded: chain Q residue 6 GLN Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 56 GLU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 10 SER Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 10 LYS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain b residue 29 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain g residue 13 LEU 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 65 THR Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain g residue 137 LYS Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain i residue 20 SER Chi-restraints excluded: chain i residue 41 THR Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 58 LYS Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 86 ARG Chi-restraints excluded: chain l residue 93 VAL Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 111 ASN Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 68 ASP Chi-restraints excluded: chain m residue 72 GLU Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 20 LYS Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 61 ILE Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 35 THR Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 48 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 572 optimal weight: 0.9980 chunk 369 optimal weight: 8.9990 chunk 552 optimal weight: 5.9990 chunk 278 optimal weight: 5.9990 chunk 181 optimal weight: 5.9990 chunk 179 optimal weight: 40.0000 chunk 588 optimal weight: 2.9990 chunk 630 optimal weight: 10.0000 chunk 457 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 727 optimal weight: 6.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS 3 35 GLN ** C 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 HIS C 163 GLN G 143 GLN J 110 GLN O 9 GLN O 13 ASN P 56 GLN P 71 GLN P 101 HIS Q 6 GLN R 37 ASN S 58 ASN V 12 ASN Y 48 ASN ** Z 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 213 GLN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN e 120 HIS e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN j 20 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.131 147527 Z= 0.593 Angle : 1.111 25.331 220639 Z= 0.536 Chirality : 0.060 2.282 28172 Planarity : 0.009 0.150 11889 Dihedral : 23.441 179.977 73474 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.19 % Allowed : 3.17 % Favored : 96.65 % Rotamer: Outliers : 7.83 % Allowed : 23.95 % Favored : 68.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.11), residues: 5401 helix: 0.82 (0.12), residues: 1849 sheet: 0.04 (0.15), residues: 1050 loop : -0.89 (0.11), residues: 2502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP s 34 HIS 0.016 0.003 HIS c 18 PHE 0.052 0.004 PHE s 10 TYR 0.037 0.004 TYR c 168 ARG 0.024 0.002 ARG i 111 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1319 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 969 time to evaluate : 5.653 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 26 ILE cc_start: 0.7271 (OUTLIER) cc_final: 0.7035 (pt) REVERT: C 67 PHE cc_start: 0.8439 (m-80) cc_final: 0.8055 (m-80) REVERT: C 114 ASP cc_start: 0.7536 (OUTLIER) cc_final: 0.7126 (m-30) REVERT: C 180 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.7272 (tt0) REVERT: D 160 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (mttm) REVERT: F 26 MET cc_start: 0.7475 (OUTLIER) cc_final: 0.6416 (mmm) REVERT: G 149 ARG cc_start: 0.7726 (OUTLIER) cc_final: 0.7308 (ttp80) REVERT: J 86 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8145 (mm) REVERT: L 41 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7209 (mtt180) REVERT: M 23 ASN cc_start: 0.8733 (OUTLIER) cc_final: 0.8222 (m-40) REVERT: N 93 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7451 (ptt90) REVERT: O 28 THR cc_start: 0.8412 (t) cc_final: 0.8068 (m) REVERT: P 12 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7144 (ttm110) REVERT: V 55 ARG cc_start: 0.8474 (ptm-80) cc_final: 0.8233 (ptm-80) REVERT: W 72 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.6525 (mpt-90) REVERT: Y 10 LYS cc_start: 0.8744 (OUTLIER) cc_final: 0.7490 (mttt) REVERT: Y 14 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.6534 (p-80) REVERT: Y 17 LYS cc_start: 0.7848 (OUTLIER) cc_final: 0.7585 (tmmt) REVERT: c 164 ARG cc_start: 0.8209 (OUTLIER) cc_final: 0.7608 (ptt-90) REVERT: d 10 LYS cc_start: 0.4613 (mptt) cc_final: 0.3633 (mptt) REVERT: e 158 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.7089 (mttp) REVERT: g 32 GLN cc_start: 0.7812 (OUTLIER) cc_final: 0.7532 (mt0) REVERT: i 58 LYS cc_start: 0.7576 (OUTLIER) cc_final: 0.7322 (ptpp) REVERT: i 125 PHE cc_start: 0.6914 (OUTLIER) cc_final: 0.6555 (t80) REVERT: j 7 ARG cc_start: 0.7590 (OUTLIER) cc_final: 0.6958 (ttm170) REVERT: j 67 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8272 (tt) REVERT: m 107 ARG cc_start: 0.8534 (OUTLIER) cc_final: 0.7816 (mmp-170) REVERT: n 4 LYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7238 (mptt) REVERT: q 7 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6362 (mmt180) REVERT: q 20 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7922 (mttm) REVERT: t 16 LYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7102 (mtpm) outliers start: 350 outliers final: 259 residues processed: 1178 average time/residue: 2.1581 time to fit residues: 3555.9982 Evaluate side-chains 1243 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 957 time to evaluate : 5.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 0 residue 23 LYS Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 13 ARG Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 116 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 134 ASN Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 145 GLU Chi-restraints excluded: chain C residue 170 SER Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 186 VAL Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 194 GLU Chi-restraints excluded: chain C residue 199 GLU Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 3 ILE Chi-restraints excluded: chain D residue 36 THR Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 52 SER Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 169 VAL Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 16 LEU Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 25 VAL Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 71 ARG Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 47 GLU Chi-restraints excluded: chain G residue 72 LEU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain I residue 73 LYS Chi-restraints excluded: chain I residue 106 LYS Chi-restraints excluded: chain J residue 9 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain K residue 78 GLU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 41 ARG Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 111 GLU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 24 LEU Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 70 THR Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain O residue 27 ASP Chi-restraints excluded: chain O residue 74 GLU Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 15 LYS Chi-restraints excluded: chain P residue 41 LYS Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain Q residue 32 THR Chi-restraints excluded: chain Q residue 34 THR Chi-restraints excluded: chain Q residue 41 VAL Chi-restraints excluded: chain R residue 13 SER Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain R residue 109 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain T residue 91 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 71 ASP Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain V residue 62 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 68 VAL Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 10 SER Chi-restraints excluded: chain X residue 17 LEU Chi-restraints excluded: chain X residue 34 THR Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 10 LYS Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Y residue 20 LYS Chi-restraints excluded: chain Z residue 11 SER Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 36 THR Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain b residue 29 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 143 MET Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain b residue 221 ASP Chi-restraints excluded: chain c residue 4 LYS Chi-restraints excluded: chain c residue 14 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 52 VAL Chi-restraints excluded: chain c residue 55 ILE Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 95 MET Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 141 THR Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 162 ILE Chi-restraints excluded: chain c residue 164 ARG Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain c residue 191 THR Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 118 GLN Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 12 GLU Chi-restraints excluded: chain e residue 13 LYS Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 78 THR Chi-restraints excluded: chain e residue 145 ASP Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain e residue 160 VAL Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 64 VAL Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain g residue 11 GLU 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 65 THR Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 73 VAL Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 112 SER Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 25 VAL Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 60 LEU Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 76 VAL Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 97 LYS Chi-restraints excluded: chain h residue 106 SER Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain h residue 126 VAL Chi-restraints excluded: chain i residue 45 VAL Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 58 LYS Chi-restraints excluded: chain i residue 116 LEU Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 7 ARG Chi-restraints excluded: chain j residue 21 SER Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 54 SER Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 66 GLU Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain j residue 98 VAL Chi-restraints excluded: chain k residue 17 GLU Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 107 VAL Chi-restraints excluded: chain l residue 111 ASN Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 4 ILE Chi-restraints excluded: chain m residue 43 THR Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 65 THR Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain m residue 107 ARG Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 34 VAL Chi-restraints excluded: chain n residue 43 GLU Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 4 THR Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain q residue 7 ARG Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 20 LYS Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain r residue 40 VAL Chi-restraints excluded: chain r residue 55 LEU Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 31 ILE Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 56 ASN Chi-restraints excluded: chain s residue 61 ILE Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 81 ARG Chi-restraints excluded: chain t residue 16 LYS Chi-restraints excluded: chain t residue 35 THR Chi-restraints excluded: chain t residue 37 SER Chi-restraints excluded: chain t residue 46 VAL Chi-restraints excluded: chain t residue 48 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 841 optimal weight: 0.2980 chunk 886 optimal weight: 0.7980 chunk 808 optimal weight: 0.5980 chunk 862 optimal weight: 0.7980 chunk 518 optimal weight: 7.9990 chunk 375 optimal weight: 20.0000 chunk 677 optimal weight: 0.5980 chunk 264 optimal weight: 3.9990 chunk 779 optimal weight: 0.9980 chunk 815 optimal weight: 9.9990 chunk 859 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS C 163 GLN E 96 ASN E 114 GLN G 143 GLN I 136 GLN J 110 GLN O 9 GLN O 13 ASN O 78 GLN P 56 GLN P 71 GLN P 101 HIS R 37 ASN S 58 ASN V 12 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 88 GLN c 123 GLN ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN j 20 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 147527 Z= 0.148 Angle : 0.660 24.292 220639 Z= 0.344 Chirality : 0.042 2.124 28172 Planarity : 0.006 0.126 11889 Dihedral : 23.071 179.868 73473 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.43 % Favored : 97.44 % Rotamer: Outliers : 4.52 % Allowed : 27.47 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.52 (0.11), residues: 5401 helix: 1.60 (0.12), residues: 1866 sheet: 0.43 (0.15), residues: 1036 loop : -0.64 (0.11), residues: 2499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP s 34 HIS 0.008 0.001 HIS s 57 PHE 0.022 0.001 PHE s 10 TYR 0.017 0.002 TYR c 168 ARG 0.011 0.001 ARG b 210 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1187 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 985 time to evaluate : 5.654 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: 3 26 ILE cc_start: 0.7203 (OUTLIER) cc_final: 0.6964 (pt) REVERT: C 67 PHE cc_start: 0.8359 (m-80) cc_final: 0.7979 (m-80) REVERT: C 114 ASP cc_start: 0.7437 (OUTLIER) cc_final: 0.6905 (m-30) REVERT: D 160 LYS cc_start: 0.8446 (OUTLIER) cc_final: 0.8230 (mttm) REVERT: F 26 MET cc_start: 0.7459 (OUTLIER) cc_final: 0.6404 (mmm) REVERT: G 149 ARG cc_start: 0.7620 (OUTLIER) cc_final: 0.7052 (ttp80) REVERT: K 4 ARG cc_start: 0.8226 (mmt180) cc_final: 0.7957 (mmt180) REVERT: M 23 ASN cc_start: 0.8705 (OUTLIER) cc_final: 0.8200 (t0) REVERT: N 93 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7388 (ptt90) REVERT: O 28 THR cc_start: 0.8215 (t) cc_final: 0.7914 (t) REVERT: P 12 ARG cc_start: 0.7769 (OUTLIER) cc_final: 0.7123 (ttm110) REVERT: V 55 ARG cc_start: 0.8473 (ptm-80) cc_final: 0.8256 (ptm-80) REVERT: W 72 ARG cc_start: 0.7700 (OUTLIER) cc_final: 0.6391 (mpt-90) REVERT: Y 14 HIS cc_start: 0.7137 (OUTLIER) cc_final: 0.6569 (p-80) REVERT: Y 17 LYS cc_start: 0.7615 (OUTLIER) cc_final: 0.7369 (tmmt) REVERT: c 16 LYS cc_start: 0.7818 (OUTLIER) cc_final: 0.7418 (mttt) REVERT: d 10 LYS cc_start: 0.4559 (mptt) cc_final: 0.3863 (mptt) REVERT: e 158 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7035 (mttp) REVERT: g 25 LYS cc_start: 0.7979 (OUTLIER) cc_final: 0.7759 (tppt) REVERT: i 125 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.6532 (t80) REVERT: p 70 LEU cc_start: 0.8288 (OUTLIER) cc_final: 0.7977 (mt) outliers start: 202 outliers final: 144 residues processed: 1102 average time/residue: 2.2140 time to fit residues: 3401.5041 Evaluate side-chains 1126 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 966 time to evaluate : 5.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 114 ASP Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 245 VAL Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain C residue 264 THR Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain M residue 116 VAL Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain R residue 105 VAL Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain b residue 29 MET Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 84 ILE Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 41 GLN Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 71 GLU Chi-restraints excluded: chain d residue 144 VAL Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 63 GLU Chi-restraints excluded: chain g residue 65 THR Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain i residue 56 THR Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 67 ILE Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 81 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 566 optimal weight: 0.2980 chunk 911 optimal weight: 5.9990 chunk 556 optimal weight: 2.9990 chunk 432 optimal weight: 2.9990 chunk 633 optimal weight: 3.9990 chunk 956 optimal weight: 50.0000 chunk 880 optimal weight: 0.0070 chunk 761 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 588 optimal weight: 3.9990 chunk 466 optimal weight: 1.9990 overall best weight: 1.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 50 HIS C 23 HIS C 163 GLN E 105 GLN G 143 GLN J 110 GLN O 9 GLN O 13 ASN P 71 GLN P 101 HIS Q 86 GLN R 37 ASN U 79 GLN Y 48 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 49 ASN c 88 GLN ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 42 GLN h 48 ASN h 86 GLN j 20 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN s 56 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 147527 Z= 0.246 Angle : 0.726 23.863 220639 Z= 0.373 Chirality : 0.045 2.197 28172 Planarity : 0.006 0.131 11889 Dihedral : 23.097 179.808 73462 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.67 % Favored : 97.20 % Rotamer: Outliers : 3.80 % Allowed : 28.16 % Favored : 68.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % 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: 0.51 (0.11), residues: 5401 helix: 1.59 (0.12), residues: 1852 sheet: 0.46 (0.16), residues: 1026 loop : -0.63 (0.11), residues: 2523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP s 34 HIS 0.008 0.001 HIS j 15 PHE 0.031 0.002 PHE s 10 TYR 0.024 0.002 TYR c 168 ARG 0.012 0.001 ARG d 58 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10802 Ramachandran restraints generated. 5401 Oldfield, 0 Emsley, 5401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1143 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 973 time to evaluate : 5.667 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: 3 26 ILE cc_start: 0.7238 (OUTLIER) cc_final: 0.6993 (pt) REVERT: C 67 PHE cc_start: 0.8389 (m-80) cc_final: 0.8018 (m-80) REVERT: C 180 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7135 (tt0) REVERT: D 160 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8250 (mttm) REVERT: F 26 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6358 (mmm) REVERT: F 47 LYS cc_start: 0.4857 (OUTLIER) cc_final: 0.4479 (ptpp) REVERT: G 149 ARG cc_start: 0.7638 (OUTLIER) cc_final: 0.7121 (ttp80) REVERT: M 23 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8210 (t0) REVERT: N 93 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7410 (ptt90) REVERT: O 28 THR cc_start: 0.8276 (t) cc_final: 0.8032 (t) REVERT: P 12 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7158 (ttm110) REVERT: V 55 ARG cc_start: 0.8476 (ptm-80) cc_final: 0.8239 (ptm-80) REVERT: W 72 ARG cc_start: 0.7718 (OUTLIER) cc_final: 0.6442 (mpt-90) REVERT: Y 14 HIS cc_start: 0.7135 (OUTLIER) cc_final: 0.6553 (p-80) REVERT: Y 17 LYS cc_start: 0.7715 (OUTLIER) cc_final: 0.7479 (tmmt) REVERT: c 16 LYS cc_start: 0.7815 (OUTLIER) cc_final: 0.7415 (mttt) REVERT: d 10 LYS cc_start: 0.4720 (mptt) cc_final: 0.3987 (mptt) REVERT: e 158 LYS cc_start: 0.7396 (OUTLIER) cc_final: 0.7048 (mttp) REVERT: i 125 PHE cc_start: 0.6880 (OUTLIER) cc_final: 0.6524 (t80) outliers start: 170 outliers final: 139 residues processed: 1069 average time/residue: 2.2474 time to fit residues: 3336.8940 Evaluate side-chains 1120 residues out of total 4471 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 966 time to evaluate : 5.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 0 residue 6 ARG Chi-restraints excluded: chain 2 residue 30 HIS Chi-restraints excluded: chain 2 residue 51 VAL Chi-restraints excluded: chain 3 residue 26 ILE Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain C residue 133 ARG Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 189 ARG Chi-restraints excluded: chain C residue 202 LEU Chi-restraints excluded: chain C residue 257 THR Chi-restraints excluded: chain C residue 261 LYS Chi-restraints excluded: chain D residue 42 GLU Chi-restraints excluded: chain D residue 59 SER Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 160 LYS Chi-restraints excluded: chain D residue 171 GLU Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 189 VAL Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 92 SER Chi-restraints excluded: chain E residue 129 LYS Chi-restraints excluded: chain E residue 172 THR Chi-restraints excluded: chain F residue 13 LYS Chi-restraints excluded: chain F residue 18 GLU Chi-restraints excluded: chain F residue 19 GLU Chi-restraints excluded: chain F residue 22 ILE Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 47 LYS Chi-restraints excluded: chain F residue 50 LEU Chi-restraints excluded: chain F residue 57 MET Chi-restraints excluded: chain F residue 90 THR Chi-restraints excluded: chain F residue 96 MET Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain G residue 18 THR Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 92 VAL Chi-restraints excluded: chain G residue 103 VAL Chi-restraints excluded: chain G residue 143 GLN Chi-restraints excluded: chain G residue 149 ARG Chi-restraints excluded: chain G residue 167 GLU Chi-restraints excluded: chain H residue 41 GLU Chi-restraints excluded: chain I residue 70 LEU Chi-restraints excluded: chain K residue 123 THR Chi-restraints excluded: chain K residue 131 LYS Chi-restraints excluded: chain L residue 28 SER Chi-restraints excluded: chain M residue 23 ASN Chi-restraints excluded: chain M residue 99 LYS Chi-restraints excluded: chain N residue 22 LEU Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 93 ARG Chi-restraints excluded: chain P residue 12 ARG Chi-restraints excluded: chain P residue 91 ASP Chi-restraints excluded: chain S residue 9 VAL Chi-restraints excluded: chain S residue 49 LEU Chi-restraints excluded: chain S residue 60 THR Chi-restraints excluded: chain T residue 18 LYS Chi-restraints excluded: chain T residue 57 VAL Chi-restraints excluded: chain T residue 62 SER Chi-restraints excluded: chain T residue 63 LEU Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain V residue 84 THR Chi-restraints excluded: chain W residue 47 VAL Chi-restraints excluded: chain W residue 51 LEU Chi-restraints excluded: chain W residue 72 ARG Chi-restraints excluded: chain X residue 5 ASP Chi-restraints excluded: chain X residue 43 VAL Chi-restraints excluded: chain X residue 44 GLN Chi-restraints excluded: chain Y residue 14 HIS Chi-restraints excluded: chain Y residue 17 LYS Chi-restraints excluded: chain Z residue 43 THR Chi-restraints excluded: chain b residue 29 MET Chi-restraints excluded: chain b residue 72 VAL Chi-restraints excluded: chain b residue 145 LYS Chi-restraints excluded: chain b residue 146 LEU Chi-restraints excluded: chain b residue 156 MET Chi-restraints excluded: chain b residue 165 VAL Chi-restraints excluded: chain b residue 189 VAL Chi-restraints excluded: chain c residue 16 LYS Chi-restraints excluded: chain c residue 56 LEU Chi-restraints excluded: chain c residue 67 THR Chi-restraints excluded: chain c residue 68 ILE Chi-restraints excluded: chain c residue 72 ARG Chi-restraints excluded: chain c residue 88 GLN Chi-restraints excluded: chain c residue 92 THR Chi-restraints excluded: chain c residue 103 ILE Chi-restraints excluded: chain c residue 152 GLU Chi-restraints excluded: chain c residue 173 VAL Chi-restraints excluded: chain d residue 17 THR Chi-restraints excluded: chain d residue 63 VAL Chi-restraints excluded: chain d residue 111 SER Chi-restraints excluded: chain d residue 162 GLU Chi-restraints excluded: chain d residue 185 LYS Chi-restraints excluded: chain d residue 193 LEU Chi-restraints excluded: chain e residue 14 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 23 VAL Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain e residue 63 LEU Chi-restraints excluded: chain e residue 158 LYS Chi-restraints excluded: chain f residue 58 HIS Chi-restraints excluded: chain f residue 70 THR Chi-restraints excluded: chain g residue 25 LYS Chi-restraints excluded: chain g residue 56 VAL Chi-restraints excluded: chain g residue 72 MET Chi-restraints excluded: chain g residue 104 LEU Chi-restraints excluded: chain g residue 123 GLU Chi-restraints excluded: chain h residue 19 MET Chi-restraints excluded: chain h residue 24 THR Chi-restraints excluded: chain h residue 47 SER Chi-restraints excluded: chain h residue 53 GLN Chi-restraints excluded: chain h residue 74 GLU Chi-restraints excluded: chain h residue 86 GLN Chi-restraints excluded: chain h residue 90 LYS Chi-restraints excluded: chain h residue 122 ILE Chi-restraints excluded: chain i residue 125 PHE Chi-restraints excluded: chain j residue 36 VAL Chi-restraints excluded: chain j residue 57 VAL Chi-restraints excluded: chain j residue 60 ASP Chi-restraints excluded: chain j residue 75 ASP Chi-restraints excluded: chain j residue 78 GLN Chi-restraints excluded: chain k residue 29 THR Chi-restraints excluded: chain k residue 34 THR Chi-restraints excluded: chain k residue 107 ASN Chi-restraints excluded: chain l residue 98 VAL Chi-restraints excluded: chain l residue 111 ASN Chi-restraints excluded: chain l residue 115 SER Chi-restraints excluded: chain l residue 116 LYS Chi-restraints excluded: chain m residue 63 VAL Chi-restraints excluded: chain m residue 74 SER Chi-restraints excluded: chain m residue 89 LEU Chi-restraints excluded: chain m residue 104 THR Chi-restraints excluded: chain n residue 80 SER Chi-restraints excluded: chain o residue 73 LYS Chi-restraints excluded: chain o residue 87 LEU Chi-restraints excluded: chain p residue 38 VAL Chi-restraints excluded: chain p residue 60 THR Chi-restraints excluded: chain p residue 70 LEU Chi-restraints excluded: chain q residue 12 LYS Chi-restraints excluded: chain q residue 15 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 24 VAL Chi-restraints excluded: chain q residue 25 LEU Chi-restraints excluded: chain q residue 42 SER Chi-restraints excluded: chain q residue 80 VAL Chi-restraints excluded: chain s residue 4 SER Chi-restraints excluded: chain s residue 35 SER Chi-restraints excluded: chain s residue 50 SER Chi-restraints excluded: chain s residue 81 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 960 random chunks: chunk 604 optimal weight: 2.9990 chunk 811 optimal weight: 20.0000 chunk 233 optimal weight: 8.9990 chunk 702 optimal weight: 1.9990 chunk 112 optimal weight: 5.9990 chunk 211 optimal weight: 6.9990 chunk 762 optimal weight: 0.1980 chunk 319 optimal weight: 9.9990 chunk 783 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 140 optimal weight: 6.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 1 6 GLN C 23 HIS C 163 GLN E 105 GLN G 143 GLN J 110 GLN O 9 GLN O 13 ASN O 78 GLN P 56 GLN P 71 GLN P 101 HIS Q 86 GLN R 37 ASN S 58 ASN V 12 ASN Y 48 ASN ** c 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 216 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 138 GLN e 120 HIS e 137 ASN ** f 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 21 GLN h 42 GLN j 20 GLN l 29 GLN m 12 ASN m 52 GLN o 40 GLN q 31 GLN s 56 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.176956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.159496 restraints weight = 152587.645| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 0.60 r_work: 0.3647 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 147527 Z= 0.445 Angle : 0.942 24.631 220639 Z= 0.465 Chirality : 0.053 2.213 28172 Planarity : 0.008 0.142 11889 Dihedral : 23.258 179.707 73461 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.91 % Favored : 96.93 % Rotamer: Outliers : 4.65 % Allowed : 27.51 % Favored : 67.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.73 % Cis-general : 0.00 % Twisted Proline : 0.58 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.11), residues: 5401 helix: 1.18 (0.12), residues: 1848 sheet: 0.27 (0.15), residues: 1028 loop : -0.78 (0.11), residues: 2525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP s 34 HIS 0.013 0.002 HIS c 18 PHE 0.043 0.003 PHE s 10 TYR 0.038 0.003 TYR h 87 ARG 0.016 0.001 ARG i 111 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46601.73 seconds wall clock time: 805 minutes 44.12 seconds (48344.12 seconds total)