Starting phenix.real_space_refine on Thu Mar 21 05:13:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nwy_3713/03_2024/5nwy_3713.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nwy_3713/03_2024/5nwy_3713.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nwy_3713/03_2024/5nwy_3713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nwy_3713/03_2024/5nwy_3713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nwy_3713/03_2024/5nwy_3713.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5nwy_3713/03_2024/5nwy_3713.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4634 5.49 5 S 152 5.16 5 C 72377 2.51 5 N 26859 2.21 5 O 40120 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "s ARG 125": "NH1" <-> "NH2" Residue "s ARG 139": "NH1" <-> "NH2" Residue "P ARG 52": "NH1" <-> "NH2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 133": "NH1" <-> "NH2" Residue "P ARG 167": "NH1" <-> "NH2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "P ARG 182": "NH1" <-> "NH2" Residue "P ARG 189": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P ARG 212": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 59": "NH1" <-> "NH2" Residue "Q ARG 77": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 169": "NH1" <-> "NH2" Residue "Q ARG 184": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 44": "NH1" <-> "NH2" Residue "R ARG 49": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R ARG 162": "NH1" <-> "NH2" Residue "R ARG 170": "NH1" <-> "NH2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "S ARG 80": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 102": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "S ARG 112": "NH1" <-> "NH2" Residue "S ARG 115": "NH1" <-> "NH2" Residue "S ARG 133": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 153": "NH1" <-> "NH2" Residue "T ARG 163": "NH1" <-> "NH2" Residue "T ARG 170": "NH1" <-> "NH2" Residue "U ARG 27": "NH1" <-> "NH2" Residue "U PHE 47": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 13": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 96": "NH1" <-> "NH2" Residue "W ARG 120": "NH1" <-> "NH2" Residue "Y ARG 21": "NH1" <-> "NH2" Residue "Y ARG 33": "NH1" <-> "NH2" Residue "Y ARG 41": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 60": "NH1" <-> "NH2" Residue "Y ARG 78": "NH1" <-> "NH2" Residue "Y ARG 126": "NH1" <-> "NH2" Residue "Z ARG 10": "NH1" <-> "NH2" Residue "Z ARG 18": "NH1" <-> "NH2" Residue "Z ARG 40": "NH1" <-> "NH2" Residue "Z ARG 44": "NH1" <-> "NH2" Residue "Z ARG 50": "NH1" <-> "NH2" Residue "Z ARG 55": "NH1" <-> "NH2" Residue "Z ARG 59": "NH1" <-> "NH2" Residue "Z TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 114": "NH1" <-> "NH2" Residue "Z PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 8": "NH1" <-> "NH2" Residue "a ARG 12": "NH1" <-> "NH2" Residue "a ARG 17": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "a ARG 46": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "a ARG 64": "NH1" <-> "NH2" Residue "a ARG 69": "NH1" <-> "NH2" Residue "a ARG 71": "NH1" <-> "NH2" Residue "a ARG 96": "NH1" <-> "NH2" Residue "a PHE 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 118": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ARG 81": "NH1" <-> "NH2" Residue "b ARG 94": "NH1" <-> "NH2" Residue "b ARG 102": "NH1" <-> "NH2" Residue "b ARG 111": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c ARG 62": "NH1" <-> "NH2" Residue "c ARG 89": "NH1" <-> "NH2" Residue "c TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 101": "NH1" <-> "NH2" Residue "c ARG 109": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 6": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 48": "NH1" <-> "NH2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "e TYR 2": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 21": "NH1" <-> "NH2" Residue "e ARG 68": "NH1" <-> "NH2" Residue "e ARG 78": "NH1" <-> "NH2" Residue "e ARG 79": "NH1" <-> "NH2" Residue "e ARG 84": "NH1" <-> "NH2" Residue "e PHE 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f PHE 75": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f ARG 84": "NH1" <-> "NH2" Residue "f ARG 88": "NH1" <-> "NH2" Residue "f ARG 92": "NH1" <-> "NH2" Residue "f ARG 110": "NH1" <-> "NH2" Residue "g ARG 73": "NH1" <-> "NH2" Residue "h ARG 6": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 82": "NH1" <-> "NH2" Residue "h ARG 86": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "i TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ARG 11": "NH1" <-> "NH2" Residue "k ARG 18": "NH1" <-> "NH2" Residue "k PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 37": "NH1" <-> "NH2" Residue "k ARG 50": "NH1" <-> "NH2" Residue "k ARG 57": "NH1" <-> "NH2" Residue "k ARG 74": "NH1" <-> "NH2" Residue "l ARG 29": "NH1" <-> "NH2" Residue "l ARG 47": "NH1" <-> "NH2" Residue "l ARG 52": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 30": "NH1" <-> "NH2" Residue "m ARG 45": "NH1" <-> "NH2" Residue "m PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 10": "NH1" <-> "NH2" Residue "n ARG 16": "NH1" <-> "NH2" Residue "n ARG 52": "NH1" <-> "NH2" Residue "o ARG 44": "NH1" <-> "NH2" Residue "p ARG 3": "NH1" <-> "NH2" Residue "p ARG 12": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 19": "NH1" <-> "NH2" Residue "p ARG 21": "NH1" <-> "NH2" Residue "p ARG 33": "NH1" <-> "NH2" Residue "p ARG 41": "NH1" <-> "NH2" Residue "q ARG 13": "NH1" <-> "NH2" Residue "q ARG 30": "NH1" <-> "NH2" Residue "q ARG 40": "NH1" <-> "NH2" Residue "q ARG 42": "NH1" <-> "NH2" Residue "r ARG 24": "NH1" <-> "NH2" Residue "L ARG 49": "NH1" <-> "NH2" Residue "L ARG 56": "NH1" <-> "NH2" Residue "1 PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 131": "NH1" <-> "NH2" Residue "5 TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 124": "NH1" <-> "NH2" Residue "A PHE 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 56": "NH1" <-> "NH2" Residue "C TYR 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 144142 Number of models: 1 Model: "" Number of chains: 56 Chain: "s" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 316 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Chain: "M" Number of atoms: 1594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1594 Classifications: {'RNA': 75} Modifications used: {'p5*END': 1, 'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 32, 'rna3p_pyr': 36} Link IDs: {'rna2p': 6, 'rna3p': 68} Chain: "O" Number of atoms: 2529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 2529 Classifications: {'RNA': 118} Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 4, 'rna3p_pur': 62, 'rna3p_pyr': 50} Link IDs: {'rna2p': 6, 'rna3p': 111} Chain: "P" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "Q" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1564 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "R" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "S" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "T" Number of atoms: 1322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1322 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "U" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 359 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 2, 'TRANS': 44} Chain: "V" Number of atoms: 1031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1031 Classifications: {'peptide': 141} Link IDs: {'PTRANS': 9, 'TRANS': 131} Chain: "W" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1128 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "X" Number of atoms: 938 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 938 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "Y" Number of atoms: 1044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 1044 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 4, 'TRANS': 138} Chain: "Z" Number of atoms: 1073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1073 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "a" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 960 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "b" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 891 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "c" Number of atoms: 915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 915 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 946 Classifications: {'peptide': 117} Link IDs: {'TRANS': 116} Chain: "e" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 815 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "f" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "g" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 738 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "h" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 779 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "i" Number of atoms: 752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 752 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "j" Number of atoms: 568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 568 Classifications: {'peptide': 75} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "k" Number of atoms: 624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 624 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "l" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 508 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "m" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "n" Number of atoms: 443 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 443 Classifications: {'peptide': 56} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 53} Chain: "o" Number of atoms: 409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 409 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "p" Number of atoms: 376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 376 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "q" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 503 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "r" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 301 Classifications: {'peptide': 38} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "N" Number of atoms: 62215 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 214, 'rna2p_pyr': 120, 'rna3p_pur': 1458, 'rna3p_pyr': 1105} Link IDs: {'rna2p': 334, 'rna3p': 2562} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 214, 'rna2p_pyr': 119, 'rna3p_pur': 1458, 'rna3p_pyr': 1106} Link IDs: {'rna2p': 333, 'rna3p': 2563} Chain breaks: 1 bond proxies already assigned to first conformer: 69636 Chain: "L" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "0" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 87, 'rna2p_pyr': 60, 'rna3p_pur': 787, 'rna3p_pyr': 605} Link IDs: {'rna2p': 147, 'rna3p': 1391} Chain: "1" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 208} Chain: "2" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "3" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "4" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "5" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "6" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "7" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "8" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "9" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "C" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "D" Number of atoms: 773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 773 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 4, 'TRANS': 91} Chain breaks: 1 Chain: "E" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 709 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 87} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 648 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "G" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "H" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 455 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "I" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 5, 'TRANS': 73} Chain: "J" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "K" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "t" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 1, 'rna3p_pyr': 2} Link IDs: {'rna3p': 3} Time building chain proxies: 77.94, per 1000 atoms: 0.54 Number of scatterers: 144142 At special positions: 0 Unit cell: (266.664, 278.588, 222.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 152 16.00 P 4634 15.00 O 40120 8.00 N 26859 7.00 C 72377 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS r 11 " - pdb=" SG CYS r 14 " distance=2.17 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: 55.52 Conformation dependent library (CDL) restraints added in 6.7 seconds 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10502 Finding SS restraints... Secondary structure from input PDB file: 175 helices and 74 sheets defined 34.0% alpha, 17.9% beta 1615 base pairs and 2583 stacking pairs defined. Time for finding SS restraints: 54.53 Creating SS restraints... Processing helix chain 's' and resid 120 through 127 Processing helix chain 's' and resid 139 through 143 Processing helix chain 's' and resid 147 through 156 Processing helix chain 'P' and resid 30 through 32 No H-bonds generated for 'chain 'P' and resid 30 through 32' Processing helix chain 'P' and resid 197 through 203 removed outlier: 3.616A pdb=" N ARG P 203 " --> pdb=" O HIS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.998A pdb=" N ALA P 211 " --> pdb=" O LYS P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 225 Processing helix chain 'Q' and resid 61 through 72 Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 120 through 125 Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 24 through 39 Processing helix chain 'R' and resid 97 through 115 Processing helix chain 'R' and resid 130 through 141 Processing helix chain 'R' and resid 154 through 161 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.560A pdb=" N LEU R 180 " --> pdb=" O ASP R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 200 Processing helix chain 'S' and resid 3 through 20 removed outlier: 5.074A pdb=" N VAL S 13 " --> pdb=" O LYS S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.762A pdb=" N ILE S 44 " --> pdb=" O GLY S 41 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA S 45 " --> pdb=" O GLU S 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 41 through 45' Processing helix chain 'S' and resid 47 through 61 Processing helix chain 'S' and resid 93 through 106 removed outlier: 3.642A pdb=" N TRP S 97 " --> pdb=" O GLY S 93 " (cutoff:3.500A) Processing helix chain 'S' and resid 142 through 146 removed outlier: 3.903A pdb=" N VAL S 146 " --> pdb=" O TYR S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 162 through 172 Processing helix chain 'T' and resid 60 through 81 Processing helix chain 'T' and resid 137 through 152 removed outlier: 4.303A pdb=" N ARG T 152 " --> pdb=" O LEU T 148 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 29 Processing helix chain 'U' and resid 43 through 47 removed outlier: 3.618A pdb=" N PHE U 46 " --> pdb=" O ASN U 43 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N PHE U 47 " --> pdb=" O ILE U 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 43 through 47' Processing helix chain 'V' and resid 24 through 29 Processing helix chain 'V' and resid 35 through 39 removed outlier: 3.677A pdb=" N PHE V 38 " --> pdb=" O ILE V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 45 Processing helix chain 'V' and resid 103 through 113 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.950A pdb=" N ILE V 129 " --> pdb=" O MET V 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 24 through 38 Processing helix chain 'W' and resid 58 through 62 removed outlier: 3.747A pdb=" N VAL W 62 " --> pdb=" O ALA W 59 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 72 removed outlier: 3.543A pdb=" N LYS W 72 " --> pdb=" O LYS W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 89 through 96 Processing helix chain 'W' and resid 97 through 109 Processing helix chain 'W' and resid 112 through 120 Processing helix chain 'X' and resid 104 through 108 removed outlier: 3.506A pdb=" N ARG X 108 " --> pdb=" O ARG X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 118 removed outlier: 3.560A pdb=" N LEU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 61 removed outlier: 3.703A pdb=" N LEU Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 138 Processing helix chain 'Z' and resid 43 through 57 Processing helix chain 'Z' and resid 109 through 121 Processing helix chain 'a' and resid 13 through 32 Processing helix chain 'a' and resid 38 through 56 removed outlier: 4.300A pdb=" N ARG a 46 " --> pdb=" O LYS a 42 " (cutoff:3.500A) Proline residue: a 50 - end of helix Processing helix chain 'a' and resid 59 through 69 removed outlier: 3.597A pdb=" N ARG a 69 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 82 removed outlier: 4.880A pdb=" N PHE a 80 " --> pdb=" O VAL a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 88 Processing helix chain 'b' and resid 3 through 22 removed outlier: 4.992A pdb=" N ARG b 13 " --> pdb=" O ARG b 9 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ALA b 14 " --> pdb=" O ARG b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 60 Processing helix chain 'b' and resid 67 through 85 Processing helix chain 'b' and resid 101 through 113 Processing helix chain 'c' and resid 3 through 10 Processing helix chain 'c' and resid 53 through 56 removed outlier: 3.514A pdb=" N HIS c 56 " --> pdb=" O ARG c 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 53 through 56' Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.525A pdb=" N ARG c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 20 removed outlier: 3.562A pdb=" N ALA d 10 " --> pdb=" O ARG d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 30 Processing helix chain 'd' and resid 31 through 72 removed outlier: 4.482A pdb=" N GLN d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS d 54 " --> pdb=" O ARG d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 86 Processing helix chain 'd' and resid 91 through 102 Processing helix chain 'd' and resid 102 through 118 Processing helix chain 'f' and resid 13 through 25 removed outlier: 4.466A pdb=" N VAL f 20 " --> pdb=" O LYS f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 38 removed outlier: 3.983A pdb=" N TYR f 38 " --> pdb=" O ASP f 34 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 62 removed outlier: 3.642A pdb=" N LEU f 46 " --> pdb=" O LYS f 42 " (cutoff:3.500A) Processing helix chain 'f' and resid 65 through 69 Processing helix chain 'f' and resid 89 through 91 No H-bonds generated for 'chain 'f' and resid 89 through 91' Processing helix chain 'g' and resid 3 through 10 removed outlier: 3.934A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL g 10 " --> pdb=" O ARG g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 28 removed outlier: 3.643A pdb=" N ASN g 28 " --> pdb=" O MET g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 51 Processing helix chain 'i' and resid 13 through 23 removed outlier: 3.619A pdb=" N ALA i 23 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 52 Processing helix chain 'k' and resid 54 through 63 Processing helix chain 'k' and resid 63 through 74 Processing helix chain 'l' and resid 9 through 23 Processing helix chain 'l' and resid 24 through 33 Processing helix chain 'l' and resid 40 through 61 removed outlier: 4.159A pdb=" N LYS l 44 " --> pdb=" O SER l 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 17 through 28 Processing helix chain 'm' and resid 41 through 51 Processing helix chain 'n' and resid 10 through 17 Processing helix chain 'n' and resid 18 through 20 No H-bonds generated for 'chain 'n' and resid 18 through 20' Processing helix chain 'p' and resid 8 through 17 Processing helix chain 'p' and resid 17 through 22 Processing helix chain 'p' and resid 24 through 38 Processing helix chain 'q' and resid 7 through 12 removed outlier: 3.640A pdb=" N LYS q 12 " --> pdb=" O ARG q 8 " (cutoff:3.500A) Processing helix chain 'q' and resid 37 through 45 Processing helix chain 'q' and resid 54 through 62 Processing helix chain 'r' and resid 30 through 33 Processing helix chain 'L' and resid 43 through 52 Processing helix chain 'L' and resid 56 through 64 Processing helix chain '1' and resid 24 through 31 Proline residue: 1 29 - end of helix Processing helix chain '1' and resid 34 through 38 removed outlier: 4.413A pdb=" N LYS 1 37 " --> pdb=" O ALA 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 62 Proline residue: 1 48 - end of helix Processing helix chain '1' and resid 78 through 87 Processing helix chain '1' and resid 103 through 123 removed outlier: 3.829A pdb=" N VAL 1 107 " --> pdb=" O ASN 1 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ASP 1 123 " --> pdb=" O THR 1 119 " (cutoff:3.500A) Processing helix chain '1' and resid 131 through 148 Processing helix chain '1' and resid 149 through 154 removed outlier: 3.737A pdb=" N LYS 1 152 " --> pdb=" O GLY 1 149 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ASP 1 153 " --> pdb=" O GLY 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 169 through 180 Processing helix chain '1' and resid 206 through 222 removed outlier: 3.628A pdb=" N ARG 1 222 " --> pdb=" O ALA 1 218 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 12 removed outlier: 3.711A pdb=" N LEU 2 12 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 46 Processing helix chain '2' and resid 72 through 78 removed outlier: 3.595A pdb=" N VAL 2 76 " --> pdb=" O ARG 2 72 " (cutoff:3.500A) Processing helix chain '2' and resid 81 through 96 Processing helix chain '2' and resid 108 through 111 Processing helix chain '2' and resid 112 through 125 Processing helix chain '2' and resid 129 through 144 removed outlier: 4.028A pdb=" N LEU 2 144 " --> pdb=" O ASN 2 140 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 15 removed outlier: 3.987A pdb=" N LEU 3 11 " --> pdb=" O PRO 3 7 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU 3 15 " --> pdb=" O LEU 3 11 " (cutoff:3.500A) Processing helix chain '3' and resid 49 through 66 Processing helix chain '3' and resid 68 through 82 Processing helix chain '3' and resid 85 through 96 Processing helix chain '3' and resid 97 through 105 Processing helix chain '3' and resid 110 through 120 Processing helix chain '3' and resid 152 through 161 removed outlier: 3.711A pdb=" N LYS 3 156 " --> pdb=" O GLN 3 152 " (cutoff:3.500A) Processing helix chain '3' and resid 187 through 191 Processing helix chain '3' and resid 196 through 205 removed outlier: 3.896A pdb=" N ILE 3 200 " --> pdb=" O ASN 3 196 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 69 removed outlier: 4.040A pdb=" N ARG 4 69 " --> pdb=" O GLU 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 118 Processing helix chain '4' and resid 132 through 137 removed outlier: 3.815A pdb=" N VAL 4 137 " --> pdb=" O PRO 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 145 Processing helix chain '4' and resid 149 through 157 removed outlier: 3.536A pdb=" N ALA 4 155 " --> pdb=" O GLU 4 151 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 16 removed outlier: 5.361A pdb=" N GLU 5 16 " --> pdb=" O ASP 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 31 Processing helix chain '5' and resid 67 through 81 removed outlier: 3.645A pdb=" N ILE 5 71 " --> pdb=" O PRO 5 67 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 31 Processing helix chain '6' and resid 35 through 55 removed outlier: 3.666A pdb=" N ALA 6 39 " --> pdb=" O LYS 6 35 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 68 Processing helix chain '6' and resid 92 through 111 Processing helix chain '6' and resid 115 through 129 removed outlier: 3.803A pdb=" N GLU 6 129 " --> pdb=" O SER 6 125 " (cutoff:3.500A) Processing helix chain '6' and resid 133 through 148 Processing helix chain '7' and resid 5 through 19 Processing helix chain '7' and resid 30 through 43 Processing helix chain '7' and resid 95 through 99 Processing helix chain '7' and resid 112 through 119 Processing helix chain '8' and resid 34 through 39 removed outlier: 3.618A pdb=" N PHE 8 39 " --> pdb=" O LEU 8 35 " (cutoff:3.500A) Processing helix chain '8' and resid 45 through 53 removed outlier: 3.678A pdb=" N VAL 8 48 " --> pdb=" O ARG 8 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN 8 50 " --> pdb=" O VAL 8 47 " (cutoff:3.500A) Proline residue: 8 51 - end of helix Processing helix chain '8' and resid 72 through 86 Processing helix chain '8' and resid 93 through 101 removed outlier: 4.092A pdb=" N GLU 8 97 " --> pdb=" O SER 8 93 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ARG 8 99 " --> pdb=" O ARG 8 95 " (cutoff:3.500A) Processing helix chain '9' and resid 14 through 33 Processing helix chain '9' and resid 80 through 86 Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.642A pdb=" N GLY A 78 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.850A pdb=" N CYS B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.527A pdb=" N LYS B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 19 Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 49 through 61 Processing helix chain 'C' and resid 65 through 84 Processing helix chain 'C' and resid 85 through 94 removed outlier: 3.585A pdb=" N GLY C 94 " --> pdb=" O ARG C 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 20 removed outlier: 3.713A pdb=" N LYS D 7 " --> pdb=" O LYS D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 31 removed outlier: 4.343A pdb=" N LYS D 28 " --> pdb=" O ARG D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 43 through 48 Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.948A pdb=" N GLN D 60 " --> pdb=" O PRO D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 91 Processing helix chain 'E' and resid 4 through 16 Processing helix chain 'E' and resid 24 through 45 removed outlier: 4.090A pdb=" N GLU E 45 " --> pdb=" O GLY E 41 " (cutoff:3.500A) Processing helix chain 'E' and resid 51 through 72 Processing helix chain 'E' and resid 74 through 86 Processing helix chain 'F' and resid 53 through 64 Processing helix chain 'F' and resid 68 through 76 Processing helix chain 'G' and resid 49 through 52 removed outlier: 4.552A pdb=" N GLU G 52 " --> pdb=" O GLU G 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 49 through 52' Processing helix chain 'H' and resid 25 through 32 Processing helix chain 'H' and resid 41 through 46 Processing helix chain 'H' and resid 48 through 65 Processing helix chain 'I' and resid 12 through 25 Processing helix chain 'I' and resid 41 through 45 removed outlier: 3.575A pdb=" N ILE I 45 " --> pdb=" O PRO I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 removed outlier: 3.956A pdb=" N VAL I 67 " --> pdb=" O ASP I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 71 through 75 Processing helix chain 'J' and resid 6 through 39 removed outlier: 3.653A pdb=" N ARG J 10 " --> pdb=" O SER J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 43 through 65 removed outlier: 3.710A pdb=" N ALA J 47 " --> pdb=" O ASP J 43 " (cutoff:3.500A) Proline residue: J 56 - end of helix removed outlier: 3.517A pdb=" N GLY J 65 " --> pdb=" O GLN J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 69 through 87 Processing helix chain 'K' and resid 27 through 32 removed outlier: 3.771A pdb=" N VAL K 32 " --> pdb=" O VAL K 28 " (cutoff:3.500A) Processing helix chain 'K' and resid 39 through 52 Processing sheet with id=AA1, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'P' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'P' and resid 101 through 105 removed outlier: 6.203A pdb=" N LEU P 95 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL P 78 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 129 through 131 removed outlier: 6.196A pdb=" N THR P 173 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET P 181 " --> pdb=" O VAL P 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 144 through 145 removed outlier: 5.979A pdb=" N VAL P 144 " --> pdb=" O GLN P 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 6.565A pdb=" N VAL Q 109 " --> pdb=" O GLN Q 173 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN Q 173 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLY Q 111 " --> pdb=" O THR Q 171 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR Q 171 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 8 through 15 removed outlier: 5.804A pdb=" N LYS Q 8 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLU Q 28 " --> pdb=" O LYS Q 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY Q 10 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU Q 186 " --> pdb=" O VAL Q 180 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 186 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N LEU Q 188 " --> pdb=" O VAL Q 178 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'Q' and resid 79 through 83 removed outlier: 6.595A pdb=" N ALA Q 47 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL Q 37 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN Q 49 " --> pdb=" O THR Q 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 117 through 119 Processing sheet with id=AB1, first strand: chain 'R' and resid 2 through 4 Processing sheet with id=AB2, first strand: chain 'R' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'S' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'T' and resid 16 through 20 Processing sheet with id=AB5, first strand: chain 'T' and resid 41 through 44 Processing sheet with id=AB6, first strand: chain 'T' and resid 122 through 124 Processing sheet with id=AB7, first strand: chain 'T' and resid 95 through 99 Processing sheet with id=AB8, first strand: chain 'U' and resid 3 through 5 Processing sheet with id=AB9, first strand: chain 'V' and resid 99 through 102 removed outlier: 6.727A pdb=" N GLY V 99 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU V 141 " --> pdb=" O GLY V 99 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ILE V 101 " --> pdb=" O GLU V 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'W' and resid 122 through 124 removed outlier: 6.425A pdb=" N ILE W 54 " --> pdb=" O LYS W 123 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR W 16 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N LEU W 57 " --> pdb=" O TYR W 16 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N VAL W 18 " --> pdb=" O LEU W 57 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'W' and resid 73 through 77 Processing sheet with id=AC3, first strand: chain 'X' and resid 7 through 10 removed outlier: 3.993A pdb=" N VAL X 10 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG X 17 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA X 16 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ALA X 46 " --> pdb=" O ALA X 16 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ARG X 18 " --> pdb=" O LYS X 44 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS X 40 " --> pdb=" O ILE X 22 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL X 24 " --> pdb=" O ILE X 38 " (cutoff:3.500A) removed outlier: 8.082A pdb=" N ILE X 38 " --> pdb=" O VAL X 24 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL X 62 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N VAL X 85 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS X 84 " --> pdb=" O MET X 7 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ASN X 9 " --> pdb=" O CYS X 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'X' and resid 69 through 70 removed outlier: 3.570A pdb=" N VAL X 76 " --> pdb=" O VAL c 73 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA c 58 " --> pdb=" O ILE c 50 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N ILE c 50 " --> pdb=" O ALA c 58 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR c 60 " --> pdb=" O ILE c 48 " (cutoff:3.500A) removed outlier: 5.624A pdb=" N ILE c 64 " --> pdb=" O GLU c 44 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLU c 44 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU c 27 " --> pdb=" O VAL c 86 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N VAL c 86 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS c 29 " --> pdb=" O ILE c 84 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N ILE c 84 " --> pdb=" O LYS c 29 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N TRP c 31 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N ASP c 82 " --> pdb=" O TRP c 31 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'Y' and resid 89 through 90 removed outlier: 5.825A pdb=" N VAL Y 90 " --> pdb=" O ARG Y 123 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 62 through 65 removed outlier: 6.460A pdb=" N LEU Z 33 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU Z 104 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N PHE Z 31 " --> pdb=" O GLU Z 104 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Z' and resid 40 through 42 removed outlier: 5.498A pdb=" N VAL Z 89 " --> pdb=" O GLU Z 75 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N GLU Z 75 " --> pdb=" O VAL Z 89 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR Z 91 " --> pdb=" O ILE Z 73 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'a' and resid 33 through 37 removed outlier: 5.888A pdb=" N MET a 110 " --> pdb=" O CYS a 100 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'b' and resid 47 through 52 removed outlier: 6.595A pdb=" N VAL b 39 " --> pdb=" O LEU b 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA b 50 " --> pdb=" O ALA b 37 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA b 37 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER b 52 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ILE b 35 " --> pdb=" O SER b 52 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'c' and resid 90 through 91 removed outlier: 4.216A pdb=" N LYS c 111 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 11 through 14 removed outlier: 6.711A pdb=" N TYR e 2 " --> pdb=" O ILE e 41 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE e 41 " --> pdb=" O TYR e 2 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL e 4 " --> pdb=" O LEU e 39 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'e' and resid 19 through 23 removed outlier: 6.670A pdb=" N PHE e 93 " --> pdb=" O HIS e 66 " (cutoff:3.500A) removed outlier: 4.781A pdb=" N HIS e 66 " --> pdb=" O PHE e 93 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP e 95 " --> pdb=" O VAL e 64 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LYS e 60 " --> pdb=" O THR e 99 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE e 101 " --> pdb=" O VAL e 58 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL e 58 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 72 through 78 removed outlier: 4.300A pdb=" N TYR e 83 " --> pdb=" O ARG e 78 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 3 through 10 removed outlier: 5.734A pdb=" N SER f 101 " --> pdb=" O HIS f 9 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N HIS f 102 " --> pdb=" O VAL f 76 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N VAL f 76 " --> pdb=" O HIS f 102 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N THR f 104 " --> pdb=" O ILE f 74 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ILE f 74 " --> pdb=" O THR f 104 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL f 106 " --> pdb=" O THR f 72 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 82 through 87 Processing sheet with id=AD7, first strand: chain 'g' and resid 11 through 14 removed outlier: 6.689A pdb=" N LYS g 33 " --> pdb=" O ARG g 12 " (cutoff:3.500A) removed outlier: 7.812A pdb=" N VAL g 31 " --> pdb=" O PRO g 14 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS g 81 " --> pdb=" O VAL g 34 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'g' and resid 67 through 70 Processing sheet with id=AD9, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AE1, first strand: chain 'h' and resid 41 through 45 Processing sheet with id=AE2, first strand: chain 'h' and resid 83 through 88 Processing sheet with id=AE3, first strand: chain 'i' and resid 3 through 8 removed outlier: 7.798A pdb=" N ASN i 5 " --> pdb=" O ASP i 43 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N ASP i 43 " --> pdb=" O ASN i 5 " (cutoff:3.500A) removed outlier: 8.931A pdb=" N LYS i 25 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 9.663A pdb=" N ILE i 89 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N PHE i 91 " --> pdb=" O PRO i 27 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N ILE i 29 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 7.240A pdb=" N ARG i 93 " --> pdb=" O ILE i 29 " (cutoff:3.500A) removed outlier: 7.805A pdb=" N TYR i 31 " --> pdb=" O ARG i 93 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N GLN i 78 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N ILE i 89 " --> pdb=" O ASP i 76 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP i 76 " --> pdb=" O ILE i 89 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE i 91 " --> pdb=" O ALA i 74 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA i 74 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG i 93 " --> pdb=" O VAL i 72 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL i 72 " --> pdb=" O ARG i 93 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 22 through 23 removed outlier: 6.798A pdb=" N LEU j 59 " --> pdb=" O ILE j 37 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'j' and resid 30 through 31 Processing sheet with id=AE6, first strand: chain 'k' and resid 13 through 17 Processing sheet with id=AE7, first strand: chain 'k' and resid 34 through 40 Processing sheet with id=AE8, first strand: chain 'm' and resid 36 through 38 Processing sheet with id=AE9, first strand: chain 'n' and resid 29 through 30 Processing sheet with id=AF1, first strand: chain 'n' and resid 48 through 49 Processing sheet with id=AF2, first strand: chain 'o' and resid 20 through 25 Processing sheet with id=AF3, first strand: chain 'q' and resid 14 through 16 Processing sheet with id=AF4, first strand: chain 'r' and resid 2 through 3 removed outlier: 6.530A pdb=" N LYS r 2 " --> pdb=" O ARG r 36 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N GLY r 38 " --> pdb=" O LYS r 2 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE r 23 " --> pdb=" O GLN r 37 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 21 through 25 removed outlier: 9.296A pdb=" N LEU L 32 " --> pdb=" O GLU L 11 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N THR L 13 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain '1' and resid 91 through 92 removed outlier: 6.640A pdb=" N PHE 1 69 " --> pdb=" O VAL 1 92 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU 1 161 " --> pdb=" O PHE 1 184 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE 1 186 " --> pdb=" O LEU 1 161 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N VAL 1 163 " --> pdb=" O ILE 1 186 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL 1 183 " --> pdb=" O PHE 1 198 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N ILE 1 200 " --> pdb=" O VAL 1 183 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA 1 185 " --> pdb=" O ILE 1 200 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain '2' and resid 52 through 56 removed outlier: 6.732A pdb=" N HIS 2 69 " --> pdb=" O SER 2 53 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 2 55 " --> pdb=" O THR 2 67 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR 2 67 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain '2' and resid 167 through 171 Processing sheet with id=AF9, first strand: chain '3' and resid 128 through 129 Processing sheet with id=AG1, first strand: chain '4' and resid 13 through 15 Processing sheet with id=AG2, first strand: chain '4' and resid 19 through 22 Processing sheet with id=AG3, first strand: chain '4' and resid 85 through 89 Processing sheet with id=AG4, first strand: chain '5' and resid 40 through 45 removed outlier: 5.325A pdb=" N ASP 5 41 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU 5 61 " --> pdb=" O ASP 5 41 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY 5 43 " --> pdb=" O TYR 5 59 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '5' and resid 40 through 45 removed outlier: 5.325A pdb=" N ASP 5 41 " --> pdb=" O LEU 5 61 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N LEU 5 61 " --> pdb=" O ASP 5 41 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY 5 43 " --> pdb=" O TYR 5 59 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N ARG 5 86 " --> pdb=" O MET 5 9 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '6' and resid 73 through 77 Processing sheet with id=AG7, first strand: chain '7' and resid 24 through 28 removed outlier: 6.221A pdb=" N GLU 7 58 " --> pdb=" O VAL 7 51 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL 7 51 " --> pdb=" O GLU 7 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU 7 60 " --> pdb=" O PHE 7 49 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N PHE 7 49 " --> pdb=" O GLU 7 60 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N THR 7 62 " --> pdb=" O GLU 7 47 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain '7' and resid 75 through 77 Processing sheet with id=AG9, first strand: chain '7' and resid 75 through 77 removed outlier: 6.559A pdb=" N VAL 7 103 " --> pdb=" O ILE 7 126 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain '8' and resid 6 through 8 removed outlier: 5.992A pdb=" N VAL 8 29 " --> pdb=" O ILE 8 65 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL 8 67 " --> pdb=" O VAL 8 29 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '9' and resid 45 through 52 Processing sheet with id=AH3, first strand: chain '9' and resid 45 through 52 Processing sheet with id=AH4, first strand: chain 'A' and resid 41 through 46 removed outlier: 6.717A pdb=" N ALA A 41 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP A 36 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 82 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ASN A 109 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 30 through 32 Processing sheet with id=AH6, first strand: chain 'B' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR B 95 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'D' and resid 73 through 74 removed outlier: 3.566A pdb=" N LEU D 79 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'F' and resid 34 through 35 Processing sheet with id=AH9, first strand: chain 'F' and resid 37 through 39 removed outlier: 3.730A pdb=" N ARG F 51 " --> pdb=" O PHE F 38 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 8 through 14 removed outlier: 7.815A pdb=" N GLN G 9 " --> pdb=" O GLU G 26 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU G 26 " --> pdb=" O GLN G 9 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL G 22 " --> pdb=" O VAL G 13 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP G 73 " --> pdb=" O HIS G 45 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU G 60 " --> pdb=" O VAL G 76 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N VAL G 78 " --> pdb=" O VAL G 58 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL G 58 " --> pdb=" O VAL G 78 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 31 through 33 1791 hydrogen bonds defined for protein. 4977 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4062 hydrogen bonds 6346 hydrogen bond angles 0 basepair planarities 1615 basepair parallelities 2583 stacking parallelities Total time for adding SS restraints: 216.24 Time building geometry restraints manager: 60.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.25: 9848 1.25 - 1.41: 56396 1.41 - 1.57: 82330 1.57 - 1.73: 7838 1.73 - 1.90: 272 Bond restraints: 156684 Sorted by residual: bond pdb=" P G N2502 " pdb=" OP2 G N2502 " ideal model delta sigma weight residual 1.485 1.769 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" P A N1156 " pdb=" OP2 A N1156 " ideal model delta sigma weight residual 1.485 1.744 -0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" P G N1333 " pdb=" OP2 G N1333 " ideal model delta sigma weight residual 1.485 1.704 -0.219 2.00e-02 2.50e+03 1.20e+02 bond pdb=" P A N 783 " pdb=" OP2 A N 783 " ideal model delta sigma weight residual 1.485 1.701 -0.216 2.00e-02 2.50e+03 1.16e+02 bond pdb=" C ALA 4 127 " pdb=" O ALA 4 127 " ideal model delta sigma weight residual 1.234 1.105 0.129 1.22e-02 6.72e+03 1.11e+02 ... (remaining 156679 not shown) Histogram of bond angle deviations from ideal: 80.72 - 93.22: 9 93.22 - 105.71: 27438 105.71 - 118.20: 123042 118.20 - 130.69: 82378 130.69 - 143.18: 1611 Bond angle restraints: 234478 Sorted by residual: angle pdb=" O3' C M 73 " pdb=" P C M 74 " pdb=" O5' C M 74 " ideal model delta sigma weight residual 104.00 131.32 -27.32 1.50e+00 4.44e-01 3.32e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" O5' C N2507 " ideal model delta sigma weight residual 104.00 80.72 23.28 1.50e+00 4.44e-01 2.41e+02 angle pdb=" C THR Q 151 " pdb=" N PRO Q 152 " pdb=" CA PRO Q 152 " ideal model delta sigma weight residual 119.47 134.30 -14.83 1.16e+00 7.43e-01 1.64e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" OP1 C N2507 " ideal model delta sigma weight residual 108.00 142.94 -34.94 3.00e+00 1.11e-01 1.36e+02 angle pdb=" C4' A N1936 " pdb=" C3' A N1936 " pdb=" O3' A N1936 " ideal model delta sigma weight residual 113.00 96.35 16.65 1.50e+00 4.44e-01 1.23e+02 ... (remaining 234473 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.86: 88803 35.86 - 71.72: 10612 71.72 - 107.58: 924 107.58 - 143.44: 21 143.44 - 179.30: 35 Dihedral angle restraints: 100395 sinusoidal: 84114 harmonic: 16281 Sorted by residual: dihedral pdb=" CA THR Q 151 " pdb=" C THR Q 151 " pdb=" N PRO Q 152 " pdb=" CA PRO Q 152 " ideal model delta harmonic sigma weight residual -180.00 -48.27 -131.73 0 5.00e+00 4.00e-02 6.94e+02 dihedral pdb=" CA ASN 5 52 " pdb=" C ASN 5 52 " pdb=" N LYS 5 53 " pdb=" CA LYS 5 53 " ideal model delta harmonic sigma weight residual 180.00 -115.03 -64.97 0 5.00e+00 4.00e-02 1.69e+02 dihedral pdb=" CA LYS A 125 " pdb=" C LYS A 125 " pdb=" N LYS A 126 " pdb=" CA LYS A 126 " ideal model delta harmonic sigma weight residual -180.00 -115.41 -64.59 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 100392 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 28451 0.216 - 0.432: 1417 0.432 - 0.648: 92 0.648 - 0.864: 11 0.864 - 1.080: 5 Chirality restraints: 29976 Sorted by residual: chirality pdb=" CA ARG j 41 " pdb=" N ARG j 41 " pdb=" C ARG j 41 " pdb=" CB ARG j 41 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.92e+01 chirality pdb=" CA VAL P 204 " pdb=" N VAL P 204 " pdb=" C VAL P 204 " pdb=" CB VAL P 204 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" C3' G 01347 " pdb=" C4' G 01347 " pdb=" O3' G 01347 " pdb=" C2' G 01347 " both_signs ideal model delta sigma weight residual False -2.74 -1.86 -0.88 2.00e-01 2.50e+01 1.95e+01 ... (remaining 29973 not shown) Planarity restraints: 12458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A N2765 " -0.012 2.00e-02 2.50e+03 8.70e-02 2.08e+02 pdb=" N9 A N2765 " 0.010 2.00e-02 2.50e+03 pdb=" C8 A N2765 " -0.062 2.00e-02 2.50e+03 pdb=" N7 A N2765 " -0.045 2.00e-02 2.50e+03 pdb=" C5 A N2765 " 0.058 2.00e-02 2.50e+03 pdb=" C6 A N2765 " 0.083 2.00e-02 2.50e+03 pdb=" N6 A N2765 " 0.070 2.00e-02 2.50e+03 pdb=" N1 A N2765 " -0.236 2.00e-02 2.50e+03 pdb=" C2 A N2765 " 0.025 2.00e-02 2.50e+03 pdb=" N3 A N2765 " 0.057 2.00e-02 2.50e+03 pdb=" C4 A N2765 " 0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A N1802 " -0.112 2.00e-02 2.50e+03 7.17e-02 1.41e+02 pdb=" N9 A N1802 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A N1802 " -0.039 2.00e-02 2.50e+03 pdb=" N7 A N1802 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A N1802 " 0.068 2.00e-02 2.50e+03 pdb=" C6 A N1802 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A N1802 " -0.024 2.00e-02 2.50e+03 pdb=" N1 A N1802 " -0.080 2.00e-02 2.50e+03 pdb=" C2 A N1802 " -0.061 2.00e-02 2.50e+03 pdb=" N3 A N1802 " 0.092 2.00e-02 2.50e+03 pdb=" C4 A N1802 " 0.134 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U N2522 " 0.020 2.00e-02 2.50e+03 7.71e-02 1.34e+02 pdb=" N1 U N2522 " -0.045 2.00e-02 2.50e+03 pdb=" C2 U N2522 " -0.038 2.00e-02 2.50e+03 pdb=" O2 U N2522 " -0.055 2.00e-02 2.50e+03 pdb=" N3 U N2522 " 0.188 2.00e-02 2.50e+03 pdb=" C4 U N2522 " -0.024 2.00e-02 2.50e+03 pdb=" O4 U N2522 " -0.092 2.00e-02 2.50e+03 pdb=" C5 U N2522 " 0.048 2.00e-02 2.50e+03 pdb=" C6 U N2522 " -0.002 2.00e-02 2.50e+03 ... (remaining 12455 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 7 2.07 - 2.78: 29344 2.78 - 3.49: 179035 3.49 - 4.19: 493496 4.19 - 4.90: 641453 Nonbonded interactions: 1343335 Sorted by model distance: nonbonded pdb=" C GLN s 156 " pdb=" O3' A M 75 " model vdw 1.364 3.270 nonbonded pdb=" N1 A M 75 " pdb=" O2' A N2450 " model vdw 1.742 2.520 nonbonded pdb=" N3 U N 306 " pdb=" N6 A N 310 " model vdw 1.856 2.560 nonbonded pdb=" N6 A 01238 " pdb=" N3 U 01301 " model vdw 2.008 2.560 nonbonded pdb=" OE2 GLU 4 101 " pdb=" OG1 THR 4 103 " model vdw 2.046 2.440 ... (remaining 1343330 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: 2.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.110 Extract box with map and model: 15.770 Check model and map are aligned: 1.560 Set scattering table: 0.990 Process input model: 506.280 Find NCS groups from input model: 2.770 Set up NCS constraints: 0.380 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:8.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 538.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 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 : 0.016 0.284 156684 Z= 0.987 Angle : 1.632 34.936 234478 Z= 0.969 Chirality : 0.112 1.080 29976 Planarity : 0.015 0.113 12458 Dihedral : 22.930 179.305 89890 Min Nonbonded Distance : 1.364 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 1.00 % Allowed : 8.71 % Favored : 90.29 % Rotamer: Outliers : 1.45 % Allowed : 4.83 % Favored : 93.72 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.04 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.03 (0.09), residues: 5614 helix: -2.80 (0.09), residues: 1787 sheet: -2.39 (0.14), residues: 1023 loop : -2.66 (0.10), residues: 2804 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.079 0.012 TRP P 213 HIS 0.068 0.008 HIS f 7 PHE 0.067 0.011 PHE 4 48 TYR 0.088 0.012 TYR Z 91 ARG 0.060 0.005 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1521 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1453 time to evaluate : 6.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 139 ARG cc_start: 0.8094 (mtt180) cc_final: 0.7688 (mpt-90) REVERT: P 4 VAL cc_start: 0.9074 (t) cc_final: 0.8827 (m) REVERT: P 5 LYS cc_start: 0.8876 (mttt) cc_final: 0.8640 (tttt) REVERT: P 110 LEU cc_start: 0.9071 (tt) cc_final: 0.8755 (tp) REVERT: P 125 LYS cc_start: 0.8968 (ptmt) cc_final: 0.8711 (ptpt) REVERT: P 133 ARG cc_start: 0.8838 (ptt-90) cc_final: 0.8612 (ptm160) REVERT: P 185 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8444 (mt-10) REVERT: P 199 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8625 (pm20) REVERT: P 270 ARG cc_start: 0.8822 (mmm160) cc_final: 0.7627 (ttp-170) REVERT: Q 11 MET cc_start: 0.9153 (mtp) cc_final: 0.8839 (mtp) REVERT: Q 89 GLU cc_start: 0.8863 (tp30) cc_final: 0.8323 (tm-30) REVERT: Q 184 ARG cc_start: 0.8928 (mtt180) cc_final: 0.8718 (mtt180) REVERT: R 2 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8027 (tp30) REVERT: R 3 LEU cc_start: 0.8918 (mt) cc_final: 0.8684 (mp) REVERT: R 69 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.7363 (ptt90) REVERT: R 122 GLU cc_start: 0.9132 (tp30) cc_final: 0.8743 (pt0) REVERT: R 144 GLU cc_start: 0.9147 (tt0) cc_final: 0.8785 (mm-30) REVERT: R 149 ILE cc_start: 0.8638 (OUTLIER) cc_final: 0.8434 (mt) REVERT: R 155 GLU cc_start: 0.8695 (tp30) cc_final: 0.8304 (tm-30) REVERT: R 173 THR cc_start: 0.9243 (m) cc_final: 0.9037 (p) REVERT: R 184 ASP cc_start: 0.8976 (m-30) cc_final: 0.8727 (m-30) REVERT: S 10 ASP cc_start: 0.8375 (p0) cc_final: 0.8127 (p0) REVERT: S 11 GLU cc_start: 0.9056 (mt-10) cc_final: 0.8736 (mt-10) REVERT: S 56 ASP cc_start: 0.8755 (m-30) cc_final: 0.8193 (m-30) REVERT: S 77 PHE cc_start: 0.8969 (m-80) cc_final: 0.8768 (m-80) REVERT: S 78 LYS cc_start: 0.9248 (mttt) cc_final: 0.9046 (mttm) REVERT: S 113 ASP cc_start: 0.8309 (m-30) cc_final: 0.8055 (t0) REVERT: S 130 MET cc_start: 0.8978 (ptm) cc_final: 0.8731 (ptp) REVERT: S 142 ASP cc_start: 0.7898 (t0) cc_final: 0.7493 (t70) REVERT: S 143 TYR cc_start: 0.8221 (t80) cc_final: 0.7997 (t80) REVERT: S 145 LYS cc_start: 0.9207 (mmtp) cc_final: 0.8823 (mmtp) REVERT: S 149 VAL cc_start: 0.8905 (m) cc_final: 0.8634 (t) REVERT: T 27 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7865 (mtpp) REVERT: T 106 SER cc_start: 0.9200 (m) cc_final: 0.8914 (t) REVERT: U 1 MET cc_start: 0.7594 (tpp) cc_final: 0.7377 (tpt) REVERT: U 27 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.8089 (ptp90) REVERT: V 117 MET cc_start: 0.2343 (mmm) cc_final: 0.1905 (mmm) REVERT: V 136 MET cc_start: 0.2683 (mtm) cc_final: 0.1579 (mtp) REVERT: W 1 MET cc_start: 0.8282 (ptp) cc_final: 0.7881 (pp-130) REVERT: W 2 LYS cc_start: 0.9033 (mttt) cc_final: 0.8826 (mtpp) REVERT: W 96 ARG cc_start: 0.8299 (ttt-90) cc_final: 0.8056 (ptm160) REVERT: W 106 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8683 (tttt) REVERT: W 108 MET cc_start: 0.9095 (mtt) cc_final: 0.8643 (mtt) REVERT: W 111 LYS cc_start: 0.8488 (pttt) cc_final: 0.8130 (mmtm) REVERT: W 129 GLU cc_start: 0.9230 (pm20) cc_final: 0.9015 (mp0) REVERT: X 20 MET cc_start: 0.9303 (ttp) cc_final: 0.9092 (ttm) REVERT: X 49 ARG cc_start: 0.8688 (ptp90) cc_final: 0.8449 (ptp90) REVERT: X 53 LYS cc_start: 0.8933 (pttp) cc_final: 0.8598 (mmtp) REVERT: X 98 ARG cc_start: 0.8345 (mmt-90) cc_final: 0.7807 (mtm180) REVERT: X 106 GLU cc_start: 0.8788 (mp0) cc_final: 0.8373 (mp0) REVERT: Y 70 LYS cc_start: 0.8479 (ttmt) cc_final: 0.8165 (ttmm) REVERT: Y 78 ARG cc_start: 0.8620 (mtp-110) cc_final: 0.8404 (mtm180) REVERT: Y 106 GLU cc_start: 0.9140 (mt-10) cc_final: 0.8879 (tt0) REVERT: Y 141 LYS cc_start: 0.8749 (tptp) cc_final: 0.8464 (tptm) REVERT: Z 6 ARG cc_start: 0.9110 (ttt-90) cc_final: 0.8731 (ttp-170) REVERT: Z 18 ARG cc_start: 0.8904 (mtp-110) cc_final: 0.8657 (mtp180) REVERT: Z 55 ARG cc_start: 0.8640 (tpp80) cc_final: 0.8374 (ttm110) REVERT: Z 73 ILE cc_start: 0.9425 (mm) cc_final: 0.9201 (mp) REVERT: Z 119 LEU cc_start: 0.9252 (mt) cc_final: 0.9030 (mt) REVERT: Z 127 LYS cc_start: 0.8669 (mtpp) cc_final: 0.8290 (tptt) REVERT: a 18 GLN cc_start: 0.9047 (tt0) cc_final: 0.8721 (tt0) REVERT: b 46 GLU cc_start: 0.8705 (tt0) cc_final: 0.8466 (mt-10) REVERT: b 56 LYS cc_start: 0.9094 (pttp) cc_final: 0.8697 (tppt) REVERT: b 78 VAL cc_start: 0.9000 (t) cc_final: 0.8777 (m) REVERT: c 13 MET cc_start: 0.9238 (mtp) cc_final: 0.9021 (mtm) REVERT: c 89 ARG cc_start: 0.8581 (ttm-80) cc_final: 0.8246 (mtp180) REVERT: d 11 ARG cc_start: 0.8331 (tpt170) cc_final: 0.7467 (ttm170) REVERT: d 15 LYS cc_start: 0.8964 (ttmm) cc_final: 0.8728 (ttpt) REVERT: d 78 LYS cc_start: 0.9202 (mtpp) cc_final: 0.8952 (mttt) REVERT: d 84 LYS cc_start: 0.8806 (ttpp) cc_final: 0.8432 (mttt) REVERT: d 85 LYS cc_start: 0.9022 (mttt) cc_final: 0.8791 (mttm) REVERT: d 102 ASP cc_start: 0.9241 (t0) cc_final: 0.8991 (t0) REVERT: e 14 VAL cc_start: 0.8985 (p) cc_final: 0.8725 (m) REVERT: e 16 GLU cc_start: 0.8807 (tt0) cc_final: 0.8429 (tm-30) REVERT: e 33 VAL cc_start: 0.8969 (m) cc_final: 0.8702 (p) REVERT: e 72 VAL cc_start: 0.8608 (p) cc_final: 0.8329 (m) REVERT: f 1 MET cc_start: 0.7957 (tpt) cc_final: 0.7607 (ttt) REVERT: f 73 LYS cc_start: 0.9105 (mttt) cc_final: 0.8779 (mttt) REVERT: f 86 MET cc_start: 0.8898 (tpt) cc_final: 0.8665 (tpt) REVERT: g 1 MET cc_start: 0.8796 (ptt) cc_final: 0.8567 (ptm) REVERT: g 49 LYS cc_start: 0.8924 (mttm) cc_final: 0.8493 (ttmm) REVERT: h 60 GLU cc_start: 0.8893 (tt0) cc_final: 0.8677 (tt0) REVERT: i 19 ARG cc_start: 0.9104 (mtm-85) cc_final: 0.8840 (mtm180) REVERT: i 43 ASP cc_start: 0.9050 (t0) cc_final: 0.8830 (t70) REVERT: i 50 MET cc_start: 0.8867 (ttm) cc_final: 0.8661 (ttm) REVERT: i 68 LYS cc_start: 0.8361 (mtmm) cc_final: 0.8047 (mptp) REVERT: i 83 LYS cc_start: 0.8781 (mttt) cc_final: 0.8538 (mttm) REVERT: k 43 GLU cc_start: 0.8449 (tt0) cc_final: 0.8138 (tt0) REVERT: k 56 MET cc_start: 0.9296 (mtp) cc_final: 0.9034 (mtt) REVERT: k 60 ASP cc_start: 0.8661 (m-30) cc_final: 0.8320 (m-30) REVERT: l 1 MET cc_start: 0.8200 (mtm) cc_final: 0.7494 (ptp) REVERT: l 30 MET cc_start: 0.9282 (mmm) cc_final: 0.8986 (mmm) REVERT: m 5 ILE cc_start: 0.8590 (tt) cc_final: 0.8313 (pt) REVERT: m 32 ILE cc_start: 0.8785 (pp) cc_final: 0.8509 (mt) REVERT: m 45 ARG cc_start: 0.9080 (mmt180) cc_final: 0.8876 (mmt180) REVERT: n 12 LYS cc_start: 0.8901 (tptt) cc_final: 0.8439 (mmtp) REVERT: n 15 MET cc_start: 0.8993 (mtt) cc_final: 0.8753 (mtp) REVERT: n 52 ARG cc_start: 0.8970 (ptp90) cc_final: 0.8653 (ptt90) REVERT: o 50 LYS cc_start: 0.9097 (mttt) cc_final: 0.8875 (mtmp) REVERT: p 25 LYS cc_start: 0.8669 (tptt) cc_final: 0.8140 (ttpp) REVERT: p 44 VAL cc_start: 0.8680 (p) cc_final: 0.8200 (m) REVERT: q 15 LYS cc_start: 0.8885 (tttm) cc_final: 0.8564 (mptp) REVERT: r 4 ARG cc_start: 0.8095 (mtp180) cc_final: 0.7765 (mtt90) REVERT: L 9 TYR cc_start: 0.8731 (t80) cc_final: 0.8441 (t80) REVERT: L 39 LYS cc_start: 0.9023 (mtmt) cc_final: 0.8732 (mtpt) REVERT: 1 9 MET cc_start: 0.6895 (mtt) cc_final: 0.6200 (pp-130) REVERT: 1 23 TRP cc_start: 0.8698 (p-90) cc_final: 0.8485 (p-90) REVERT: 1 27 MET cc_start: 0.9112 (mmp) cc_final: 0.8854 (mmm) REVERT: 1 52 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8802 (mp0) REVERT: 1 56 GLU cc_start: 0.8346 (mp0) cc_final: 0.8045 (mp0) REVERT: 1 78 GLU cc_start: 0.8420 (pt0) cc_final: 0.7950 (pp20) REVERT: 1 137 ARG cc_start: 0.7732 (ttm170) cc_final: 0.6167 (tmt170) REVERT: 1 145 GLU cc_start: 0.9017 (tp30) cc_final: 0.8774 (tp30) REVERT: 1 165 ASP cc_start: 0.8818 (t0) cc_final: 0.8440 (t70) REVERT: 1 169 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8452 (mp0) REVERT: 1 222 ARG cc_start: 0.8796 (ptt-90) cc_final: 0.8418 (ptt90) REVERT: 2 28 GLU cc_start: 0.8603 (pm20) cc_final: 0.8213 (pm20) REVERT: 2 105 GLU cc_start: 0.8910 (tt0) cc_final: 0.8574 (tt0) REVERT: 2 135 LYS cc_start: 0.8570 (tttt) cc_final: 0.8365 (ttmm) REVERT: 2 162 ILE cc_start: 0.8789 (pp) cc_final: 0.8567 (mt) REVERT: 2 169 ARG cc_start: 0.8299 (ptt90) cc_final: 0.7948 (ppt170) REVERT: 3 31 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8569 (pmtt) REVERT: 3 44 ARG cc_start: 0.8248 (mmt-90) cc_final: 0.7546 (mtp180) REVERT: 3 70 ARG cc_start: 0.8594 (ttm110) cc_final: 0.8314 (ttm110) REVERT: 3 73 ARG cc_start: 0.8849 (tpt170) cc_final: 0.8294 (ttp-110) REVERT: 3 128 ARG cc_start: 0.8336 (mtp180) cc_final: 0.7733 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8607 (mp0) REVERT: 3 156 LYS cc_start: 0.8669 (mttt) cc_final: 0.8331 (mtmm) REVERT: 3 166 GLU cc_start: 0.8704 (pt0) cc_final: 0.8481 (mm-30) REVERT: 3 172 GLU cc_start: 0.9137 (tp30) cc_final: 0.8573 (mm-30) REVERT: 3 177 LYS cc_start: 0.8480 (mtmt) cc_final: 0.7464 (tptt) REVERT: 3 179 GLU cc_start: 0.8843 (pt0) cc_final: 0.8544 (pp20) REVERT: 3 190 ASP cc_start: 0.8925 (m-30) cc_final: 0.8210 (m-30) REVERT: 4 46 VAL cc_start: 0.8629 (t) cc_final: 0.8310 (p) REVERT: 4 61 GLN cc_start: 0.9137 (tt0) cc_final: 0.8798 (mm110) REVERT: 4 69 ARG cc_start: 0.8791 (ptp90) cc_final: 0.8531 (ptt90) REVERT: 4 70 ASN cc_start: 0.8809 (m110) cc_final: 0.8597 (t0) REVERT: 4 78 ASN cc_start: 0.9056 (t0) cc_final: 0.8834 (t0) REVERT: 4 111 MET cc_start: 0.9195 (ttt) cc_final: 0.8867 (ttp) REVERT: 4 134 ILE cc_start: 0.8595 (mp) cc_final: 0.8319 (tp) REVERT: 4 141 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.8330 (mm) REVERT: 4 152 MET cc_start: 0.8945 (mmt) cc_final: 0.8699 (mtp) REVERT: 5 42 TRP cc_start: 0.8986 (m-10) cc_final: 0.8779 (m-10) REVERT: 5 63 ASN cc_start: 0.8875 (m110) cc_final: 0.8564 (m110) REVERT: 6 32 VAL cc_start: 0.8948 (p) cc_final: 0.8656 (m) REVERT: 6 33 ASP cc_start: 0.8776 (m-30) cc_final: 0.8545 (m-30) REVERT: 6 47 LEU cc_start: 0.8392 (mp) cc_final: 0.8054 (mt) REVERT: 6 48 GLU cc_start: 0.8328 (tt0) cc_final: 0.8110 (tm-30) REVERT: 6 74 GLU cc_start: 0.8051 (pt0) cc_final: 0.7410 (pm20) REVERT: 6 90 GLU cc_start: 0.8821 (mp0) cc_final: 0.8546 (pp20) REVERT: 6 92 ARG cc_start: 0.8028 (mmm160) cc_final: 0.7558 (mtp180) REVERT: 6 106 GLU cc_start: 0.8480 (tt0) cc_final: 0.8198 (pt0) REVERT: 6 110 LYS cc_start: 0.8807 (mmtm) cc_final: 0.8309 (mmpt) REVERT: 6 118 LEU cc_start: 0.8463 (mt) cc_final: 0.8018 (tp) REVERT: 6 122 ASN cc_start: 0.8608 (m-40) cc_final: 0.8072 (m110) REVERT: 6 136 LYS cc_start: 0.8812 (tttm) cc_final: 0.8534 (tppt) REVERT: 6 139 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8556 (mt-10) REVERT: 6 148 ASN cc_start: 0.9138 (m110) cc_final: 0.8752 (m-40) REVERT: 7 31 LYS cc_start: 0.8898 (mmmt) cc_final: 0.8533 (mtpp) REVERT: 7 50 LYS cc_start: 0.8850 (ttmm) cc_final: 0.8636 (ttpp) REVERT: 7 76 GLN cc_start: 0.8568 (mm110) cc_final: 0.8349 (tt0) REVERT: 7 108 LYS cc_start: 0.9289 (ttmm) cc_final: 0.9056 (mmmt) REVERT: 7 118 GLN cc_start: 0.8834 (tt0) cc_final: 0.8377 (mp10) REVERT: 8 22 LYS cc_start: 0.8184 (mtmt) cc_final: 0.7629 (mttp) REVERT: 8 61 LEU cc_start: 0.8630 (pp) cc_final: 0.8391 (mp) REVERT: 8 100 LYS cc_start: 0.8937 (ttpp) cc_final: 0.8443 (mmtm) REVERT: 8 119 ARG cc_start: 0.8662 (mtm110) cc_final: 0.8453 (mtm180) REVERT: 9 5 ARG cc_start: 0.7427 (tpt170) cc_final: 0.7224 (mmm160) REVERT: 9 7 ARG cc_start: 0.8042 (mtt-85) cc_final: 0.7302 (mpt-90) REVERT: 9 16 ARG cc_start: 0.8424 (mtm180) cc_final: 0.8155 (mtm-85) REVERT: 9 45 ARG cc_start: 0.7876 (tpp-160) cc_final: 0.6079 (tmm-80) REVERT: B 10 LYS cc_start: 0.8838 (ttpp) cc_final: 0.8629 (ptmt) REVERT: B 54 ARG cc_start: 0.8457 (ttp-170) cc_final: 0.7992 (ttm-80) REVERT: B 56 ARG cc_start: 0.8830 (tpp-160) cc_final: 0.8402 (ttm-80) REVERT: B 70 GLU cc_start: 0.8302 (mt-10) cc_final: 0.7764 (mp0) REVERT: B 89 ASP cc_start: 0.9077 (t70) cc_final: 0.8762 (t0) REVERT: C 63 PHE cc_start: 0.5988 (t80) cc_final: 0.5427 (t80) REVERT: C 89 LEU cc_start: 0.9004 (mt) cc_final: 0.8741 (mm) REVERT: D 41 ARG cc_start: 0.7161 (ptt90) cc_final: 0.6334 (ptm-80) REVERT: E 79 THR cc_start: 0.9263 (m) cc_final: 0.8998 (p) REVERT: F 79 ASN cc_start: 0.6007 (m-40) cc_final: 0.5646 (t0) REVERT: G 6 ARG cc_start: 0.8477 (mtp-110) cc_final: 0.7842 (mtt-85) REVERT: G 27 ARG cc_start: 0.8261 (ptt90) cc_final: 0.7980 (ptt90) REVERT: G 48 ASP cc_start: 0.8497 (p0) cc_final: 0.8126 (p0) REVERT: G 57 ASP cc_start: 0.9052 (m-30) cc_final: 0.8826 (m-30) REVERT: G 61 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8154 (pt) REVERT: H 42 SER cc_start: 0.9199 (p) cc_final: 0.8849 (t) REVERT: I 7 LYS cc_start: 0.7436 (mmtt) cc_final: 0.7057 (pmtt) REVERT: I 61 PHE cc_start: 0.8699 (t80) cc_final: 0.8442 (t80) REVERT: I 81 ARG cc_start: 0.7808 (tpp80) cc_final: 0.6622 (ppt170) REVERT: J 44 LYS cc_start: 0.8696 (mttt) cc_final: 0.8449 (tmtt) REVERT: K 34 ARG cc_start: 0.8126 (ttt-90) cc_final: 0.6658 (mmp80) outliers start: 68 outliers final: 20 residues processed: 1498 average time/residue: 2.3644 time to fit residues: 4885.9086 Evaluate side-chains 1145 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1120 time to evaluate : 6.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 218 PRO Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 149 ILE Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain U residue 27 ARG Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain q residue 2 PRO Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 123 VAL Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 125 ILE Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain H residue 25 ASP Chi-restraints excluded: chain I residue 58 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 852 optimal weight: 0.9980 chunk 764 optimal weight: 0.8980 chunk 424 optimal weight: 20.0000 chunk 261 optimal weight: 8.9990 chunk 515 optimal weight: 0.8980 chunk 408 optimal weight: 0.7980 chunk 790 optimal weight: 6.9990 chunk 306 optimal weight: 0.9990 chunk 480 optimal weight: 7.9990 chunk 588 optimal weight: 0.7980 chunk 916 optimal weight: 10.0000 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 126 HIS P 53 HIS P 86 ASN P 115 GLN P 134 ASN Q 32 ASN Q 49 GLN Q 150 GLN T 22 GLN T 88 GLN T 143 GLN U 11 ASN V 12 GLN V 43 ASN W 40 HIS W 80 HIS W 128 ASN X 29 HIS a 3 HIS a 18 GLN b 19 GLN b 29 HIS b 38 GLN d 20 GLN d 37 GLN d 44 GLN e 18 GLN f 15 GLN g 15 HIS h 66 GLN j 57 HIS l 27 ASN l 31 GLN n 6 ASN o 19 HIS ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN 2 19 ASN 2 190 HIS 3 164 GLN 4 77 ASN 4 89 HIS 4 132 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 11 HIS 5 46 GLN 6 68 ASN 8 32 GLN 8 110 GLN 9 56 HIS A 29 ASN C 8 ASN C 105 ASN D 4 GLN D 49 GLN E 40 GLN F 63 GLN G 31 HIS H 52 GLN J 21 ASN J 55 GLN J 61 GLN Total number of N/Q/H flips: 60 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 156684 Z= 0.146 Angle : 0.601 12.905 234478 Z= 0.317 Chirality : 0.036 0.343 29976 Planarity : 0.005 0.134 12458 Dihedral : 23.454 179.428 78668 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.34 % Favored : 92.43 % Rotamer: Outliers : 3.72 % Allowed : 15.95 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.04 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.10), residues: 5614 helix: -0.76 (0.11), residues: 1801 sheet: -1.87 (0.15), residues: 961 loop : -2.20 (0.10), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP P 213 HIS 0.004 0.001 HIS P 230 PHE 0.016 0.002 PHE I 74 TYR 0.018 0.002 TYR f 38 ARG 0.010 0.001 ARG 4 93 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 174 poor density : 1246 time to evaluate : 6.153 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: s 139 ARG cc_start: 0.7752 (mtt180) cc_final: 0.7386 (mpt-90) REVERT: P 5 LYS cc_start: 0.8812 (mttt) cc_final: 0.8582 (tppp) REVERT: P 110 LEU cc_start: 0.9061 (tt) cc_final: 0.8675 (tp) REVERT: P 133 ARG cc_start: 0.8914 (ptt-90) cc_final: 0.8685 (ptp-110) REVERT: P 147 LYS cc_start: 0.8875 (mtpp) cc_final: 0.8595 (mttm) REVERT: P 180 GLU cc_start: 0.8657 (tt0) cc_final: 0.8399 (tt0) REVERT: P 199 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8577 (pm20) REVERT: P 236 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7580 (mt-10) REVERT: P 270 ARG cc_start: 0.8698 (mmm160) cc_final: 0.7519 (ttp-110) REVERT: Q 89 GLU cc_start: 0.8737 (tp30) cc_final: 0.8209 (tm-30) REVERT: Q 199 SER cc_start: 0.8767 (OUTLIER) cc_final: 0.8521 (p) REVERT: R 2 GLU cc_start: 0.8240 (mm-30) cc_final: 0.8033 (tp30) REVERT: R 3 LEU cc_start: 0.9026 (mt) cc_final: 0.8796 (mp) REVERT: R 16 GLU cc_start: 0.8472 (tt0) cc_final: 0.8265 (tp30) REVERT: R 22 ASP cc_start: 0.8815 (OUTLIER) cc_final: 0.8370 (p0) REVERT: R 51 GLU cc_start: 0.9153 (mt-10) cc_final: 0.8937 (mt-10) REVERT: R 77 ILE cc_start: 0.8554 (pt) cc_final: 0.8342 (pt) REVERT: R 122 GLU cc_start: 0.9071 (tp30) cc_final: 0.8772 (tt0) REVERT: R 139 LYS cc_start: 0.9290 (tppp) cc_final: 0.9037 (ttpp) REVERT: R 144 GLU cc_start: 0.8980 (tt0) cc_final: 0.8726 (mm-30) REVERT: R 155 GLU cc_start: 0.8528 (tp30) cc_final: 0.8216 (tm-30) REVERT: R 171 ASP cc_start: 0.8925 (t70) cc_final: 0.8589 (m-30) REVERT: R 184 ASP cc_start: 0.8999 (m-30) cc_final: 0.8577 (t0) REVERT: S 11 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8760 (tp30) REVERT: S 56 ASP cc_start: 0.8695 (m-30) cc_final: 0.8068 (m-30) REVERT: S 78 LYS cc_start: 0.9262 (mttt) cc_final: 0.9016 (mttm) REVERT: S 113 ASP cc_start: 0.8161 (m-30) cc_final: 0.7947 (t0) REVERT: S 142 ASP cc_start: 0.7820 (t0) cc_final: 0.7534 (t70) REVERT: S 143 TYR cc_start: 0.8129 (t80) cc_final: 0.7763 (t80) REVERT: S 164 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: T 3 ARG cc_start: 0.8594 (mtm-85) cc_final: 0.7783 (ttm170) REVERT: T 106 SER cc_start: 0.9138 (m) cc_final: 0.8906 (t) REVERT: T 175 LYS cc_start: 0.7505 (ttmt) cc_final: 0.7080 (tttp) REVERT: U 25 TYR cc_start: 0.8972 (t80) cc_final: 0.8659 (t80) REVERT: U 35 LYS cc_start: 0.8756 (mttt) cc_final: 0.8409 (mtpp) REVERT: V 117 MET cc_start: 0.2699 (mmm) cc_final: 0.2419 (mmm) REVERT: V 136 MET cc_start: 0.2638 (mtm) cc_final: 0.1903 (mtp) REVERT: W 1 MET cc_start: 0.8353 (ptp) cc_final: 0.7941 (pp-130) REVERT: W 106 LYS cc_start: 0.8835 (ttmm) cc_final: 0.8462 (tttt) REVERT: W 111 LYS cc_start: 0.8268 (pttt) cc_final: 0.7962 (mmtm) REVERT: X 49 ARG cc_start: 0.8505 (ptp90) cc_final: 0.8214 (mtm-85) REVERT: X 53 LYS cc_start: 0.9018 (pttp) cc_final: 0.8570 (mmtp) REVERT: X 98 ARG cc_start: 0.8071 (mmt-90) cc_final: 0.7718 (mmm160) REVERT: X 106 GLU cc_start: 0.8591 (mp0) cc_final: 0.8259 (mp0) REVERT: X 121 GLU cc_start: 0.8418 (mt-10) cc_final: 0.7904 (mt-10) REVERT: Y 7 SER cc_start: 0.9238 (t) cc_final: 0.8976 (p) REVERT: Y 42 SER cc_start: 0.8796 (t) cc_final: 0.8585 (t) REVERT: Y 55 MET cc_start: 0.8511 (tpt) cc_final: 0.8252 (tpt) REVERT: Y 106 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8793 (tt0) REVERT: Y 111 ILE cc_start: 0.8279 (mp) cc_final: 0.7974 (pt) REVERT: Y 129 LYS cc_start: 0.8736 (tttp) cc_final: 0.8486 (mttt) REVERT: Y 136 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8473 (mm-30) REVERT: Z 1 MET cc_start: 0.8519 (mtm) cc_final: 0.8228 (mtm) REVERT: Z 6 ARG cc_start: 0.8940 (ttt-90) cc_final: 0.8331 (tmt170) REVERT: Z 30 SER cc_start: 0.9281 (t) cc_final: 0.9002 (p) REVERT: Z 55 ARG cc_start: 0.8498 (tpp80) cc_final: 0.8294 (ttp-170) REVERT: Z 70 ASP cc_start: 0.8812 (p0) cc_final: 0.8557 (p0) REVERT: Z 73 ILE cc_start: 0.9369 (mm) cc_final: 0.9092 (mp) REVERT: Z 91 TYR cc_start: 0.9207 (p90) cc_final: 0.8928 (p90) REVERT: Z 118 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8709 (tttm) REVERT: Z 127 LYS cc_start: 0.8708 (mtpp) cc_final: 0.8310 (tptt) REVERT: b 45 SER cc_start: 0.9266 (t) cc_final: 0.8976 (m) REVERT: b 46 GLU cc_start: 0.8621 (tt0) cc_final: 0.8338 (mt-10) REVERT: c 10 GLN cc_start: 0.8775 (pt0) cc_final: 0.8392 (mt0) REVERT: d 11 ARG cc_start: 0.8313 (tpt170) cc_final: 0.7551 (ttm170) REVERT: d 78 LYS cc_start: 0.9152 (mtpp) cc_final: 0.8905 (mttt) REVERT: d 84 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8301 (mttt) REVERT: e 45 GLU cc_start: 0.8335 (pp20) cc_final: 0.7525 (pp20) REVERT: e 72 VAL cc_start: 0.8565 (p) cc_final: 0.8307 (m) REVERT: g 1 MET cc_start: 0.8650 (ptt) cc_final: 0.8425 (ptm) REVERT: h 79 LYS cc_start: 0.8765 (mttm) cc_final: 0.8309 (mtpp) REVERT: i 43 ASP cc_start: 0.8983 (t0) cc_final: 0.8782 (t70) REVERT: i 83 LYS cc_start: 0.8640 (mttt) cc_final: 0.8411 (mttm) REVERT: k 43 GLU cc_start: 0.8056 (tt0) cc_final: 0.7743 (tm-30) REVERT: l 1 MET cc_start: 0.8252 (mtm) cc_final: 0.7697 (ptp) REVERT: l 30 MET cc_start: 0.9189 (mmm) cc_final: 0.8818 (mmm) REVERT: l 31 GLN cc_start: 0.8453 (tt0) cc_final: 0.8171 (tt0) REVERT: m 5 ILE cc_start: 0.8304 (tt) cc_final: 0.8007 (pt) REVERT: n 12 LYS cc_start: 0.8788 (tptt) cc_final: 0.8363 (mmtt) REVERT: n 15 MET cc_start: 0.8868 (mtt) cc_final: 0.8588 (mtp) REVERT: o 35 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8533 (pt0) REVERT: o 50 LYS cc_start: 0.8677 (mttt) cc_final: 0.8464 (mtmp) REVERT: p 25 LYS cc_start: 0.8637 (tptt) cc_final: 0.8172 (ttpp) REVERT: p 28 ARG cc_start: 0.9057 (mtp180) cc_final: 0.8771 (mtt90) REVERT: r 15 LYS cc_start: 0.8708 (ttpp) cc_final: 0.8469 (tttp) REVERT: L 9 TYR cc_start: 0.8543 (t80) cc_final: 0.8337 (t80) REVERT: L 39 LYS cc_start: 0.8915 (mtmt) cc_final: 0.8673 (mtpt) REVERT: L 59 ARG cc_start: 0.7906 (ppp80) cc_final: 0.7614 (ptm160) REVERT: 1 9 MET cc_start: 0.6471 (mtt) cc_final: 0.6039 (pp-130) REVERT: 1 27 MET cc_start: 0.9066 (mmp) cc_final: 0.8800 (mmm) REVERT: 1 52 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8811 (mp0) REVERT: 1 56 GLU cc_start: 0.8306 (mp0) cc_final: 0.7987 (mp0) REVERT: 1 78 GLU cc_start: 0.8510 (pt0) cc_final: 0.7572 (tm-30) REVERT: 1 82 ASP cc_start: 0.9198 (t0) cc_final: 0.8957 (m-30) REVERT: 1 117 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8242 (tp) REVERT: 1 128 LYS cc_start: 0.7257 (mmmm) cc_final: 0.6713 (mppt) REVERT: 1 145 GLU cc_start: 0.8926 (tp30) cc_final: 0.8717 (tp30) REVERT: 1 165 ASP cc_start: 0.8777 (t0) cc_final: 0.8476 (t70) REVERT: 1 167 ASP cc_start: 0.8497 (p0) cc_final: 0.8168 (m-30) REVERT: 1 192 ASP cc_start: 0.8494 (t0) cc_final: 0.8079 (t0) REVERT: 2 28 GLU cc_start: 0.8571 (pm20) cc_final: 0.8220 (pm20) REVERT: 2 86 LYS cc_start: 0.8448 (ttpp) cc_final: 0.8086 (tptm) REVERT: 2 105 GLU cc_start: 0.8804 (tt0) cc_final: 0.8567 (tt0) REVERT: 2 106 VAL cc_start: 0.8999 (p) cc_final: 0.8706 (m) REVERT: 2 135 LYS cc_start: 0.8442 (tttt) cc_final: 0.8238 (mtpp) REVERT: 3 44 ARG cc_start: 0.8101 (mmt-90) cc_final: 0.7337 (mtp180) REVERT: 3 70 ARG cc_start: 0.8244 (ttm110) cc_final: 0.7779 (ttm-80) REVERT: 3 73 ARG cc_start: 0.8722 (tpt170) cc_final: 0.8250 (ttp-110) REVERT: 3 128 ARG cc_start: 0.8374 (mtp180) cc_final: 0.7760 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8530 (mp0) REVERT: 3 166 GLU cc_start: 0.8767 (pt0) cc_final: 0.8547 (mm-30) REVERT: 3 172 GLU cc_start: 0.9019 (tp30) cc_final: 0.8466 (mm-30) REVERT: 3 177 LYS cc_start: 0.8387 (mtmt) cc_final: 0.7416 (tptt) REVERT: 3 178 MET cc_start: 0.8844 (mtt) cc_final: 0.8578 (mtt) REVERT: 3 179 GLU cc_start: 0.8853 (pt0) cc_final: 0.8569 (pp20) REVERT: 4 61 GLN cc_start: 0.9169 (tt0) cc_final: 0.8814 (mm110) REVERT: 4 103 THR cc_start: 0.7762 (m) cc_final: 0.7478 (m) REVERT: 4 152 MET cc_start: 0.8869 (mmt) cc_final: 0.8611 (mtp) REVERT: 5 42 TRP cc_start: 0.8996 (m-10) cc_final: 0.8779 (m-10) REVERT: 5 45 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8706 (mtp85) REVERT: 5 79 ARG cc_start: 0.7957 (mmt-90) cc_final: 0.7378 (ttp-110) REVERT: 6 48 GLU cc_start: 0.8448 (tt0) cc_final: 0.8155 (tm-30) REVERT: 6 66 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8105 (tt) REVERT: 6 74 GLU cc_start: 0.8104 (pt0) cc_final: 0.7503 (pm20) REVERT: 6 90 GLU cc_start: 0.8763 (mp0) cc_final: 0.8455 (pp20) REVERT: 6 92 ARG cc_start: 0.8011 (mmm160) cc_final: 0.7553 (mtp180) REVERT: 6 136 LYS cc_start: 0.8860 (tttm) cc_final: 0.8512 (tppt) REVERT: 6 139 GLU cc_start: 0.8719 (mt-10) cc_final: 0.8384 (mt-10) REVERT: 7 31 LYS cc_start: 0.8845 (mmmt) cc_final: 0.8518 (mtpp) REVERT: 7 108 LYS cc_start: 0.9152 (ttmm) cc_final: 0.8932 (mmmt) REVERT: 7 118 GLN cc_start: 0.8703 (tt0) cc_final: 0.8275 (mp10) REVERT: 7 125 ILE cc_start: 0.8625 (tt) cc_final: 0.8307 (mt) REVERT: 8 18 ARG cc_start: 0.7559 (OUTLIER) cc_final: 0.7335 (mtm180) REVERT: 8 22 LYS cc_start: 0.8247 (mtmt) cc_final: 0.7681 (mtpp) REVERT: 8 32 GLN cc_start: 0.8885 (OUTLIER) cc_final: 0.8605 (mp10) REVERT: 8 61 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8100 (mp) REVERT: 9 7 ARG cc_start: 0.8068 (mtt-85) cc_final: 0.7404 (mpt-90) REVERT: 9 16 ARG cc_start: 0.8275 (mtm180) cc_final: 0.8029 (mtm-85) REVERT: A 127 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7886 (mmm160) REVERT: B 10 LYS cc_start: 0.8465 (ttpp) cc_final: 0.8235 (ptmt) REVERT: B 54 ARG cc_start: 0.7969 (ttp-170) cc_final: 0.7599 (ttm-80) REVERT: B 56 ARG cc_start: 0.8746 (tpp-160) cc_final: 0.8301 (ttm-80) REVERT: B 70 GLU cc_start: 0.8195 (mt-10) cc_final: 0.7695 (mp0) REVERT: B 108 LYS cc_start: 0.9014 (ttmm) cc_final: 0.8751 (tppt) REVERT: C 63 PHE cc_start: 0.5514 (t80) cc_final: 0.5160 (t80) REVERT: D 27 LEU cc_start: 0.7094 (mt) cc_final: 0.6873 (mp) REVERT: E 77 ARG cc_start: 0.8711 (mtp180) cc_final: 0.8483 (mtp180) REVERT: E 79 THR cc_start: 0.9268 (m) cc_final: 0.8987 (p) REVERT: G 27 ARG cc_start: 0.8042 (ptt90) cc_final: 0.7755 (ptt90) REVERT: H 42 SER cc_start: 0.8989 (p) cc_final: 0.8524 (t) REVERT: I 32 ARG cc_start: 0.8320 (mmm160) cc_final: 0.7624 (mtm180) REVERT: I 65 GLU cc_start: 0.7893 (pm20) cc_final: 0.7593 (pm20) REVERT: J 48 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8601 (mm-40) REVERT: K 34 ARG cc_start: 0.7536 (ttt-90) cc_final: 0.6250 (mmp80) outliers start: 174 outliers final: 45 residues processed: 1325 average time/residue: 2.3816 time to fit residues: 4501.3208 Evaluate side-chains 1146 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1092 time to evaluate : 6.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 164 GLU Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain e residue 43 ASN Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain 1 residue 110 SER Chi-restraints excluded: chain 1 residue 117 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 2 residue 51 SER Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 5 residue 14 GLN Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 66 LEU Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 8 residue 18 ARG Chi-restraints excluded: chain 8 residue 32 GLN Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 509 optimal weight: 10.0000 chunk 284 optimal weight: 0.0670 chunk 762 optimal weight: 10.0000 chunk 623 optimal weight: 10.0000 chunk 252 optimal weight: 0.4980 chunk 917 optimal weight: 1.9990 chunk 991 optimal weight: 30.0000 chunk 817 optimal weight: 3.9990 chunk 910 optimal weight: 10.0000 chunk 312 optimal weight: 9.9990 chunk 736 optimal weight: 10.0000 overall best weight: 3.3124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 115 GLN P 260 ASN Q 150 GLN R 115 GLN V 94 ASN W 128 ASN b 19 GLN c 7 GLN ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 66 GLN i 12 GLN i 49 ASN n 38 HIS L 41 HIS ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 164 GLN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 37 HIS 8 75 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN E 40 GLN E 46 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 156684 Z= 0.258 Angle : 0.604 12.121 234478 Z= 0.318 Chirality : 0.038 0.336 29976 Planarity : 0.005 0.105 12458 Dihedral : 23.339 179.469 78643 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.75 % Favored : 92.02 % Rotamer: Outliers : 4.62 % Allowed : 18.70 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.24 % 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: -1.91 (0.11), residues: 5614 helix: 0.01 (0.12), residues: 1810 sheet: -1.65 (0.15), residues: 1010 loop : -1.99 (0.11), residues: 2794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 213 HIS 0.007 0.001 HIS h 45 PHE 0.017 0.002 PHE 9 49 TYR 0.019 0.002 TYR 1 213 ARG 0.011 0.001 ARG G 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1311 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1095 time to evaluate : 6.140 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: P 5 LYS cc_start: 0.8931 (mttt) cc_final: 0.8726 (tttt) REVERT: P 110 LEU cc_start: 0.9083 (tt) cc_final: 0.8846 (tp) REVERT: P 125 LYS cc_start: 0.8758 (ptpp) cc_final: 0.8487 (ptpt) REVERT: P 147 LYS cc_start: 0.8856 (mtpp) cc_final: 0.8539 (mttm) REVERT: P 180 GLU cc_start: 0.8793 (tt0) cc_final: 0.8543 (tt0) REVERT: P 199 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8568 (pm20) REVERT: P 203 ARG cc_start: 0.8719 (OUTLIER) cc_final: 0.8128 (ptt180) REVERT: P 236 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7540 (mt-10) REVERT: P 239 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7989 (m110) REVERT: P 270 ARG cc_start: 0.8686 (mmm160) cc_final: 0.7449 (ttp-170) REVERT: Q 59 ARG cc_start: 0.8448 (OUTLIER) cc_final: 0.8245 (ttm-80) REVERT: Q 89 GLU cc_start: 0.8791 (tp30) cc_final: 0.8252 (tm-30) REVERT: Q 199 SER cc_start: 0.8718 (OUTLIER) cc_final: 0.8395 (p) REVERT: R 2 GLU cc_start: 0.8265 (mm-30) cc_final: 0.8063 (tp30) REVERT: R 3 LEU cc_start: 0.9043 (mt) cc_final: 0.8804 (mp) REVERT: R 22 ASP cc_start: 0.8848 (OUTLIER) cc_final: 0.8403 (p0) REVERT: R 77 ILE cc_start: 0.8670 (OUTLIER) cc_final: 0.8433 (pt) REVERT: R 122 GLU cc_start: 0.9164 (tp30) cc_final: 0.8797 (pt0) REVERT: R 139 LYS cc_start: 0.9284 (tppp) cc_final: 0.9048 (ttpp) REVERT: R 144 GLU cc_start: 0.8979 (tt0) cc_final: 0.8684 (mm-30) REVERT: R 155 GLU cc_start: 0.8456 (tp30) cc_final: 0.8158 (tm-30) REVERT: R 171 ASP cc_start: 0.8829 (t70) cc_final: 0.8521 (m-30) REVERT: R 184 ASP cc_start: 0.8975 (m-30) cc_final: 0.8602 (t0) REVERT: S 11 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8804 (tp30) REVERT: S 19 GLU cc_start: 0.8859 (tm-30) cc_final: 0.8623 (tm-30) REVERT: S 56 ASP cc_start: 0.8674 (m-30) cc_final: 0.8115 (m-30) REVERT: S 78 LYS cc_start: 0.9208 (mttt) cc_final: 0.8967 (mttm) REVERT: S 113 ASP cc_start: 0.8255 (m-30) cc_final: 0.7949 (t0) REVERT: S 142 ASP cc_start: 0.7973 (t0) cc_final: 0.7651 (t70) REVERT: S 143 TYR cc_start: 0.8102 (t80) cc_final: 0.7782 (t80) REVERT: T 3 ARG cc_start: 0.8609 (mtm-85) cc_final: 0.7986 (ttm170) REVERT: T 106 SER cc_start: 0.9168 (m) cc_final: 0.8927 (t) REVERT: T 175 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7200 (tttp) REVERT: U 35 LYS cc_start: 0.8781 (mttt) cc_final: 0.8442 (mtpp) REVERT: V 117 MET cc_start: 0.2578 (mmm) cc_final: 0.2270 (mmm) REVERT: V 136 MET cc_start: 0.2561 (mtm) cc_final: 0.1778 (mtp) REVERT: W 1 MET cc_start: 0.8338 (ptp) cc_final: 0.7869 (pp-130) REVERT: W 16 TYR cc_start: 0.9224 (m-80) cc_final: 0.8897 (m-80) REVERT: W 106 LYS cc_start: 0.9007 (ttmm) cc_final: 0.8641 (tttt) REVERT: W 111 LYS cc_start: 0.8279 (pttt) cc_final: 0.8005 (mmtm) REVERT: X 49 ARG cc_start: 0.8496 (ptp90) cc_final: 0.8127 (mtm-85) REVERT: X 53 LYS cc_start: 0.9020 (pttp) cc_final: 0.8560 (mmtp) REVERT: X 106 GLU cc_start: 0.8623 (mp0) cc_final: 0.8303 (mp0) REVERT: X 121 GLU cc_start: 0.8481 (mt-10) cc_final: 0.8013 (mt-10) REVERT: Y 7 SER cc_start: 0.9140 (OUTLIER) cc_final: 0.8908 (m) REVERT: Y 55 MET cc_start: 0.8529 (tpt) cc_final: 0.8270 (tpt) REVERT: Y 106 GLU cc_start: 0.9038 (mt-10) cc_final: 0.8814 (tt0) REVERT: Y 111 ILE cc_start: 0.8191 (mp) cc_final: 0.7864 (pt) REVERT: Y 129 LYS cc_start: 0.8808 (tttp) cc_final: 0.8567 (mttt) REVERT: Y 136 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8561 (mm-30) REVERT: Z 6 ARG cc_start: 0.8977 (ttt-90) cc_final: 0.8378 (tmt-80) REVERT: Z 30 SER cc_start: 0.9240 (t) cc_final: 0.9013 (p) REVERT: Z 55 ARG cc_start: 0.8403 (tpp80) cc_final: 0.8168 (ttp-110) REVERT: Z 118 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8701 (tttm) REVERT: Z 127 LYS cc_start: 0.8741 (mtpp) cc_final: 0.8306 (tptt) REVERT: b 45 SER cc_start: 0.9230 (t) cc_final: 0.8955 (m) REVERT: b 46 GLU cc_start: 0.8641 (tt0) cc_final: 0.8344 (mt-10) REVERT: b 56 LYS cc_start: 0.9086 (ptmm) cc_final: 0.8475 (tppt) REVERT: c 10 GLN cc_start: 0.8828 (pt0) cc_final: 0.8473 (mt0) REVERT: d 11 ARG cc_start: 0.8372 (tpt170) cc_final: 0.7585 (ttm170) REVERT: d 78 LYS cc_start: 0.9162 (mtpp) cc_final: 0.8956 (mttt) REVERT: d 84 LYS cc_start: 0.8599 (ttpp) cc_final: 0.8284 (mttt) REVERT: e 37 GLU cc_start: 0.8353 (mt-10) cc_final: 0.7886 (mm-30) REVERT: e 45 GLU cc_start: 0.8385 (pp20) cc_final: 0.7958 (pp20) REVERT: e 72 VAL cc_start: 0.8624 (p) cc_final: 0.8342 (m) REVERT: f 1 MET cc_start: 0.7967 (tpt) cc_final: 0.7613 (ttt) REVERT: g 1 MET cc_start: 0.8620 (ptt) cc_final: 0.8415 (ptm) REVERT: g 54 GLU cc_start: 0.8786 (mt-10) cc_final: 0.8196 (mp0) REVERT: h 45 HIS cc_start: 0.8437 (OUTLIER) cc_final: 0.6296 (p90) REVERT: h 79 LYS cc_start: 0.8825 (mttm) cc_final: 0.8386 (mtpp) REVERT: i 1 MET cc_start: 0.7299 (pmm) cc_final: 0.6876 (pmm) REVERT: i 43 ASP cc_start: 0.8920 (t0) cc_final: 0.8704 (t70) REVERT: i 59 GLU cc_start: 0.8881 (tt0) cc_final: 0.8595 (pt0) REVERT: j 29 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8732 (tp30) REVERT: k 43 GLU cc_start: 0.8108 (tt0) cc_final: 0.7742 (tm-30) REVERT: l 1 MET cc_start: 0.8230 (mtm) cc_final: 0.7697 (ptp) REVERT: l 30 MET cc_start: 0.9143 (mmm) cc_final: 0.8874 (mmm) REVERT: l 31 GLN cc_start: 0.8418 (tt0) cc_final: 0.8133 (tt0) REVERT: m 5 ILE cc_start: 0.8375 (tt) cc_final: 0.8090 (pt) REVERT: n 12 LYS cc_start: 0.8721 (tptt) cc_final: 0.8239 (mmtt) REVERT: n 15 MET cc_start: 0.8891 (mtt) cc_final: 0.8597 (mtp) REVERT: o 35 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8565 (pt0) REVERT: p 14 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8475 (mtt180) REVERT: p 25 LYS cc_start: 0.8666 (tptt) cc_final: 0.8170 (ttpp) REVERT: p 28 ARG cc_start: 0.9119 (mtp180) cc_final: 0.8815 (mtt90) REVERT: r 8 LYS cc_start: 0.8311 (mttt) cc_final: 0.8091 (mtmp) REVERT: L 39 LYS cc_start: 0.9118 (mtmt) cc_final: 0.8792 (mtpt) REVERT: L 59 ARG cc_start: 0.7864 (ppp80) cc_final: 0.7645 (ptm160) REVERT: 1 9 MET cc_start: 0.6479 (mtt) cc_final: 0.5955 (pp-130) REVERT: 1 27 MET cc_start: 0.9112 (mmp) cc_final: 0.8768 (mmm) REVERT: 1 56 GLU cc_start: 0.8399 (mp0) cc_final: 0.8186 (tp30) REVERT: 1 59 LYS cc_start: 0.9079 (tttp) cc_final: 0.8821 (ttpt) REVERT: 1 78 GLU cc_start: 0.8530 (pt0) cc_final: 0.7814 (pp20) REVERT: 1 128 LYS cc_start: 0.7239 (mmmm) cc_final: 0.6691 (mppt) REVERT: 1 145 GLU cc_start: 0.8911 (tp30) cc_final: 0.8707 (tp30) REVERT: 1 167 ASP cc_start: 0.8469 (p0) cc_final: 0.8063 (m-30) REVERT: 2 28 GLU cc_start: 0.8603 (pm20) cc_final: 0.8212 (pm20) REVERT: 2 86 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8096 (tptm) REVERT: 2 105 GLU cc_start: 0.8768 (tt0) cc_final: 0.8560 (tt0) REVERT: 2 106 VAL cc_start: 0.8952 (p) cc_final: 0.8696 (m) REVERT: 2 164 ARG cc_start: 0.8965 (OUTLIER) cc_final: 0.8756 (mtm110) REVERT: 3 44 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7472 (mtp180) REVERT: 3 70 ARG cc_start: 0.8343 (ttm110) cc_final: 0.7885 (ttm-80) REVERT: 3 73 ARG cc_start: 0.8725 (tpt170) cc_final: 0.8254 (ttp-110) REVERT: 3 128 ARG cc_start: 0.8303 (mtp180) cc_final: 0.7655 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8892 (mm-30) cc_final: 0.8522 (mp0) REVERT: 3 172 GLU cc_start: 0.9039 (tp30) cc_final: 0.8490 (mm-30) REVERT: 3 177 LYS cc_start: 0.8436 (mtmt) cc_final: 0.7443 (tptt) REVERT: 3 178 MET cc_start: 0.8824 (mtt) cc_final: 0.8509 (mtt) REVERT: 3 179 GLU cc_start: 0.8833 (pt0) cc_final: 0.8463 (pp20) REVERT: 4 12 GLN cc_start: 0.8784 (tp40) cc_final: 0.8392 (tt0) REVERT: 4 54 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8475 (tpp80) REVERT: 4 61 GLN cc_start: 0.9163 (tt0) cc_final: 0.8845 (mm110) REVERT: 4 122 ASN cc_start: 0.7651 (OUTLIER) cc_final: 0.7403 (m110) REVERT: 4 152 MET cc_start: 0.8973 (mmt) cc_final: 0.8733 (mtp) REVERT: 4 157 ARG cc_start: 0.9275 (OUTLIER) cc_final: 0.7440 (ptm-80) REVERT: 5 44 ARG cc_start: 0.8821 (mpt-90) cc_final: 0.8543 (mpt-90) REVERT: 5 79 ARG cc_start: 0.7994 (mmt-90) cc_final: 0.7420 (ttp-170) REVERT: 6 48 GLU cc_start: 0.8462 (tt0) cc_final: 0.8226 (tm-30) REVERT: 6 66 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.8109 (tt) REVERT: 6 74 GLU cc_start: 0.8113 (pt0) cc_final: 0.7543 (pm20) REVERT: 6 90 GLU cc_start: 0.8824 (mp0) cc_final: 0.8518 (pp20) REVERT: 6 92 ARG cc_start: 0.8177 (mmm160) cc_final: 0.7778 (mtp180) REVERT: 6 136 LYS cc_start: 0.8902 (tttm) cc_final: 0.8547 (tppt) REVERT: 6 144 MET cc_start: 0.8527 (tpp) cc_final: 0.8226 (tpp) REVERT: 7 31 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8532 (mtpm) REVERT: 7 118 GLN cc_start: 0.8750 (tt0) cc_final: 0.8296 (mp10) REVERT: 7 125 ILE cc_start: 0.8734 (OUTLIER) cc_final: 0.8497 (mt) REVERT: 8 22 LYS cc_start: 0.8212 (mtmt) cc_final: 0.7614 (mttt) REVERT: 8 61 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8135 (mp) REVERT: 8 120 LYS cc_start: 0.9081 (OUTLIER) cc_final: 0.8148 (ptmm) REVERT: 9 7 ARG cc_start: 0.8072 (mtt-85) cc_final: 0.7252 (mpt-90) REVERT: 9 11 LYS cc_start: 0.8610 (mtmt) cc_final: 0.8263 (mtmt) REVERT: 9 16 ARG cc_start: 0.8324 (mtm180) cc_final: 0.8091 (mtm-85) REVERT: A 127 ARG cc_start: 0.8207 (mmm160) cc_final: 0.7891 (mmm160) REVERT: B 10 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8326 (ptmt) REVERT: B 54 ARG cc_start: 0.8000 (ttp-170) cc_final: 0.7578 (ttm-80) REVERT: B 56 ARG cc_start: 0.8852 (tpp-160) cc_final: 0.8476 (ttp80) REVERT: B 70 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7639 (mp0) REVERT: C 31 LYS cc_start: 0.8675 (OUTLIER) cc_final: 0.8371 (mtmp) REVERT: C 63 PHE cc_start: 0.5520 (t80) cc_final: 0.5079 (t80) REVERT: C 113 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.5756 (ptp90) REVERT: D 27 LEU cc_start: 0.7284 (mt) cc_final: 0.7009 (mp) REVERT: E 77 ARG cc_start: 0.8726 (mtp180) cc_final: 0.8472 (mtp180) REVERT: F 18 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8786 (mt0) REVERT: F 77 GLU cc_start: 0.8853 (tt0) cc_final: 0.7990 (mp0) REVERT: G 6 ARG cc_start: 0.7989 (ttm110) cc_final: 0.6949 (mtt90) REVERT: G 15 ASP cc_start: 0.8368 (t70) cc_final: 0.7784 (p0) REVERT: G 65 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8361 (ptt180) REVERT: H 42 SER cc_start: 0.8975 (p) cc_final: 0.8529 (t) REVERT: I 32 ARG cc_start: 0.8308 (mmm160) cc_final: 0.7834 (mtm180) REVERT: J 33 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8213 (ttmt) REVERT: J 48 GLN cc_start: 0.8792 (tp-100) cc_final: 0.8499 (mm-40) REVERT: K 34 ARG cc_start: 0.7546 (ttt-90) cc_final: 0.6265 (mmp80) outliers start: 216 outliers final: 81 residues processed: 1201 average time/residue: 2.2633 time to fit residues: 3810.0964 Evaluate side-chains 1147 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 1042 time to evaluate : 6.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain Q residue 59 ARG Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 97 SER Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 111 LYS Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Z residue 118 LYS Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 78 SER Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 43 LYS Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 41 ARG Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain m residue 7 ILE Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 110 SER Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 164 ARG Chi-restraints excluded: chain 3 residue 148 LYS Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 54 ARG Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 122 ASN Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 66 LEU Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 125 ILE Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 18 GLN Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 53 CYS Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain J residue 54 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 906 optimal weight: 10.0000 chunk 690 optimal weight: 10.0000 chunk 476 optimal weight: 10.0000 chunk 101 optimal weight: 10.0000 chunk 438 optimal weight: 10.0000 chunk 616 optimal weight: 8.9990 chunk 921 optimal weight: 4.9990 chunk 975 optimal weight: 4.9990 chunk 481 optimal weight: 10.0000 chunk 873 optimal weight: 5.9990 chunk 262 optimal weight: 5.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** s 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 GLN Q 32 ASN Q 150 GLN R 115 GLN T 88 GLN T 116 GLN V 94 ASN W 128 ASN Z 60 GLN a 18 GLN b 19 GLN c 7 GLN ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 12 HIS ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 12 GLN i 49 ASN p 29 GLN ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 178 ASN 2 139 GLN 2 176 HIS 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 55 HIS 9 58 ASN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 ASN C 105 ASN D 60 GLN H 54 GLN J 75 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.076 156684 Z= 0.445 Angle : 0.709 12.344 234478 Z= 0.369 Chirality : 0.045 0.388 29976 Planarity : 0.006 0.115 12458 Dihedral : 23.350 179.537 78641 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.25 % Favored : 91.50 % Rotamer: Outliers : 5.58 % Allowed : 19.43 % Favored : 74.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.27 % 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: -1.74 (0.11), residues: 5614 helix: 0.16 (0.12), residues: 1826 sheet: -1.64 (0.15), residues: 1021 loop : -1.87 (0.11), residues: 2767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP P 213 HIS 0.011 0.002 HIS h 45 PHE 0.021 0.002 PHE A 52 TYR 0.019 0.002 TYR 2 184 ARG 0.010 0.001 ARG 8 124 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1063 time to evaluate : 6.274 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: P 5 LYS cc_start: 0.8927 (mttt) cc_final: 0.8722 (tttt) REVERT: P 125 LYS cc_start: 0.8823 (ptpp) cc_final: 0.8588 (ptpt) REVERT: P 147 LYS cc_start: 0.8925 (mtpp) cc_final: 0.8622 (mttm) REVERT: P 199 GLU cc_start: 0.8913 (mt-10) cc_final: 0.8577 (pm20) REVERT: P 203 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8216 (ptt180) REVERT: P 239 ASN cc_start: 0.8222 (OUTLIER) cc_final: 0.7916 (m110) REVERT: P 270 ARG cc_start: 0.8718 (mmm160) cc_final: 0.7499 (ttt-90) REVERT: Q 59 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.8379 (ttm-80) REVERT: Q 88 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.8662 (mt-10) REVERT: Q 89 GLU cc_start: 0.8875 (tp30) cc_final: 0.8322 (tm-30) REVERT: R 3 LEU cc_start: 0.9043 (mt) cc_final: 0.8813 (mp) REVERT: R 22 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8439 (p0) REVERT: R 77 ILE cc_start: 0.8669 (OUTLIER) cc_final: 0.8354 (pt) REVERT: R 122 GLU cc_start: 0.9114 (tp30) cc_final: 0.8803 (pt0) REVERT: R 139 LYS cc_start: 0.9278 (tppp) cc_final: 0.9042 (ttpp) REVERT: R 144 GLU cc_start: 0.9037 (tt0) cc_final: 0.8736 (mm-30) REVERT: R 155 GLU cc_start: 0.8458 (tp30) cc_final: 0.8160 (tm-30) REVERT: R 171 ASP cc_start: 0.8898 (t70) cc_final: 0.8657 (m-30) REVERT: R 184 ASP cc_start: 0.9023 (m-30) cc_final: 0.8698 (t0) REVERT: S 11 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8719 (tp30) REVERT: S 19 GLU cc_start: 0.8856 (tm-30) cc_final: 0.8605 (tm-30) REVERT: S 30 ARG cc_start: 0.8468 (OUTLIER) cc_final: 0.8211 (ptp90) REVERT: S 78 LYS cc_start: 0.9167 (mttt) cc_final: 0.8942 (mttm) REVERT: S 113 ASP cc_start: 0.8213 (m-30) cc_final: 0.7937 (t0) REVERT: S 142 ASP cc_start: 0.8058 (t0) cc_final: 0.7732 (t70) REVERT: S 143 TYR cc_start: 0.8127 (t80) cc_final: 0.7822 (t80) REVERT: T 3 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.7946 (ttm170) REVERT: T 106 SER cc_start: 0.9104 (m) cc_final: 0.8849 (t) REVERT: U 35 LYS cc_start: 0.8892 (mttt) cc_final: 0.8489 (mtpp) REVERT: V 117 MET cc_start: 0.2302 (mmm) cc_final: 0.1984 (mmm) REVERT: V 136 MET cc_start: 0.2580 (mtm) cc_final: 0.1769 (mtp) REVERT: W 1 MET cc_start: 0.8311 (ptp) cc_final: 0.7827 (pp-130) REVERT: W 16 TYR cc_start: 0.9276 (m-80) cc_final: 0.8946 (m-80) REVERT: W 108 MET cc_start: 0.8738 (mtt) cc_final: 0.8242 (mtt) REVERT: W 111 LYS cc_start: 0.8279 (pttt) cc_final: 0.8021 (mmtm) REVERT: X 53 LYS cc_start: 0.9086 (pttp) cc_final: 0.8614 (mmtp) REVERT: X 106 GLU cc_start: 0.8818 (mp0) cc_final: 0.8375 (mp0) REVERT: Y 7 SER cc_start: 0.9172 (OUTLIER) cc_final: 0.8938 (p) REVERT: Y 55 MET cc_start: 0.8635 (tpt) cc_final: 0.8432 (tpt) REVERT: Y 106 GLU cc_start: 0.9060 (mt-10) cc_final: 0.8823 (tt0) REVERT: Y 111 ILE cc_start: 0.8238 (mp) cc_final: 0.7944 (pt) REVERT: Y 129 LYS cc_start: 0.8835 (tttp) cc_final: 0.8543 (mttt) REVERT: Z 6 ARG cc_start: 0.9095 (ttt-90) cc_final: 0.8542 (tmt-80) REVERT: Z 30 SER cc_start: 0.9269 (t) cc_final: 0.9000 (p) REVERT: Z 55 ARG cc_start: 0.8442 (tpp80) cc_final: 0.8143 (ttp-170) REVERT: Z 60 GLN cc_start: 0.8661 (pt0) cc_final: 0.8318 (pp30) REVERT: Z 127 LYS cc_start: 0.8705 (mtpp) cc_final: 0.8172 (tptt) REVERT: b 46 GLU cc_start: 0.8608 (tt0) cc_final: 0.8368 (mt-10) REVERT: c 10 GLN cc_start: 0.8752 (pt0) cc_final: 0.8432 (mt0) REVERT: d 11 ARG cc_start: 0.8525 (tpt170) cc_final: 0.7726 (ttm170) REVERT: d 78 LYS cc_start: 0.9182 (mtpp) cc_final: 0.8973 (mttt) REVERT: d 84 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8324 (mttt) REVERT: e 45 GLU cc_start: 0.8546 (pp20) cc_final: 0.8169 (pp20) REVERT: e 72 VAL cc_start: 0.8721 (OUTLIER) cc_final: 0.8425 (m) REVERT: g 21 SER cc_start: 0.8883 (t) cc_final: 0.8645 (m) REVERT: g 76 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8545 (ttp80) REVERT: h 45 HIS cc_start: 0.8478 (OUTLIER) cc_final: 0.6539 (p90) REVERT: h 79 LYS cc_start: 0.8835 (mttm) cc_final: 0.8435 (mtpp) REVERT: i 43 ASP cc_start: 0.8910 (t0) cc_final: 0.8697 (t70) REVERT: i 59 GLU cc_start: 0.8952 (tt0) cc_final: 0.8671 (mt-10) REVERT: k 43 GLU cc_start: 0.8110 (tt0) cc_final: 0.7723 (tm-30) REVERT: l 1 MET cc_start: 0.8171 (mtm) cc_final: 0.7616 (ptp) REVERT: l 31 GLN cc_start: 0.8408 (tt0) cc_final: 0.8205 (tt0) REVERT: m 5 ILE cc_start: 0.8300 (tt) cc_final: 0.7977 (pt) REVERT: m 37 GLU cc_start: 0.9126 (pt0) cc_final: 0.8885 (tt0) REVERT: m 45 ARG cc_start: 0.9043 (mmt180) cc_final: 0.8816 (mmt180) REVERT: n 12 LYS cc_start: 0.8771 (tptt) cc_final: 0.8303 (mmtt) REVERT: n 15 MET cc_start: 0.8922 (mtt) cc_final: 0.8633 (mtp) REVERT: n 28 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8624 (pp) REVERT: o 45 GLN cc_start: 0.9026 (OUTLIER) cc_final: 0.8504 (mp10) REVERT: p 14 ARG cc_start: 0.9083 (OUTLIER) cc_final: 0.8514 (mtt180) REVERT: p 25 LYS cc_start: 0.8822 (tptt) cc_final: 0.8322 (ttpp) REVERT: p 28 ARG cc_start: 0.9120 (mtp180) cc_final: 0.8793 (mtt90) REVERT: r 8 LYS cc_start: 0.8295 (mttt) cc_final: 0.8068 (mtmp) REVERT: L 25 ARG cc_start: 0.8301 (mtm-85) cc_final: 0.7816 (mtp85) REVERT: 1 9 MET cc_start: 0.6461 (mtt) cc_final: 0.6038 (pp-130) REVERT: 1 27 MET cc_start: 0.9180 (mmp) cc_final: 0.8871 (mmm) REVERT: 1 59 LYS cc_start: 0.9089 (tttp) cc_final: 0.8883 (tttm) REVERT: 1 78 GLU cc_start: 0.8560 (pt0) cc_final: 0.7827 (pp20) REVERT: 1 82 ASP cc_start: 0.9378 (OUTLIER) cc_final: 0.9123 (m-30) REVERT: 1 145 GLU cc_start: 0.8910 (tp30) cc_final: 0.8710 (tp30) REVERT: 1 167 ASP cc_start: 0.8517 (p0) cc_final: 0.8239 (m-30) REVERT: 1 192 ASP cc_start: 0.8682 (t0) cc_final: 0.8279 (t0) REVERT: 2 28 GLU cc_start: 0.8596 (pm20) cc_final: 0.8190 (pm20) REVERT: 2 86 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8111 (tptm) REVERT: 2 105 GLU cc_start: 0.8771 (tt0) cc_final: 0.8566 (tt0) REVERT: 3 44 ARG cc_start: 0.8085 (mmt-90) cc_final: 0.7368 (mtp180) REVERT: 3 70 ARG cc_start: 0.8450 (ttm110) cc_final: 0.8016 (ttm-80) REVERT: 3 128 ARG cc_start: 0.8273 (mtp180) cc_final: 0.7611 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8570 (mp0) REVERT: 3 172 GLU cc_start: 0.9021 (tp30) cc_final: 0.8544 (mm-30) REVERT: 3 177 LYS cc_start: 0.8502 (mtmt) cc_final: 0.7581 (tptp) REVERT: 3 179 GLU cc_start: 0.8804 (pt0) cc_final: 0.8465 (pp20) REVERT: 4 12 GLN cc_start: 0.8762 (tp40) cc_final: 0.8419 (tt0) REVERT: 4 29 ARG cc_start: 0.8803 (mtt-85) cc_final: 0.8555 (mtm-85) REVERT: 4 54 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8534 (tpp80) REVERT: 4 61 GLN cc_start: 0.9148 (tt0) cc_final: 0.8845 (mm110) REVERT: 4 141 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8568 (mm) REVERT: 4 152 MET cc_start: 0.9009 (mmt) cc_final: 0.8764 (mtp) REVERT: 4 157 ARG cc_start: 0.9321 (OUTLIER) cc_final: 0.8213 (ptm160) REVERT: 5 9 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7318 (mpt) REVERT: 5 17 GLN cc_start: 0.8539 (OUTLIER) cc_final: 0.8318 (mp-120) REVERT: 5 79 ARG cc_start: 0.7899 (mmt-90) cc_final: 0.7364 (ttp-170) REVERT: 6 48 GLU cc_start: 0.8458 (tt0) cc_final: 0.8218 (tm-30) REVERT: 6 74 GLU cc_start: 0.8090 (pt0) cc_final: 0.7617 (pm20) REVERT: 6 90 GLU cc_start: 0.8703 (mp0) cc_final: 0.8429 (pp20) REVERT: 6 92 ARG cc_start: 0.8194 (mmm160) cc_final: 0.7844 (mtp180) REVERT: 6 136 LYS cc_start: 0.8902 (tttm) cc_final: 0.8557 (tppt) REVERT: 6 144 MET cc_start: 0.8547 (tpp) cc_final: 0.8264 (tpp) REVERT: 6 148 ASN cc_start: 0.9054 (m110) cc_final: 0.8847 (m-40) REVERT: 7 31 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8624 (mtpm) REVERT: 7 56 LYS cc_start: 0.8534 (mtmt) cc_final: 0.8078 (mttt) REVERT: 7 80 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8596 (ptm-80) REVERT: 7 118 GLN cc_start: 0.8829 (tt0) cc_final: 0.8423 (mp10) REVERT: 8 22 LYS cc_start: 0.8220 (mtmt) cc_final: 0.7621 (mttt) REVERT: 8 61 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.8094 (mp) REVERT: 8 88 MET cc_start: 0.7709 (ptt) cc_final: 0.7171 (mmp) REVERT: 8 120 LYS cc_start: 0.9092 (OUTLIER) cc_final: 0.7743 (ptmm) REVERT: 9 7 ARG cc_start: 0.8043 (mtt-85) cc_final: 0.6993 (mpt-90) REVERT: 9 11 LYS cc_start: 0.8640 (mtmt) cc_final: 0.8429 (mtmt) REVERT: A 69 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8352 (mtp-110) REVERT: A 127 ARG cc_start: 0.8329 (mmm160) cc_final: 0.8016 (mmm160) REVERT: B 10 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8447 (ptmt) REVERT: B 54 ARG cc_start: 0.8124 (ttp-170) cc_final: 0.7526 (tpt170) REVERT: B 56 ARG cc_start: 0.8956 (tpp-160) cc_final: 0.8584 (ttp80) REVERT: B 70 GLU cc_start: 0.8203 (mt-10) cc_final: 0.7722 (mp0) REVERT: B 123 LYS cc_start: 0.8852 (mmtp) cc_final: 0.8613 (mmpt) REVERT: C 31 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8556 (mtmp) REVERT: C 63 PHE cc_start: 0.5587 (t80) cc_final: 0.5091 (t80) REVERT: C 109 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.7944 (tpt-90) REVERT: C 113 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.5743 (ptp90) REVERT: E 72 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8695 (ptp90) REVERT: E 77 ARG cc_start: 0.8746 (mtp180) cc_final: 0.8457 (mtp180) REVERT: G 15 ASP cc_start: 0.8322 (t70) cc_final: 0.8037 (p0) REVERT: G 65 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8342 (ptt180) REVERT: I 81 ARG cc_start: 0.8367 (tpp80) cc_final: 0.6575 (pmt-80) REVERT: J 33 LYS cc_start: 0.8766 (OUTLIER) cc_final: 0.8258 (ttmt) REVERT: K 34 ARG cc_start: 0.7674 (ttt-90) cc_final: 0.6243 (mmp80) outliers start: 261 outliers final: 119 residues processed: 1190 average time/residue: 2.2188 time to fit residues: 3729.4918 Evaluate side-chains 1172 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 1024 time to evaluate : 6.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain Q residue 59 ARG Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain Y residue 7 SER Chi-restraints excluded: chain Z residue 24 THR Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain Z residue 128 THR Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain c residue 110 ILE Chi-restraints excluded: chain e residue 34 GLU Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 78 SER Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 83 LYS Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 45 GLN Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 106 THR Chi-restraints excluded: chain 1 residue 110 SER Chi-restraints excluded: chain 1 residue 118 GLU Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 54 ARG Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 9 MET Chi-restraints excluded: chain 5 residue 17 GLN Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 23 LEU Chi-restraints excluded: chain 6 residue 66 LEU Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 7 residue 21 ASN Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 76 GLN Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 91 HIS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 72 ARG Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain I residue 38 SER Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 812 optimal weight: 8.9990 chunk 553 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 726 optimal weight: 10.0000 chunk 402 optimal weight: 3.9990 chunk 832 optimal weight: 6.9990 chunk 674 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 498 optimal weight: 7.9990 chunk 875 optimal weight: 3.9990 chunk 246 optimal weight: 0.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 138 HIS P 115 GLN Q 32 ASN Q 150 GLN R 115 GLN T 88 GLN V 94 ASN W 128 ASN X 3 GLN b 19 GLN b 98 GLN c 7 GLN i 12 GLN i 49 ASN r 35 GLN ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 178 ASN 2 139 GLN 4 19 ASN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN H 54 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 156684 Z= 0.263 Angle : 0.602 12.158 234478 Z= 0.316 Chirality : 0.038 0.342 29976 Planarity : 0.005 0.109 12458 Dihedral : 23.308 178.882 78641 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.21 % Allowed : 7.89 % Favored : 91.90 % Rotamer: Outliers : 5.17 % Allowed : 20.63 % Favored : 74.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.22 % 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: -1.41 (0.11), residues: 5614 helix: 0.55 (0.12), residues: 1812 sheet: -1.44 (0.15), residues: 1030 loop : -1.76 (0.11), residues: 2772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 213 HIS 0.006 0.001 HIS h 45 PHE 0.020 0.002 PHE 1 69 TYR 0.018 0.002 TYR J 36 ARG 0.008 0.001 ARG C 93 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1305 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1063 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 5 LYS cc_start: 0.8908 (mttt) cc_final: 0.8702 (tttt) REVERT: P 110 LEU cc_start: 0.9101 (tt) cc_final: 0.8844 (tp) REVERT: P 125 LYS cc_start: 0.8769 (ptpp) cc_final: 0.8529 (ptpt) REVERT: P 147 LYS cc_start: 0.8903 (mtpp) cc_final: 0.8607 (mttm) REVERT: P 199 GLU cc_start: 0.8875 (mt-10) cc_final: 0.8563 (pm20) REVERT: P 203 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8134 (ptt-90) REVERT: P 236 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7498 (mt-10) REVERT: P 239 ASN cc_start: 0.8169 (OUTLIER) cc_final: 0.7866 (m110) REVERT: P 270 ARG cc_start: 0.8698 (mmm160) cc_final: 0.7420 (ttt-90) REVERT: Q 88 GLU cc_start: 0.8875 (OUTLIER) cc_final: 0.8663 (mt-10) REVERT: Q 89 GLU cc_start: 0.8893 (tp30) cc_final: 0.8319 (tm-30) REVERT: Q 104 VAL cc_start: 0.8273 (m) cc_final: 0.8032 (t) REVERT: Q 105 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8390 (mtpt) REVERT: Q 199 SER cc_start: 0.8725 (OUTLIER) cc_final: 0.8363 (p) REVERT: R 22 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8408 (p0) REVERT: R 77 ILE cc_start: 0.8551 (OUTLIER) cc_final: 0.8296 (pt) REVERT: R 122 GLU cc_start: 0.9137 (tp30) cc_final: 0.8831 (pt0) REVERT: R 139 LYS cc_start: 0.9281 (tppp) cc_final: 0.9054 (ttpp) REVERT: R 144 GLU cc_start: 0.8987 (tt0) cc_final: 0.8674 (pm20) REVERT: R 145 ASP cc_start: 0.8993 (t0) cc_final: 0.8619 (t0) REVERT: R 155 GLU cc_start: 0.8457 (tp30) cc_final: 0.8178 (tm-30) REVERT: R 171 ASP cc_start: 0.8870 (t70) cc_final: 0.8647 (m-30) REVERT: R 184 ASP cc_start: 0.8963 (m-30) cc_final: 0.8664 (t0) REVERT: R 197 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: S 11 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8787 (tp30) REVERT: S 19 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8612 (tm-30) REVERT: S 23 ASN cc_start: 0.8926 (m110) cc_final: 0.8613 (m110) REVERT: S 56 ASP cc_start: 0.8609 (m-30) cc_final: 0.8078 (m-30) REVERT: S 78 LYS cc_start: 0.9161 (mttt) cc_final: 0.8935 (mttm) REVERT: S 94 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8603 (mm-30) REVERT: S 98 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8452 (mt-10) REVERT: S 113 ASP cc_start: 0.8247 (m-30) cc_final: 0.7991 (t70) REVERT: S 120 LYS cc_start: 0.8961 (OUTLIER) cc_final: 0.8718 (mtpp) REVERT: S 142 ASP cc_start: 0.8032 (t0) cc_final: 0.7718 (t70) REVERT: S 143 TYR cc_start: 0.8103 (t80) cc_final: 0.7824 (t80) REVERT: T 3 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7816 (ttm170) REVERT: T 106 SER cc_start: 0.9173 (m) cc_final: 0.8927 (t) REVERT: U 1 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6877 (mmm) REVERT: U 35 LYS cc_start: 0.8768 (mttt) cc_final: 0.8402 (mtpp) REVERT: V 117 MET cc_start: 0.1961 (mmm) cc_final: 0.1656 (mmm) REVERT: V 136 MET cc_start: 0.2390 (mtm) cc_final: 0.1983 (ptt) REVERT: W 1 MET cc_start: 0.8362 (ptp) cc_final: 0.7793 (pp-130) REVERT: W 16 TYR cc_start: 0.9285 (m-80) cc_final: 0.8990 (m-80) REVERT: W 111 LYS cc_start: 0.8256 (pttt) cc_final: 0.8006 (mmtm) REVERT: X 53 LYS cc_start: 0.9075 (pttp) cc_final: 0.8594 (mmtp) REVERT: X 106 GLU cc_start: 0.8631 (mp0) cc_final: 0.8190 (mp0) REVERT: Y 55 MET cc_start: 0.8610 (tpt) cc_final: 0.8310 (tpt) REVERT: Z 6 ARG cc_start: 0.9044 (ttt-90) cc_final: 0.8476 (tmt-80) REVERT: Z 55 ARG cc_start: 0.8395 (tpp80) cc_final: 0.8092 (ttm110) REVERT: Z 60 GLN cc_start: 0.8565 (pt0) cc_final: 0.8220 (pp30) REVERT: Z 127 LYS cc_start: 0.8727 (mtpp) cc_final: 0.8171 (tptt) REVERT: b 46 GLU cc_start: 0.8676 (tt0) cc_final: 0.8370 (mt-10) REVERT: b 56 LYS cc_start: 0.8856 (pmtt) cc_final: 0.8475 (tppt) REVERT: c 10 GLN cc_start: 0.8649 (pt0) cc_final: 0.8355 (mt0) REVERT: d 11 ARG cc_start: 0.8450 (tpt170) cc_final: 0.7645 (ttm170) REVERT: d 84 LYS cc_start: 0.8612 (ttpp) cc_final: 0.8303 (mttt) REVERT: e 45 GLU cc_start: 0.8502 (pp20) cc_final: 0.8107 (pp20) REVERT: e 72 VAL cc_start: 0.8631 (OUTLIER) cc_final: 0.8317 (m) REVERT: e 79 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8261 (ptp-170) REVERT: f 82 MET cc_start: 0.8937 (mtp) cc_final: 0.8717 (mtm) REVERT: g 69 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7925 (ttp80) REVERT: g 76 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8424 (ttp80) REVERT: h 45 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.6769 (p90) REVERT: h 79 LYS cc_start: 0.8842 (mttm) cc_final: 0.8443 (mtpp) REVERT: i 43 ASP cc_start: 0.8938 (t0) cc_final: 0.8737 (t70) REVERT: i 55 GLU cc_start: 0.9129 (mp0) cc_final: 0.8871 (pm20) REVERT: j 25 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.8423 (mmt90) REVERT: k 40 VAL cc_start: 0.8442 (OUTLIER) cc_final: 0.8235 (m) REVERT: k 43 GLU cc_start: 0.8075 (tt0) cc_final: 0.7622 (tm-30) REVERT: k 54 LYS cc_start: 0.8575 (OUTLIER) cc_final: 0.8359 (ttmt) REVERT: l 1 MET cc_start: 0.8143 (mtm) cc_final: 0.7637 (ptp) REVERT: m 5 ILE cc_start: 0.8283 (tt) cc_final: 0.8026 (pt) REVERT: n 12 LYS cc_start: 0.8812 (tptt) cc_final: 0.8380 (mmtt) REVERT: n 15 MET cc_start: 0.8874 (mtt) cc_final: 0.8598 (mtp) REVERT: n 28 LEU cc_start: 0.8889 (OUTLIER) cc_final: 0.8601 (pp) REVERT: p 14 ARG cc_start: 0.9025 (OUTLIER) cc_final: 0.8451 (mtt180) REVERT: p 25 LYS cc_start: 0.8673 (tptt) cc_final: 0.8220 (ttpp) REVERT: p 28 ARG cc_start: 0.9104 (mtp180) cc_final: 0.8783 (mtt90) REVERT: r 8 LYS cc_start: 0.8321 (mttt) cc_final: 0.8081 (mtmp) REVERT: 1 9 MET cc_start: 0.6314 (mtt) cc_final: 0.5931 (pp-130) REVERT: 1 78 GLU cc_start: 0.8517 (pt0) cc_final: 0.7662 (pp20) REVERT: 1 82 ASP cc_start: 0.9406 (OUTLIER) cc_final: 0.9121 (m-30) REVERT: 1 113 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8651 (tpp80) REVERT: 1 133 GLU cc_start: 0.7280 (pp20) cc_final: 0.6769 (pm20) REVERT: 1 145 GLU cc_start: 0.8907 (tp30) cc_final: 0.8696 (tp30) REVERT: 1 165 ASP cc_start: 0.8602 (t0) cc_final: 0.8368 (t70) REVERT: 1 167 ASP cc_start: 0.8499 (p0) cc_final: 0.8229 (m-30) REVERT: 1 192 ASP cc_start: 0.8699 (t0) cc_final: 0.8341 (t0) REVERT: 1 205 ASP cc_start: 0.8174 (p0) cc_final: 0.7588 (p0) REVERT: 2 28 GLU cc_start: 0.8582 (pm20) cc_final: 0.8174 (pm20) REVERT: 2 86 LYS cc_start: 0.8449 (ttpp) cc_final: 0.8109 (tptm) REVERT: 3 44 ARG cc_start: 0.8202 (mmt-90) cc_final: 0.7467 (mtp180) REVERT: 3 70 ARG cc_start: 0.8313 (ttm110) cc_final: 0.8024 (ttm-80) REVERT: 3 128 ARG cc_start: 0.8265 (mtp180) cc_final: 0.7657 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8885 (mm-30) cc_final: 0.8559 (mp0) REVERT: 3 172 GLU cc_start: 0.8979 (tp30) cc_final: 0.8474 (mm-30) REVERT: 3 177 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7468 (tptt) REVERT: 3 179 GLU cc_start: 0.8791 (pt0) cc_final: 0.8493 (pp20) REVERT: 4 12 GLN cc_start: 0.8752 (tp40) cc_final: 0.8451 (tt0) REVERT: 4 29 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8463 (mtm-85) REVERT: 4 61 GLN cc_start: 0.9127 (tt0) cc_final: 0.8840 (mm110) REVERT: 4 152 MET cc_start: 0.8990 (mmt) cc_final: 0.8761 (mtp) REVERT: 4 157 ARG cc_start: 0.9332 (OUTLIER) cc_final: 0.7621 (ptm-80) REVERT: 5 79 ARG cc_start: 0.7807 (mmt-90) cc_final: 0.7434 (ttp-170) REVERT: 6 48 GLU cc_start: 0.8462 (tt0) cc_final: 0.8051 (mp0) REVERT: 6 74 GLU cc_start: 0.8113 (pt0) cc_final: 0.7672 (pm20) REVERT: 6 90 GLU cc_start: 0.8808 (mp0) cc_final: 0.8512 (pp20) REVERT: 6 92 ARG cc_start: 0.8227 (mmm160) cc_final: 0.7852 (mtp180) REVERT: 6 136 LYS cc_start: 0.8902 (tttm) cc_final: 0.8552 (tppt) REVERT: 6 144 MET cc_start: 0.8509 (tpp) cc_final: 0.8207 (tpp) REVERT: 6 148 ASN cc_start: 0.9016 (m110) cc_final: 0.8811 (m-40) REVERT: 7 31 LYS cc_start: 0.8931 (mmmt) cc_final: 0.8617 (mtpm) REVERT: 7 56 LYS cc_start: 0.8560 (mtmt) cc_final: 0.8146 (mttt) REVERT: 7 118 GLN cc_start: 0.8802 (tt0) cc_final: 0.8378 (mp10) REVERT: 8 22 LYS cc_start: 0.8249 (mtmt) cc_final: 0.7650 (mtpp) REVERT: 8 61 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8157 (mp) REVERT: 8 88 MET cc_start: 0.7648 (ptt) cc_final: 0.7189 (mmp) REVERT: 8 120 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.7656 (ptmm) REVERT: 8 127 PHE cc_start: 0.8413 (OUTLIER) cc_final: 0.7859 (p90) REVERT: 9 7 ARG cc_start: 0.8083 (mtt-85) cc_final: 0.7318 (mpt-90) REVERT: A 69 ARG cc_start: 0.8516 (ttm110) cc_final: 0.8301 (mtp-110) REVERT: A 127 ARG cc_start: 0.8220 (mmm160) cc_final: 0.7918 (mmm160) REVERT: B 10 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8334 (ptmt) REVERT: B 54 ARG cc_start: 0.8045 (ttp-170) cc_final: 0.7466 (tpt170) REVERT: B 56 ARG cc_start: 0.8892 (tpp-160) cc_final: 0.8507 (ttp80) REVERT: B 70 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7701 (mp0) REVERT: B 123 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8609 (mmpt) REVERT: C 92 ARG cc_start: 0.6631 (ttm-80) cc_final: 0.6135 (tpp-160) REVERT: C 109 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.7923 (tpt-90) REVERT: C 113 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.5757 (ptp90) REVERT: F 77 GLU cc_start: 0.8838 (tt0) cc_final: 0.8164 (mp0) REVERT: G 65 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8345 (ptt180) REVERT: H 32 TYR cc_start: 0.8599 (m-80) cc_final: 0.8321 (m-80) REVERT: I 32 ARG cc_start: 0.8080 (mtm180) cc_final: 0.7831 (mtm180) REVERT: I 81 ARG cc_start: 0.8489 (tpp80) cc_final: 0.6630 (pmt-80) REVERT: J 33 LYS cc_start: 0.8728 (OUTLIER) cc_final: 0.8216 (ttmt) REVERT: K 33 ARG cc_start: 0.7731 (ttt180) cc_final: 0.7481 (ttp-170) REVERT: K 34 ARG cc_start: 0.7407 (ttt-90) cc_final: 0.6051 (mmp80) outliers start: 242 outliers final: 118 residues processed: 1182 average time/residue: 2.3626 time to fit residues: 4020.6251 Evaluate side-chains 1184 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1037 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 137 ILE Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain U residue 1 MET Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain Y residue 141 LYS Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 69 ARG Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 83 LYS Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 39 LEU Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain q residue 34 THR Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 110 SER Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 213 TYR Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 71 MET Chi-restraints excluded: chain 4 residue 105 ILE Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 7 residue 21 ASN Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 76 GLN Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 94 LYS Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 7 residue 125 ILE Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 65 ILE Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 22 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 23 LYS Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 79 ASN Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 328 optimal weight: 8.9990 chunk 878 optimal weight: 7.9990 chunk 192 optimal weight: 10.0000 chunk 572 optimal weight: 10.0000 chunk 240 optimal weight: 7.9990 chunk 976 optimal weight: 9.9990 chunk 810 optimal weight: 10.0000 chunk 452 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 322 optimal weight: 5.9990 chunk 512 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 154 ASN s 156 GLN P 115 GLN Q 32 ASN Q 150 GLN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN b 19 GLN c 7 GLN i 49 ASN o 19 HIS ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 178 ASN 2 139 GLN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 46 GLN 8 110 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN D 35 ASN D 60 GLN I 14 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.084 156684 Z= 0.512 Angle : 0.741 13.101 234478 Z= 0.384 Chirality : 0.047 0.402 29976 Planarity : 0.006 0.119 12458 Dihedral : 23.339 179.838 78639 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.71 % Favored : 91.00 % Rotamer: Outliers : 5.86 % Allowed : 20.71 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.26 % 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: -1.49 (0.11), residues: 5614 helix: 0.38 (0.12), residues: 1829 sheet: -1.45 (0.15), residues: 1051 loop : -1.75 (0.11), residues: 2734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 213 HIS 0.012 0.002 HIS h 45 PHE 0.022 0.002 PHE A 52 TYR 0.020 0.002 TYR 2 184 ARG 0.015 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1302 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 274 poor density : 1028 time to evaluate : 5.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 125 LYS cc_start: 0.8850 (ptpp) cc_final: 0.8624 (ptpt) REVERT: P 199 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8596 (pm20) REVERT: P 205 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8862 (mp) REVERT: P 236 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7796 (mt-10) REVERT: P 239 ASN cc_start: 0.8329 (OUTLIER) cc_final: 0.8028 (m110) REVERT: P 251 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8000 (tt0) REVERT: P 270 ARG cc_start: 0.8768 (mmm160) cc_final: 0.7432 (ttt-90) REVERT: Q 88 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8344 (mt-10) REVERT: R 22 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8444 (p0) REVERT: R 77 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8318 (pt) REVERT: R 122 GLU cc_start: 0.9127 (tp30) cc_final: 0.8804 (pt0) REVERT: R 144 GLU cc_start: 0.9023 (tt0) cc_final: 0.8705 (mm-30) REVERT: R 155 GLU cc_start: 0.8472 (tp30) cc_final: 0.8183 (tm-30) REVERT: R 171 ASP cc_start: 0.8886 (t70) cc_final: 0.8625 (m-30) REVERT: R 184 ASP cc_start: 0.8931 (m-30) cc_final: 0.8677 (t0) REVERT: R 198 GLU cc_start: 0.9042 (mt-10) cc_final: 0.8725 (tm-30) REVERT: S 11 GLU cc_start: 0.8991 (mt-10) cc_final: 0.8726 (tp30) REVERT: S 19 GLU cc_start: 0.8854 (tm-30) cc_final: 0.8591 (tm-30) REVERT: S 23 ASN cc_start: 0.9036 (m110) cc_final: 0.8755 (m110) REVERT: S 30 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7660 (ptp-110) REVERT: S 78 LYS cc_start: 0.9080 (mttt) cc_final: 0.8847 (mttm) REVERT: S 94 GLU cc_start: 0.8871 (mm-30) cc_final: 0.8602 (mm-30) REVERT: S 98 GLU cc_start: 0.8717 (mt-10) cc_final: 0.8456 (mt-10) REVERT: S 113 ASP cc_start: 0.8263 (m-30) cc_final: 0.7989 (t0) REVERT: S 142 ASP cc_start: 0.8075 (t0) cc_final: 0.7786 (t70) REVERT: S 143 TYR cc_start: 0.8135 (t80) cc_final: 0.7837 (t80) REVERT: T 3 ARG cc_start: 0.8212 (mtm-85) cc_final: 0.7858 (ttm170) REVERT: T 106 SER cc_start: 0.9079 (m) cc_final: 0.8809 (t) REVERT: U 35 LYS cc_start: 0.8875 (mttt) cc_final: 0.8504 (mtpp) REVERT: V 117 MET cc_start: 0.1899 (mmm) cc_final: 0.1596 (mmm) REVERT: V 136 MET cc_start: 0.2377 (mtm) cc_final: 0.1986 (ptt) REVERT: W 1 MET cc_start: 0.8313 (ptp) cc_final: 0.7785 (pp-130) REVERT: W 108 MET cc_start: 0.8754 (mtt) cc_final: 0.8248 (mtt) REVERT: W 111 LYS cc_start: 0.8265 (pttt) cc_final: 0.7990 (mmtm) REVERT: X 53 LYS cc_start: 0.9144 (pttp) cc_final: 0.8656 (mmtp) REVERT: X 106 GLU cc_start: 0.8798 (mp0) cc_final: 0.8405 (mp0) REVERT: Y 55 MET cc_start: 0.8698 (tpt) cc_final: 0.8443 (tpt) REVERT: Z 5 LYS cc_start: 0.9101 (OUTLIER) cc_final: 0.8815 (mtpt) REVERT: Z 55 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8240 (ttp-170) REVERT: Z 60 GLN cc_start: 0.8526 (pt0) cc_final: 0.8231 (pp30) REVERT: Z 127 LYS cc_start: 0.8679 (mtpp) cc_final: 0.8101 (tptt) REVERT: b 46 GLU cc_start: 0.8673 (tt0) cc_final: 0.8391 (mt-10) REVERT: b 56 LYS cc_start: 0.8872 (pmtt) cc_final: 0.8499 (tppt) REVERT: c 10 GLN cc_start: 0.8718 (pt0) cc_final: 0.8407 (mt0) REVERT: d 11 ARG cc_start: 0.8545 (tpt170) cc_final: 0.7687 (ttm170) REVERT: d 15 LYS cc_start: 0.8929 (ttmm) cc_final: 0.8664 (ttpt) REVERT: d 84 LYS cc_start: 0.8636 (ttpp) cc_final: 0.8331 (mttt) REVERT: e 22 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9133 (mt) REVERT: e 45 GLU cc_start: 0.8489 (pp20) cc_final: 0.8136 (pp20) REVERT: e 72 VAL cc_start: 0.8682 (OUTLIER) cc_final: 0.8363 (m) REVERT: e 79 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8378 (ptp-170) REVERT: f 4 ILE cc_start: 0.9141 (mp) cc_final: 0.8911 (mp) REVERT: g 76 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.8507 (ttp80) REVERT: h 45 HIS cc_start: 0.8469 (OUTLIER) cc_final: 0.6786 (p90) REVERT: h 79 LYS cc_start: 0.8861 (mttm) cc_final: 0.8441 (mtpp) REVERT: i 1 MET cc_start: 0.7715 (ppp) cc_final: 0.7460 (pmm) REVERT: i 55 GLU cc_start: 0.9112 (mp0) cc_final: 0.8819 (pm20) REVERT: i 68 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7807 (tppt) REVERT: i 71 LYS cc_start: 0.8876 (mmtm) cc_final: 0.8584 (mptt) REVERT: j 25 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8407 (mmt90) REVERT: k 40 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8323 (m) REVERT: k 43 GLU cc_start: 0.8130 (tt0) cc_final: 0.7637 (tm-30) REVERT: k 54 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.8122 (tttm) REVERT: l 1 MET cc_start: 0.8125 (mtm) cc_final: 0.7587 (ptp) REVERT: m 5 ILE cc_start: 0.8419 (tt) cc_final: 0.8125 (pt) REVERT: n 12 LYS cc_start: 0.8842 (tptt) cc_final: 0.8362 (mmtt) REVERT: n 15 MET cc_start: 0.8917 (mtt) cc_final: 0.8603 (mtp) REVERT: n 28 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8682 (pp) REVERT: o 45 GLN cc_start: 0.9042 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: p 14 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8511 (mtt180) REVERT: p 25 LYS cc_start: 0.8809 (tptt) cc_final: 0.8314 (ttpp) REVERT: p 28 ARG cc_start: 0.9134 (mtp180) cc_final: 0.8803 (mtt90) REVERT: L 25 ARG cc_start: 0.8302 (mtm-85) cc_final: 0.8039 (mtm-85) REVERT: 1 9 MET cc_start: 0.6510 (mtt) cc_final: 0.6112 (pp-130) REVERT: 1 78 GLU cc_start: 0.8526 (pt0) cc_final: 0.7622 (pp20) REVERT: 1 82 ASP cc_start: 0.9427 (OUTLIER) cc_final: 0.9099 (m-30) REVERT: 1 113 ARG cc_start: 0.8885 (tpp-160) cc_final: 0.8651 (tpp80) REVERT: 1 145 GLU cc_start: 0.8899 (tp30) cc_final: 0.8687 (tp30) REVERT: 1 165 ASP cc_start: 0.8696 (t0) cc_final: 0.8475 (t70) REVERT: 1 167 ASP cc_start: 0.8583 (p0) cc_final: 0.8347 (t0) REVERT: 1 192 ASP cc_start: 0.8794 (t0) cc_final: 0.8412 (t0) REVERT: 2 28 GLU cc_start: 0.8487 (pm20) cc_final: 0.7973 (pm20) REVERT: 2 86 LYS cc_start: 0.8479 (ttpp) cc_final: 0.8151 (tptm) REVERT: 2 105 GLU cc_start: 0.8651 (tt0) cc_final: 0.7914 (pm20) REVERT: 2 107 ARG cc_start: 0.8285 (ptp-110) cc_final: 0.8063 (ptp90) REVERT: 3 44 ARG cc_start: 0.8189 (mmt-90) cc_final: 0.7471 (mtp180) REVERT: 3 70 ARG cc_start: 0.8382 (ttm110) cc_final: 0.8068 (ttm-80) REVERT: 3 128 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7679 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8615 (mp0) REVERT: 3 172 GLU cc_start: 0.8962 (tp30) cc_final: 0.8522 (mm-30) REVERT: 3 177 LYS cc_start: 0.8388 (mtmt) cc_final: 0.7530 (tptt) REVERT: 3 179 GLU cc_start: 0.8832 (pt0) cc_final: 0.8538 (pp20) REVERT: 4 12 GLN cc_start: 0.8754 (tp40) cc_final: 0.8401 (tt0) REVERT: 4 29 ARG cc_start: 0.8791 (mtt-85) cc_final: 0.8531 (mtm-85) REVERT: 4 61 GLN cc_start: 0.9143 (tt0) cc_final: 0.8861 (mm110) REVERT: 4 152 MET cc_start: 0.9021 (mmt) cc_final: 0.8758 (mtp) REVERT: 4 157 ARG cc_start: 0.9366 (OUTLIER) cc_final: 0.8406 (ptm160) REVERT: 5 79 ARG cc_start: 0.7849 (mmt-90) cc_final: 0.7461 (ttp-110) REVERT: 6 48 GLU cc_start: 0.8453 (tt0) cc_final: 0.8228 (tm-30) REVERT: 6 74 GLU cc_start: 0.8204 (pt0) cc_final: 0.7700 (pm20) REVERT: 6 90 GLU cc_start: 0.8693 (mp0) cc_final: 0.8419 (pp20) REVERT: 6 92 ARG cc_start: 0.8306 (mmm160) cc_final: 0.7966 (mtp180) REVERT: 6 136 LYS cc_start: 0.8923 (tttm) cc_final: 0.8567 (tppt) REVERT: 6 144 MET cc_start: 0.8536 (tpp) cc_final: 0.8260 (tpp) REVERT: 6 148 ASN cc_start: 0.9046 (m110) cc_final: 0.8829 (m-40) REVERT: 7 31 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8647 (mtpm) REVERT: 7 50 LYS cc_start: 0.8806 (ttpt) cc_final: 0.8603 (ptmm) REVERT: 7 56 LYS cc_start: 0.8559 (mtmt) cc_final: 0.8134 (mttt) REVERT: 7 80 ARG cc_start: 0.9152 (OUTLIER) cc_final: 0.8583 (ptm-80) REVERT: 7 92 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8091 (mp) REVERT: 7 118 GLN cc_start: 0.8823 (tt0) cc_final: 0.8380 (mp10) REVERT: 8 22 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7637 (mttt) REVERT: 8 36 GLU cc_start: 0.9102 (mm-30) cc_final: 0.8719 (mm-30) REVERT: 8 61 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8187 (mp) REVERT: 8 88 MET cc_start: 0.7708 (ptt) cc_final: 0.7178 (mmp) REVERT: 8 120 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.7693 (ptmm) REVERT: 8 127 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8183 (p90) REVERT: 9 7 ARG cc_start: 0.8111 (mtt-85) cc_final: 0.7148 (mpt-90) REVERT: A 127 ARG cc_start: 0.8342 (mmm160) cc_final: 0.8018 (mmm160) REVERT: B 10 LYS cc_start: 0.8668 (ttpp) cc_final: 0.8442 (ptmt) REVERT: B 54 ARG cc_start: 0.8088 (ttp-170) cc_final: 0.7495 (tpt170) REVERT: B 56 ARG cc_start: 0.8965 (tpp-160) cc_final: 0.8614 (ttp80) REVERT: B 70 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7690 (mp0) REVERT: B 123 LYS cc_start: 0.8857 (mmtp) cc_final: 0.8606 (mmpt) REVERT: C 31 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8493 (mtmp) REVERT: C 92 ARG cc_start: 0.6481 (ttm-80) cc_final: 0.6020 (tpp-160) REVERT: C 109 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7905 (tpt-90) REVERT: C 113 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.5844 (ptp90) REVERT: E 77 ARG cc_start: 0.8796 (mtp180) cc_final: 0.8481 (mtp180) REVERT: G 48 ASP cc_start: 0.8124 (p0) cc_final: 0.7691 (p0) REVERT: G 65 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8385 (ptt180) REVERT: H 67 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8530 (mp) REVERT: I 61 PHE cc_start: 0.8479 (t80) cc_final: 0.8066 (t80) REVERT: I 81 ARG cc_start: 0.8504 (tpp80) cc_final: 0.6696 (pmt-80) REVERT: J 33 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8262 (ttmt) REVERT: K 33 ARG cc_start: 0.7808 (ttt180) cc_final: 0.7589 (ttp-170) REVERT: K 34 ARG cc_start: 0.7603 (ttt-90) cc_final: 0.6225 (mmp80) outliers start: 274 outliers final: 147 residues processed: 1167 average time/residue: 2.1221 time to fit residues: 3504.3975 Evaluate side-chains 1188 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1008 time to evaluate : 6.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 205 LEU Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 251 GLN Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 88 GLU Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 176 ASP Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 35 THR Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 121 GLU Chi-restraints excluded: chain Y residue 14 LYS Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 24 THR Chi-restraints excluded: chain Z residue 27 SER Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain c residue 110 ILE Chi-restraints excluded: chain d residue 33 ARG Chi-restraints excluded: chain d residue 87 SER Chi-restraints excluded: chain e residue 22 LEU Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 78 SER Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 68 LYS Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 45 GLN Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 64 LYS Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 106 THR Chi-restraints excluded: chain 1 residue 110 SER Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 213 TYR Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 187 SER Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 71 MET Chi-restraints excluded: chain 4 residue 90 THR Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 110 LYS Chi-restraints excluded: chain 7 residue 21 ASN Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 76 GLN Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 7 residue 89 LYS Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 92 LEU Chi-restraints excluded: chain 7 residue 94 LYS Chi-restraints excluded: chain 7 residue 101 ILE Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 65 ILE Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 22 THR Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain 9 residue 83 THR Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 941 optimal weight: 6.9990 chunk 110 optimal weight: 9.9990 chunk 556 optimal weight: 10.0000 chunk 712 optimal weight: 6.9990 chunk 552 optimal weight: 50.0000 chunk 821 optimal weight: 1.9990 chunk 545 optimal weight: 50.0000 chunk 972 optimal weight: 0.8980 chunk 608 optimal weight: 7.9990 chunk 592 optimal weight: 3.9990 chunk 448 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 154 ASN s 156 GLN Q 32 ASN Q 150 GLN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN W 128 ASN b 19 GLN c 7 GLN e 18 GLN i 49 ASN ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 18 HIS 1 178 ASN 2 139 GLN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 110 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 GLN E 38 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8773 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 156684 Z= 0.278 Angle : 0.636 12.362 234478 Z= 0.335 Chirality : 0.040 0.344 29976 Planarity : 0.005 0.112 12458 Dihedral : 23.386 179.525 78639 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.05 % Favored : 91.72 % Rotamer: Outliers : 5.28 % Allowed : 21.93 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.22 % 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: -1.33 (0.11), residues: 5614 helix: 0.53 (0.12), residues: 1825 sheet: -1.39 (0.15), residues: 1043 loop : -1.66 (0.11), residues: 2746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP P 213 HIS 0.011 0.001 HIS C 12 PHE 0.022 0.002 PHE A 52 TYR 0.021 0.002 TYR 7 128 ARG 0.010 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1284 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 1037 time to evaluate : 6.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 147 LYS cc_start: 0.8914 (mtpp) cc_final: 0.8617 (mttm) REVERT: P 199 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8589 (pm20) REVERT: P 203 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8152 (ptt180) REVERT: P 236 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7712 (mt-10) REVERT: P 239 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7897 (m110) REVERT: P 251 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7960 (tt0) REVERT: P 270 ARG cc_start: 0.8725 (mmm160) cc_final: 0.7390 (ttt-90) REVERT: Q 89 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8402 (tm-30) REVERT: Q 104 VAL cc_start: 0.8338 (m) cc_final: 0.8117 (t) REVERT: Q 199 SER cc_start: 0.8685 (OUTLIER) cc_final: 0.8330 (p) REVERT: R 22 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8421 (p0) REVERT: R 77 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.8259 (pt) REVERT: R 122 GLU cc_start: 0.9124 (tp30) cc_final: 0.8806 (pt0) REVERT: R 144 GLU cc_start: 0.9004 (tt0) cc_final: 0.8707 (mm-30) REVERT: R 155 GLU cc_start: 0.8469 (tp30) cc_final: 0.8171 (tm-30) REVERT: R 171 ASP cc_start: 0.8869 (OUTLIER) cc_final: 0.8609 (m-30) REVERT: R 184 ASP cc_start: 0.8824 (m-30) cc_final: 0.8594 (t0) REVERT: S 11 GLU cc_start: 0.8994 (mt-10) cc_final: 0.8716 (tp30) REVERT: S 19 GLU cc_start: 0.8850 (tm-30) cc_final: 0.8577 (tm-30) REVERT: S 23 ASN cc_start: 0.9017 (m110) cc_final: 0.8720 (m110) REVERT: S 30 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7633 (ptp-110) REVERT: S 56 ASP cc_start: 0.8645 (m-30) cc_final: 0.8114 (m-30) REVERT: S 78 LYS cc_start: 0.9088 (mttt) cc_final: 0.8833 (mttm) REVERT: S 94 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8609 (mm-30) REVERT: S 113 ASP cc_start: 0.8246 (m-30) cc_final: 0.7968 (t0) REVERT: S 120 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8722 (mtpp) REVERT: S 142 ASP cc_start: 0.8089 (t0) cc_final: 0.7784 (t70) REVERT: S 143 TYR cc_start: 0.8113 (t80) cc_final: 0.7839 (t80) REVERT: T 3 ARG cc_start: 0.8161 (mtm-85) cc_final: 0.7831 (ttm170) REVERT: T 106 SER cc_start: 0.9112 (m) cc_final: 0.8852 (t) REVERT: U 35 LYS cc_start: 0.8855 (mttt) cc_final: 0.8502 (mtpp) REVERT: V 117 MET cc_start: 0.1888 (mmm) cc_final: 0.1588 (mmm) REVERT: V 136 MET cc_start: 0.2383 (mtm) cc_final: 0.1990 (ptt) REVERT: W 1 MET cc_start: 0.8307 (ptp) cc_final: 0.7816 (pp-130) REVERT: W 108 MET cc_start: 0.8676 (mtt) cc_final: 0.8223 (mtt) REVERT: W 111 LYS cc_start: 0.8253 (pttt) cc_final: 0.7973 (mmtm) REVERT: X 53 LYS cc_start: 0.9127 (pttp) cc_final: 0.8635 (mmtp) REVERT: X 106 GLU cc_start: 0.8732 (mp0) cc_final: 0.8252 (mp0) REVERT: X 114 LYS cc_start: 0.9079 (tppp) cc_final: 0.8745 (tttt) REVERT: Y 55 MET cc_start: 0.8661 (tpt) cc_final: 0.8385 (tpt) REVERT: Y 91 ASP cc_start: 0.8623 (t0) cc_final: 0.8256 (p0) REVERT: Z 5 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8795 (mtpt) REVERT: Z 6 ARG cc_start: 0.8972 (ttp80) cc_final: 0.8319 (tmt-80) REVERT: Z 55 ARG cc_start: 0.8517 (tpp80) cc_final: 0.8211 (ttp-170) REVERT: Z 60 GLN cc_start: 0.8532 (pt0) cc_final: 0.8229 (pp30) REVERT: Z 127 LYS cc_start: 0.8655 (mtpp) cc_final: 0.8088 (tptt) REVERT: b 46 GLU cc_start: 0.8669 (tt0) cc_final: 0.8383 (mt-10) REVERT: b 56 LYS cc_start: 0.8890 (pmtt) cc_final: 0.8552 (tppt) REVERT: b 80 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8353 (mm-30) REVERT: c 7 GLN cc_start: 0.8956 (tt0) cc_final: 0.8365 (tp-100) REVERT: c 10 GLN cc_start: 0.8685 (pt0) cc_final: 0.8422 (mt0) REVERT: d 11 ARG cc_start: 0.8408 (tpt170) cc_final: 0.7531 (ttm170) REVERT: d 15 LYS cc_start: 0.8898 (ttmm) cc_final: 0.8623 (ttpt) REVERT: d 84 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8314 (mttt) REVERT: e 45 GLU cc_start: 0.8451 (pp20) cc_final: 0.8062 (pp20) REVERT: e 72 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8387 (m) REVERT: e 79 ARG cc_start: 0.8818 (OUTLIER) cc_final: 0.8271 (ptp-170) REVERT: f 4 ILE cc_start: 0.9108 (mp) cc_final: 0.8885 (mp) REVERT: g 76 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8434 (ttp80) REVERT: h 45 HIS cc_start: 0.8428 (OUTLIER) cc_final: 0.6701 (p90) REVERT: h 79 LYS cc_start: 0.8856 (mttm) cc_final: 0.8451 (mtpp) REVERT: i 1 MET cc_start: 0.7680 (ppp) cc_final: 0.7463 (pmm) REVERT: i 55 GLU cc_start: 0.9123 (mp0) cc_final: 0.8835 (pm20) REVERT: i 68 LYS cc_start: 0.8013 (OUTLIER) cc_final: 0.7809 (tppt) REVERT: j 25 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8427 (mmt90) REVERT: k 40 VAL cc_start: 0.8481 (OUTLIER) cc_final: 0.8264 (m) REVERT: k 43 GLU cc_start: 0.8083 (tt0) cc_final: 0.7593 (tm-30) REVERT: k 54 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8143 (tttm) REVERT: l 1 MET cc_start: 0.8066 (mtm) cc_final: 0.7537 (ptp) REVERT: m 5 ILE cc_start: 0.8347 (tt) cc_final: 0.8024 (pt) REVERT: m 31 ARG cc_start: 0.8816 (OUTLIER) cc_final: 0.7961 (ptp-170) REVERT: n 12 LYS cc_start: 0.8799 (tptt) cc_final: 0.8349 (mmtt) REVERT: n 15 MET cc_start: 0.8863 (mtt) cc_final: 0.8636 (mtp) REVERT: n 28 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8636 (pp) REVERT: o 35 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8547 (pt0) REVERT: p 14 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.8445 (mtt180) REVERT: p 25 LYS cc_start: 0.8770 (tptt) cc_final: 0.8267 (ttpp) REVERT: p 28 ARG cc_start: 0.9126 (mtp180) cc_final: 0.8797 (mtt90) REVERT: 1 9 MET cc_start: 0.6426 (mtt) cc_final: 0.6056 (pp-130) REVERT: 1 74 ARG cc_start: 0.7405 (mtm-85) cc_final: 0.7140 (mtm110) REVERT: 1 78 GLU cc_start: 0.8515 (pt0) cc_final: 0.7752 (pp20) REVERT: 1 82 ASP cc_start: 0.9425 (OUTLIER) cc_final: 0.9176 (m-30) REVERT: 1 113 ARG cc_start: 0.8897 (tpp-160) cc_final: 0.8691 (tpp80) REVERT: 1 167 ASP cc_start: 0.8554 (p0) cc_final: 0.8268 (m-30) REVERT: 1 192 ASP cc_start: 0.8771 (t0) cc_final: 0.8383 (t0) REVERT: 2 28 GLU cc_start: 0.8552 (pm20) cc_final: 0.8132 (pm20) REVERT: 2 86 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8121 (tptm) REVERT: 3 44 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7432 (mtp180) REVERT: 3 70 ARG cc_start: 0.8326 (ttm110) cc_final: 0.8065 (ttm-80) REVERT: 3 128 ARG cc_start: 0.8270 (mtp180) cc_final: 0.7650 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8608 (mp0) REVERT: 3 172 GLU cc_start: 0.8943 (tp30) cc_final: 0.8464 (mm-30) REVERT: 3 177 LYS cc_start: 0.8300 (mtmt) cc_final: 0.7455 (tptt) REVERT: 3 179 GLU cc_start: 0.8819 (pt0) cc_final: 0.8517 (pp20) REVERT: 4 12 GLN cc_start: 0.8778 (tp40) cc_final: 0.8402 (tt0) REVERT: 4 29 ARG cc_start: 0.8741 (mtt-85) cc_final: 0.8498 (mtm-85) REVERT: 4 61 GLN cc_start: 0.9126 (tt0) cc_final: 0.8848 (mm110) REVERT: 4 152 MET cc_start: 0.9009 (mmt) cc_final: 0.8740 (mtp) REVERT: 4 157 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8337 (ptm160) REVERT: 5 79 ARG cc_start: 0.7814 (mmt-90) cc_final: 0.7399 (ttp-170) REVERT: 6 48 GLU cc_start: 0.8457 (tt0) cc_final: 0.8061 (mp0) REVERT: 6 74 GLU cc_start: 0.8195 (pt0) cc_final: 0.7712 (pm20) REVERT: 6 90 GLU cc_start: 0.8683 (mp0) cc_final: 0.8412 (pp20) REVERT: 6 92 ARG cc_start: 0.8291 (mmm160) cc_final: 0.7940 (mtp180) REVERT: 6 136 LYS cc_start: 0.8919 (tttm) cc_final: 0.8551 (tppt) REVERT: 6 144 MET cc_start: 0.8539 (tpp) cc_final: 0.8265 (tpp) REVERT: 6 148 ASN cc_start: 0.9021 (m110) cc_final: 0.8806 (m-40) REVERT: 7 31 LYS cc_start: 0.8949 (mmmt) cc_final: 0.8612 (mtpm) REVERT: 7 50 LYS cc_start: 0.8787 (OUTLIER) cc_final: 0.8578 (ptmm) REVERT: 7 56 LYS cc_start: 0.8574 (mtmt) cc_final: 0.8229 (mttt) REVERT: 7 58 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8333 (tt0) REVERT: 7 80 ARG cc_start: 0.9124 (OUTLIER) cc_final: 0.8576 (ptm-80) REVERT: 7 118 GLN cc_start: 0.8819 (tt0) cc_final: 0.8399 (mp10) REVERT: 8 22 LYS cc_start: 0.8251 (mtmt) cc_final: 0.7605 (mttt) REVERT: 8 61 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.8130 (mp) REVERT: 8 88 MET cc_start: 0.7697 (ptt) cc_final: 0.7209 (mmp) REVERT: 8 120 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.7679 (ptmm) REVERT: 8 127 PHE cc_start: 0.8581 (OUTLIER) cc_final: 0.8074 (p90) REVERT: 9 7 ARG cc_start: 0.8131 (mtt-85) cc_final: 0.7420 (mpt-90) REVERT: A 127 ARG cc_start: 0.8174 (mmm160) cc_final: 0.7884 (mmm160) REVERT: B 10 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8363 (ptmt) REVERT: B 54 ARG cc_start: 0.8030 (ttp-170) cc_final: 0.7456 (tpt170) REVERT: B 56 ARG cc_start: 0.8895 (tpp-160) cc_final: 0.8533 (ttp80) REVERT: B 70 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7705 (mp0) REVERT: B 123 LYS cc_start: 0.8859 (mmtp) cc_final: 0.8640 (mmpt) REVERT: C 31 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8537 (mtmp) REVERT: C 92 ARG cc_start: 0.6360 (ttm-80) cc_final: 0.5990 (mtp85) REVERT: C 109 ARG cc_start: 0.8756 (OUTLIER) cc_final: 0.7874 (tpt-90) REVERT: C 113 ARG cc_start: 0.7747 (OUTLIER) cc_final: 0.5794 (ptp90) REVERT: D 4 GLN cc_start: 0.8665 (mm110) cc_final: 0.8438 (tp40) REVERT: E 77 ARG cc_start: 0.8795 (mtp180) cc_final: 0.8440 (mtp180) REVERT: F 77 GLU cc_start: 0.8881 (tt0) cc_final: 0.8193 (mp0) REVERT: G 48 ASP cc_start: 0.8167 (p0) cc_final: 0.7686 (p0) REVERT: G 65 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8356 (ptt180) REVERT: H 67 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8409 (mp) REVERT: I 61 PHE cc_start: 0.8490 (t80) cc_final: 0.8086 (t80) REVERT: I 81 ARG cc_start: 0.8509 (tpp80) cc_final: 0.6714 (pmt-80) REVERT: J 24 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8596 (mmt90) REVERT: J 33 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8233 (ttmt) REVERT: K 33 ARG cc_start: 0.7768 (ttt180) cc_final: 0.7515 (ttp-170) REVERT: K 34 ARG cc_start: 0.7373 (ttt-90) cc_final: 0.6139 (mmp80) outliers start: 247 outliers final: 145 residues processed: 1158 average time/residue: 2.1791 time to fit residues: 3577.8297 Evaluate side-chains 1181 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1001 time to evaluate : 6.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 251 GLN Chi-restraints excluded: chain P residue 255 LYS Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain W residue 57 LEU Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain X residue 111 LYS Chi-restraints excluded: chain X residue 117 SER Chi-restraints excluded: chain X residue 121 GLU Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain c residue 110 ILE Chi-restraints excluded: chain d residue 87 SER Chi-restraints excluded: chain e residue 34 GLU Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 7 LEU Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 78 SER Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 37 GLU Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 61 LYS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 68 LYS Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 40 VAL Chi-restraints excluded: chain k residue 54 LYS Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain m residue 31 ARG Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 64 LYS Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 213 TYR Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 71 MET Chi-restraints excluded: chain 4 residue 90 THR Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 147 MET Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 39 LEU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 110 LYS Chi-restraints excluded: chain 7 residue 21 ASN Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 76 GLN Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 7 residue 89 LYS Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 94 LYS Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 22 THR Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain 9 residue 83 THR Chi-restraints excluded: chain 9 residue 92 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 74 ASP Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 14 SER Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 601 optimal weight: 10.0000 chunk 388 optimal weight: 10.0000 chunk 580 optimal weight: 8.9990 chunk 292 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 188 optimal weight: 6.9990 chunk 618 optimal weight: 10.0000 chunk 662 optimal weight: 10.0000 chunk 480 optimal weight: 10.0000 chunk 90 optimal weight: 9.9990 chunk 764 optimal weight: 10.0000 overall best weight: 7.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 154 ASN s 156 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN b 19 GLN e 18 GLN i 49 ASN ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 177 ASN 2 139 GLN 3 152 GLN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 110 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 52 GLN D 60 GLN H 54 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 156684 Z= 0.509 Angle : 0.740 13.672 234478 Z= 0.384 Chirality : 0.047 0.401 29976 Planarity : 0.006 0.119 12458 Dihedral : 23.356 179.937 78639 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.84 % Favored : 90.86 % Rotamer: Outliers : 5.47 % Allowed : 21.72 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 5614 helix: 0.39 (0.12), residues: 1831 sheet: -1.40 (0.15), residues: 1046 loop : -1.70 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP P 213 HIS 0.012 0.002 HIS h 45 PHE 0.023 0.002 PHE C 63 TYR 0.025 0.002 TYR 7 128 ARG 0.015 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 256 poor density : 1012 time to evaluate : 6.164 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: P 199 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8601 (pm20) REVERT: P 203 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8226 (ptt180) REVERT: P 236 GLU cc_start: 0.7989 (mm-30) cc_final: 0.7769 (mt-10) REVERT: P 239 ASN cc_start: 0.8320 (OUTLIER) cc_final: 0.8027 (m110) REVERT: P 251 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: P 252 THR cc_start: 0.8233 (OUTLIER) cc_final: 0.7875 (p) REVERT: P 270 ARG cc_start: 0.8784 (mmm160) cc_final: 0.7424 (ttt-90) REVERT: Q 89 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8438 (tm-30) REVERT: Q 104 VAL cc_start: 0.8377 (m) cc_final: 0.8159 (t) REVERT: R 22 ASP cc_start: 0.8974 (OUTLIER) cc_final: 0.8444 (p0) REVERT: R 77 ILE cc_start: 0.8640 (OUTLIER) cc_final: 0.8297 (pt) REVERT: R 122 GLU cc_start: 0.9132 (tp30) cc_final: 0.8798 (pt0) REVERT: R 139 LYS cc_start: 0.9266 (tptp) cc_final: 0.8971 (ttpp) REVERT: R 144 GLU cc_start: 0.9015 (tt0) cc_final: 0.8605 (mm-30) REVERT: R 155 GLU cc_start: 0.8498 (tp30) cc_final: 0.8203 (tm-30) REVERT: R 171 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: R 184 ASP cc_start: 0.8881 (m-30) cc_final: 0.8621 (t0) REVERT: R 197 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: S 11 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8741 (tp30) REVERT: S 19 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8555 (tm-30) REVERT: S 23 ASN cc_start: 0.9086 (m110) cc_final: 0.8815 (m110) REVERT: S 30 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7749 (ptp-110) REVERT: S 78 LYS cc_start: 0.9055 (mttt) cc_final: 0.8803 (mttm) REVERT: S 113 ASP cc_start: 0.8059 (m-30) cc_final: 0.7794 (t0) REVERT: S 120 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8813 (mtpp) REVERT: S 130 MET cc_start: 0.9011 (ptm) cc_final: 0.8785 (ptp) REVERT: S 142 ASP cc_start: 0.8091 (t0) cc_final: 0.7782 (t70) REVERT: S 143 TYR cc_start: 0.8084 (t80) cc_final: 0.7797 (t80) REVERT: T 3 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7865 (ttm170) REVERT: T 99 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7768 (mmmm) REVERT: T 106 SER cc_start: 0.9078 (m) cc_final: 0.8806 (t) REVERT: U 35 LYS cc_start: 0.8903 (mttt) cc_final: 0.8537 (mtpp) REVERT: V 117 MET cc_start: 0.1990 (mmm) cc_final: 0.1704 (mmm) REVERT: V 136 MET cc_start: 0.2125 (mtm) cc_final: 0.1806 (ptt) REVERT: W 1 MET cc_start: 0.8224 (ptp) cc_final: 0.7798 (pp-130) REVERT: W 108 MET cc_start: 0.8755 (mtt) cc_final: 0.8241 (mtt) REVERT: X 53 LYS cc_start: 0.9179 (pttp) cc_final: 0.8672 (mmtp) REVERT: X 106 GLU cc_start: 0.8805 (mp0) cc_final: 0.8424 (mp0) REVERT: Y 55 MET cc_start: 0.8684 (tpt) cc_final: 0.8427 (tpt) REVERT: Y 91 ASP cc_start: 0.8605 (t0) cc_final: 0.8220 (p0) REVERT: Z 5 LYS cc_start: 0.9120 (OUTLIER) cc_final: 0.8833 (mtpt) REVERT: Z 6 ARG cc_start: 0.8893 (ttp80) cc_final: 0.8315 (tmt-80) REVERT: Z 55 ARG cc_start: 0.8546 (tpp80) cc_final: 0.8239 (ttp-170) REVERT: Z 60 GLN cc_start: 0.8520 (pt0) cc_final: 0.8198 (pp30) REVERT: Z 127 LYS cc_start: 0.8668 (mtpp) cc_final: 0.8104 (tptt) REVERT: b 46 GLU cc_start: 0.8637 (tt0) cc_final: 0.8365 (mt-10) REVERT: b 56 LYS cc_start: 0.8895 (pmtt) cc_final: 0.8595 (tppt) REVERT: c 7 GLN cc_start: 0.8963 (tt0) cc_final: 0.8350 (tp-100) REVERT: c 10 GLN cc_start: 0.8653 (pt0) cc_final: 0.8386 (mt0) REVERT: d 11 ARG cc_start: 0.8447 (tpt170) cc_final: 0.7609 (ttm170) REVERT: d 15 LYS cc_start: 0.8953 (ttmm) cc_final: 0.8716 (ttpt) REVERT: d 49 ASP cc_start: 0.8670 (m-30) cc_final: 0.8412 (m-30) REVERT: d 84 LYS cc_start: 0.8634 (ttpp) cc_final: 0.8330 (mttt) REVERT: e 45 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8103 (pp20) REVERT: e 72 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8357 (m) REVERT: e 79 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8387 (ptp-170) REVERT: f 4 ILE cc_start: 0.9156 (mp) cc_final: 0.8919 (mp) REVERT: f 82 MET cc_start: 0.8953 (mtp) cc_final: 0.8752 (mtm) REVERT: g 76 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8489 (ttp80) REVERT: h 45 HIS cc_start: 0.8488 (OUTLIER) cc_final: 0.6814 (p90) REVERT: h 79 LYS cc_start: 0.8869 (mttm) cc_final: 0.8456 (mtpp) REVERT: i 1 MET cc_start: 0.7808 (ppp) cc_final: 0.7587 (pmm) REVERT: i 55 GLU cc_start: 0.9172 (mp0) cc_final: 0.8849 (pm20) REVERT: i 68 LYS cc_start: 0.8108 (OUTLIER) cc_final: 0.7907 (tppt) REVERT: j 25 ARG cc_start: 0.9052 (OUTLIER) cc_final: 0.8420 (mmt90) REVERT: k 43 GLU cc_start: 0.8067 (tt0) cc_final: 0.7444 (tm-30) REVERT: l 1 MET cc_start: 0.8092 (mtm) cc_final: 0.7542 (ptp) REVERT: m 5 ILE cc_start: 0.8333 (tt) cc_final: 0.8014 (pt) REVERT: m 31 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8025 (ptp-170) REVERT: n 12 LYS cc_start: 0.8841 (tptt) cc_final: 0.8367 (mmtt) REVERT: n 15 MET cc_start: 0.8905 (mtt) cc_final: 0.8586 (mtp) REVERT: n 28 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8659 (pp) REVERT: p 14 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8506 (mtt180) REVERT: p 25 LYS cc_start: 0.8802 (tptt) cc_final: 0.8304 (ttpp) REVERT: p 28 ARG cc_start: 0.9144 (mtp180) cc_final: 0.8819 (mtt90) REVERT: L 25 ARG cc_start: 0.8338 (mtm-85) cc_final: 0.7827 (mtp85) REVERT: 1 9 MET cc_start: 0.6560 (mtt) cc_final: 0.6135 (ppp) REVERT: 1 56 GLU cc_start: 0.8495 (tp30) cc_final: 0.8278 (tp30) REVERT: 1 78 GLU cc_start: 0.8511 (pt0) cc_final: 0.7656 (pp20) REVERT: 1 82 ASP cc_start: 0.9408 (OUTLIER) cc_final: 0.9091 (m-30) REVERT: 1 113 ARG cc_start: 0.8887 (tpp-160) cc_final: 0.8660 (tpp80) REVERT: 1 167 ASP cc_start: 0.8547 (p0) cc_final: 0.8183 (m-30) REVERT: 2 3 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.8657 (pt0) REVERT: 2 28 GLU cc_start: 0.8474 (pm20) cc_final: 0.7957 (pm20) REVERT: 2 86 LYS cc_start: 0.8483 (ttpp) cc_final: 0.8152 (tptm) REVERT: 3 44 ARG cc_start: 0.8187 (mmt-90) cc_final: 0.7482 (mtp180) REVERT: 3 70 ARG cc_start: 0.8335 (ttm110) cc_final: 0.8048 (ttm-80) REVERT: 3 128 ARG cc_start: 0.8382 (mtp180) cc_final: 0.7757 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8628 (mp0) REVERT: 3 172 GLU cc_start: 0.8945 (tp30) cc_final: 0.8478 (mm-30) REVERT: 3 177 LYS cc_start: 0.8340 (mtmt) cc_final: 0.7465 (tptt) REVERT: 3 179 GLU cc_start: 0.8817 (pt0) cc_final: 0.8508 (pp20) REVERT: 4 12 GLN cc_start: 0.8715 (tp40) cc_final: 0.8371 (tt0) REVERT: 4 29 ARG cc_start: 0.8792 (mtt-85) cc_final: 0.8526 (mtm-85) REVERT: 4 61 GLN cc_start: 0.9137 (tt0) cc_final: 0.8857 (mm110) REVERT: 4 152 MET cc_start: 0.8991 (mmt) cc_final: 0.8731 (mtp) REVERT: 4 157 ARG cc_start: 0.9360 (OUTLIER) cc_final: 0.8471 (ptm160) REVERT: 5 79 ARG cc_start: 0.7902 (mmt-90) cc_final: 0.7460 (ttp-110) REVERT: 6 18 PHE cc_start: 0.8483 (m-80) cc_final: 0.8165 (m-80) REVERT: 6 48 GLU cc_start: 0.8456 (tt0) cc_final: 0.8056 (mp0) REVERT: 6 74 GLU cc_start: 0.8171 (pt0) cc_final: 0.7671 (pm20) REVERT: 6 90 GLU cc_start: 0.8679 (mp0) cc_final: 0.8423 (pp20) REVERT: 6 92 ARG cc_start: 0.8307 (mmm160) cc_final: 0.7976 (mtp180) REVERT: 6 99 LEU cc_start: 0.8947 (OUTLIER) cc_final: 0.8706 (mt) REVERT: 6 136 LYS cc_start: 0.8910 (tttm) cc_final: 0.8555 (tppt) REVERT: 6 144 MET cc_start: 0.8540 (tpp) cc_final: 0.8259 (tpp) REVERT: 6 148 ASN cc_start: 0.9043 (m110) cc_final: 0.8826 (m-40) REVERT: 7 31 LYS cc_start: 0.9038 (mmmt) cc_final: 0.8666 (mtpm) REVERT: 7 50 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8636 (ptmm) REVERT: 7 56 LYS cc_start: 0.8592 (mtmt) cc_final: 0.8229 (mttt) REVERT: 7 58 GLU cc_start: 0.8699 (mm-30) cc_final: 0.8335 (tt0) REVERT: 7 80 ARG cc_start: 0.9149 (OUTLIER) cc_final: 0.8576 (ptm-80) REVERT: 7 92 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8234 (mp) REVERT: 7 118 GLN cc_start: 0.8814 (tt0) cc_final: 0.8401 (mp10) REVERT: 8 22 LYS cc_start: 0.8235 (mtmt) cc_final: 0.7649 (mttt) REVERT: 8 36 GLU cc_start: 0.9110 (mm-30) cc_final: 0.8755 (mm-30) REVERT: 8 61 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8203 (mp) REVERT: 8 88 MET cc_start: 0.7642 (ptt) cc_final: 0.7169 (mmp) REVERT: 8 120 LYS cc_start: 0.9046 (OUTLIER) cc_final: 0.7616 (ptmm) REVERT: 8 127 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.8216 (p90) REVERT: 9 7 ARG cc_start: 0.7988 (mtt-85) cc_final: 0.7079 (mpt-90) REVERT: A 127 ARG cc_start: 0.8335 (mmm160) cc_final: 0.8030 (mmm160) REVERT: B 10 LYS cc_start: 0.8690 (ttpp) cc_final: 0.8470 (ptmt) REVERT: B 54 ARG cc_start: 0.8103 (ttp-170) cc_final: 0.7596 (tpt170) REVERT: B 56 ARG cc_start: 0.8959 (tpp-160) cc_final: 0.8542 (ttp80) REVERT: B 62 GLU cc_start: 0.9144 (tp30) cc_final: 0.8780 (tp30) REVERT: B 70 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7727 (mp0) REVERT: C 31 LYS cc_start: 0.8747 (OUTLIER) cc_final: 0.8486 (mtmp) REVERT: C 109 ARG cc_start: 0.8784 (OUTLIER) cc_final: 0.7908 (tpt-90) REVERT: C 113 ARG cc_start: 0.7802 (OUTLIER) cc_final: 0.5865 (ptp90) REVERT: D 4 GLN cc_start: 0.8771 (mm110) cc_final: 0.8547 (tp40) REVERT: D 41 ARG cc_start: 0.6473 (ptt90) cc_final: 0.5884 (ptm-80) REVERT: E 77 ARG cc_start: 0.8805 (mtp180) cc_final: 0.8462 (mtp180) REVERT: F 77 GLU cc_start: 0.8880 (tt0) cc_final: 0.8201 (mp0) REVERT: G 65 ARG cc_start: 0.8911 (OUTLIER) cc_final: 0.8390 (ptt180) REVERT: H 67 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8608 (mp) REVERT: I 61 PHE cc_start: 0.8492 (t80) cc_final: 0.8015 (t80) REVERT: I 81 ARG cc_start: 0.8526 (tpp80) cc_final: 0.6761 (pmt-80) REVERT: J 24 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8582 (mmt90) REVERT: J 33 LYS cc_start: 0.8768 (OUTLIER) cc_final: 0.8257 (ttmt) REVERT: K 33 ARG cc_start: 0.7916 (ttt180) cc_final: 0.7668 (ttp-170) REVERT: K 34 ARG cc_start: 0.7359 (ttt-90) cc_final: 0.6204 (mmp80) outliers start: 256 outliers final: 157 residues processed: 1143 average time/residue: 2.2365 time to fit residues: 3616.0209 Evaluate side-chains 1196 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1000 time to evaluate : 6.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 141 VAL Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 251 GLN Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 255 LYS Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain Y residue 46 VAL Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 24 THR Chi-restraints excluded: chain Z residue 27 SER Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain c residue 110 ILE Chi-restraints excluded: chain d residue 31 VAL Chi-restraints excluded: chain d residue 87 SER Chi-restraints excluded: chain e residue 34 GLU Chi-restraints excluded: chain e residue 45 GLU Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 78 SER Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 61 LYS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 4 ILE Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 68 LYS Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain l residue 6 LEU Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 31 ARG Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain o residue 25 LYS Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 64 LYS Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 213 TYR Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 3 GLN Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 2 residue 187 SER Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 71 MET Chi-restraints excluded: chain 4 residue 90 THR Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 110 LYS Chi-restraints excluded: chain 7 residue 21 ASN Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 76 GLN Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 7 residue 89 LYS Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 92 LEU Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 65 ILE Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 22 THR Chi-restraints excluded: chain 9 residue 83 THR Chi-restraints excluded: chain 9 residue 92 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 40 GLN Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 23 SER Chi-restraints excluded: chain J residue 24 ARG Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 36 TYR Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 884 optimal weight: 1.9990 chunk 931 optimal weight: 0.9990 chunk 850 optimal weight: 8.9990 chunk 906 optimal weight: 9.9990 chunk 545 optimal weight: 50.0000 chunk 394 optimal weight: 5.9990 chunk 711 optimal weight: 6.9990 chunk 278 optimal weight: 5.9990 chunk 818 optimal weight: 4.9990 chunk 857 optimal weight: 3.9990 chunk 903 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 154 ASN s 156 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN T 88 GLN W 128 ASN b 19 GLN e 18 GLN i 49 ASN ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 131 ASN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 110 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN D 60 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 156684 Z= 0.283 Angle : 0.628 12.516 234478 Z= 0.330 Chirality : 0.039 0.353 29976 Planarity : 0.005 0.113 12458 Dihedral : 23.333 179.193 78637 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.09 % Favored : 91.68 % Rotamer: Outliers : 4.66 % Allowed : 22.98 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.18 % 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: -1.26 (0.11), residues: 5614 helix: 0.60 (0.12), residues: 1824 sheet: -1.35 (0.15), residues: 1035 loop : -1.62 (0.11), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP P 213 HIS 0.013 0.001 HIS C 12 PHE 0.020 0.002 PHE C 63 TYR 0.023 0.002 TYR 7 128 ARG 0.010 0.001 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1254 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1036 time to evaluate : 6.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 147 LYS cc_start: 0.8911 (mtpp) cc_final: 0.8610 (mttm) REVERT: P 199 GLU cc_start: 0.8900 (mt-10) cc_final: 0.8555 (pm20) REVERT: P 203 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8140 (ptt-90) REVERT: P 236 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7672 (mt-10) REVERT: P 239 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7911 (m110) REVERT: P 251 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: P 252 THR cc_start: 0.8110 (OUTLIER) cc_final: 0.7809 (p) REVERT: P 270 ARG cc_start: 0.8744 (mmm160) cc_final: 0.7381 (ttt-90) REVERT: Q 104 VAL cc_start: 0.8303 (m) cc_final: 0.8095 (t) REVERT: Q 199 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8328 (p) REVERT: R 22 ASP cc_start: 0.8879 (OUTLIER) cc_final: 0.8422 (p0) REVERT: R 77 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8263 (pt) REVERT: R 122 GLU cc_start: 0.9133 (tp30) cc_final: 0.8803 (pt0) REVERT: R 144 GLU cc_start: 0.9001 (tt0) cc_final: 0.8590 (mm-30) REVERT: R 155 GLU cc_start: 0.8469 (tp30) cc_final: 0.8184 (tm-30) REVERT: R 171 ASP cc_start: 0.8860 (OUTLIER) cc_final: 0.8620 (m-30) REVERT: R 184 ASP cc_start: 0.8936 (m-30) cc_final: 0.8670 (t0) REVERT: R 197 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: S 11 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8742 (tp30) REVERT: S 19 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8557 (tm-30) REVERT: S 23 ASN cc_start: 0.9105 (m110) cc_final: 0.8832 (m110) REVERT: S 30 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7698 (ptp-110) REVERT: S 78 LYS cc_start: 0.9039 (mttt) cc_final: 0.8782 (mttm) REVERT: S 98 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8507 (mt-10) REVERT: S 113 ASP cc_start: 0.8085 (m-30) cc_final: 0.7825 (t0) REVERT: S 120 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8704 (mtpp) REVERT: S 142 ASP cc_start: 0.8120 (t0) cc_final: 0.7793 (t70) REVERT: S 143 TYR cc_start: 0.8099 (t80) cc_final: 0.7822 (t80) REVERT: T 3 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7833 (ttm170) REVERT: T 42 GLU cc_start: 0.8621 (tp30) cc_final: 0.8270 (mp0) REVERT: T 58 TYR cc_start: 0.8468 (m-80) cc_final: 0.8260 (m-80) REVERT: T 99 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7774 (mmmm) REVERT: T 106 SER cc_start: 0.9164 (m) cc_final: 0.8901 (t) REVERT: U 35 LYS cc_start: 0.8832 (mttt) cc_final: 0.8442 (mtpp) REVERT: V 117 MET cc_start: 0.1910 (mmm) cc_final: 0.1645 (mmm) REVERT: V 136 MET cc_start: 0.2120 (mtm) cc_final: 0.1785 (ptt) REVERT: W 1 MET cc_start: 0.8216 (ptp) cc_final: 0.7794 (pp-130) REVERT: W 111 LYS cc_start: 0.8250 (pttt) cc_final: 0.7967 (mmtm) REVERT: X 53 LYS cc_start: 0.9156 (pttp) cc_final: 0.8663 (mmtp) REVERT: X 106 GLU cc_start: 0.8647 (mp0) cc_final: 0.8216 (mp0) REVERT: Y 55 MET cc_start: 0.8669 (tpt) cc_final: 0.8389 (tpt) REVERT: Y 91 ASP cc_start: 0.8610 (t0) cc_final: 0.8233 (p0) REVERT: Z 2 LEU cc_start: 0.8675 (mp) cc_final: 0.8473 (mt) REVERT: Z 5 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8838 (mtpt) REVERT: Z 6 ARG cc_start: 0.8892 (ttp80) cc_final: 0.8420 (tmt-80) REVERT: Z 55 ARG cc_start: 0.8502 (tpp80) cc_final: 0.8186 (ttm110) REVERT: Z 60 GLN cc_start: 0.8447 (pt0) cc_final: 0.8138 (pp30) REVERT: Z 127 LYS cc_start: 0.8711 (mtpp) cc_final: 0.8118 (tptt) REVERT: b 46 GLU cc_start: 0.8616 (tt0) cc_final: 0.8344 (mt-10) REVERT: b 56 LYS cc_start: 0.8862 (pmtt) cc_final: 0.8568 (tppt) REVERT: b 102 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8014 (ptt90) REVERT: c 7 GLN cc_start: 0.8941 (tt0) cc_final: 0.8338 (tp-100) REVERT: c 10 GLN cc_start: 0.8678 (pt0) cc_final: 0.8400 (mt0) REVERT: d 11 ARG cc_start: 0.8396 (tpt170) cc_final: 0.7552 (ttm170) REVERT: d 15 LYS cc_start: 0.8890 (ttmm) cc_final: 0.8634 (ttpt) REVERT: d 49 ASP cc_start: 0.8563 (m-30) cc_final: 0.8310 (m-30) REVERT: d 84 LYS cc_start: 0.8622 (ttpp) cc_final: 0.8320 (mttt) REVERT: e 45 GLU cc_start: 0.8436 (pp20) cc_final: 0.7688 (pp20) REVERT: e 72 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8356 (m) REVERT: e 79 ARG cc_start: 0.8817 (OUTLIER) cc_final: 0.8278 (ptp-170) REVERT: f 4 ILE cc_start: 0.9118 (mp) cc_final: 0.8905 (mp) REVERT: g 76 ARG cc_start: 0.8638 (OUTLIER) cc_final: 0.8394 (ttp80) REVERT: h 45 HIS cc_start: 0.8361 (OUTLIER) cc_final: 0.6726 (p90) REVERT: h 79 LYS cc_start: 0.8854 (mttm) cc_final: 0.8467 (mtpp) REVERT: i 1 MET cc_start: 0.7736 (ppp) cc_final: 0.7502 (pmm) REVERT: i 55 GLU cc_start: 0.9185 (mp0) cc_final: 0.8883 (pm20) REVERT: j 25 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8429 (mmt90) REVERT: k 43 GLU cc_start: 0.8135 (tt0) cc_final: 0.7710 (tm-30) REVERT: l 1 MET cc_start: 0.7983 (mtm) cc_final: 0.7505 (ptp) REVERT: m 5 ILE cc_start: 0.8294 (tt) cc_final: 0.7968 (pt) REVERT: m 31 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7987 (ptp-170) REVERT: n 12 LYS cc_start: 0.8818 (tptt) cc_final: 0.8354 (mmtt) REVERT: n 15 MET cc_start: 0.8865 (mtt) cc_final: 0.8560 (mtp) REVERT: n 28 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8616 (pp) REVERT: o 35 GLU cc_start: 0.8957 (mt-10) cc_final: 0.8533 (pt0) REVERT: p 14 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8452 (mtt180) REVERT: p 25 LYS cc_start: 0.8763 (tptt) cc_final: 0.8276 (ttpp) REVERT: p 28 ARG cc_start: 0.9122 (mtp180) cc_final: 0.8791 (mtt90) REVERT: L 25 ARG cc_start: 0.8266 (mtm-85) cc_final: 0.8058 (mtm-85) REVERT: 1 78 GLU cc_start: 0.8513 (pt0) cc_final: 0.7657 (pp20) REVERT: 1 82 ASP cc_start: 0.9394 (OUTLIER) cc_final: 0.9103 (m-30) REVERT: 1 113 ARG cc_start: 0.8861 (tpp-160) cc_final: 0.8509 (tpp80) REVERT: 1 165 ASP cc_start: 0.8476 (t70) cc_final: 0.8061 (t0) REVERT: 1 167 ASP cc_start: 0.8535 (p0) cc_final: 0.8138 (m-30) REVERT: 1 192 ASP cc_start: 0.8796 (t0) cc_final: 0.8557 (t0) REVERT: 2 28 GLU cc_start: 0.8438 (pm20) cc_final: 0.7958 (pm20) REVERT: 2 86 LYS cc_start: 0.8464 (ttpp) cc_final: 0.8119 (tptm) REVERT: 2 105 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7918 (pm20) REVERT: 3 44 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7468 (mtp180) REVERT: 3 70 ARG cc_start: 0.8254 (ttm110) cc_final: 0.8027 (ttt-90) REVERT: 3 128 ARG cc_start: 0.8306 (mtp180) cc_final: 0.7692 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8613 (mp0) REVERT: 3 172 GLU cc_start: 0.8932 (tp30) cc_final: 0.8468 (mm-30) REVERT: 3 177 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7399 (tptt) REVERT: 3 179 GLU cc_start: 0.8800 (pt0) cc_final: 0.8487 (pp20) REVERT: 4 12 GLN cc_start: 0.8678 (tp40) cc_final: 0.8336 (tt0) REVERT: 4 29 ARG cc_start: 0.8696 (mtt-85) cc_final: 0.8446 (mtm-85) REVERT: 4 61 GLN cc_start: 0.9115 (tt0) cc_final: 0.8842 (mm110) REVERT: 4 152 MET cc_start: 0.8995 (mmt) cc_final: 0.8758 (mtp) REVERT: 4 157 ARG cc_start: 0.9342 (OUTLIER) cc_final: 0.7754 (ptm-80) REVERT: 5 79 ARG cc_start: 0.7872 (mmt-90) cc_final: 0.7411 (ttp-170) REVERT: 6 48 GLU cc_start: 0.8465 (tt0) cc_final: 0.8068 (mp0) REVERT: 6 58 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7277 (mm-30) REVERT: 6 74 GLU cc_start: 0.8218 (pt0) cc_final: 0.7762 (pm20) REVERT: 6 90 GLU cc_start: 0.8703 (mp0) cc_final: 0.8436 (pp20) REVERT: 6 92 ARG cc_start: 0.8253 (mmm160) cc_final: 0.7939 (mtp180) REVERT: 6 99 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8567 (mt) REVERT: 6 136 LYS cc_start: 0.8899 (tttm) cc_final: 0.8537 (tppt) REVERT: 6 144 MET cc_start: 0.8525 (tpp) cc_final: 0.8255 (tpp) REVERT: 6 148 ASN cc_start: 0.9021 (m110) cc_final: 0.8818 (m-40) REVERT: 7 31 LYS cc_start: 0.8956 (mmmt) cc_final: 0.8641 (mtpm) REVERT: 7 50 LYS cc_start: 0.8823 (OUTLIER) cc_final: 0.8605 (ptmm) REVERT: 7 56 LYS cc_start: 0.8543 (mtmt) cc_final: 0.8229 (mttt) REVERT: 7 58 GLU cc_start: 0.8697 (mm-30) cc_final: 0.8337 (tt0) REVERT: 7 80 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.8566 (ptm-80) REVERT: 7 92 LEU cc_start: 0.8562 (OUTLIER) cc_final: 0.8170 (mp) REVERT: 7 118 GLN cc_start: 0.8807 (tt0) cc_final: 0.8390 (mp10) REVERT: 8 22 LYS cc_start: 0.8292 (mtmt) cc_final: 0.7650 (mttt) REVERT: 8 61 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8134 (mp) REVERT: 8 88 MET cc_start: 0.7602 (ptt) cc_final: 0.7165 (mmp) REVERT: 8 120 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.7622 (ptmm) REVERT: 8 127 PHE cc_start: 0.8531 (OUTLIER) cc_final: 0.8025 (p90) REVERT: 9 7 ARG cc_start: 0.8114 (mtt-85) cc_final: 0.7490 (mpt-90) REVERT: 9 45 ARG cc_start: 0.7869 (tpp-160) cc_final: 0.6057 (ttp-170) REVERT: A 127 ARG cc_start: 0.8228 (mmm160) cc_final: 0.7937 (mmm160) REVERT: B 54 ARG cc_start: 0.8048 (ttp-170) cc_final: 0.7502 (tpt170) REVERT: B 56 ARG cc_start: 0.8937 (tpp-160) cc_final: 0.8582 (ttp80) REVERT: B 70 GLU cc_start: 0.8202 (mt-10) cc_final: 0.7711 (mp0) REVERT: C 31 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8542 (mtmp) REVERT: C 109 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7902 (tpt-90) REVERT: C 113 ARG cc_start: 0.7758 (OUTLIER) cc_final: 0.5977 (ptp90) REVERT: D 4 GLN cc_start: 0.8637 (mm110) cc_final: 0.8387 (tp40) REVERT: D 41 ARG cc_start: 0.6410 (ptt90) cc_final: 0.6054 (ptt90) REVERT: E 58 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8279 (ttt90) REVERT: E 77 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8458 (mtp180) REVERT: E 83 GLU cc_start: 0.9024 (mm-30) cc_final: 0.8784 (pp20) REVERT: F 77 GLU cc_start: 0.8833 (tt0) cc_final: 0.8157 (mp0) REVERT: G 65 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8390 (ptt180) REVERT: I 61 PHE cc_start: 0.8453 (t80) cc_final: 0.8006 (t80) REVERT: I 81 ARG cc_start: 0.8653 (tpp80) cc_final: 0.6783 (pmt-80) REVERT: J 33 LYS cc_start: 0.8737 (OUTLIER) cc_final: 0.8219 (ttmt) REVERT: K 33 ARG cc_start: 0.7937 (ttt180) cc_final: 0.7655 (ttp-170) REVERT: K 34 ARG cc_start: 0.7283 (ttt-90) cc_final: 0.6095 (mmp80) outliers start: 218 outliers final: 133 residues processed: 1143 average time/residue: 2.2025 time to fit residues: 3573.9320 Evaluate side-chains 1203 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1033 time to evaluate : 5.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 251 GLN Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 255 LYS Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain Z residue 5 LYS Chi-restraints excluded: chain Z residue 27 SER Chi-restraints excluded: chain Z residue 30 SER Chi-restraints excluded: chain a residue 6 SER Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 102 ARG Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain c residue 110 ILE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 61 LYS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 25 ARG Chi-restraints excluded: chain j residue 29 GLU Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain m residue 31 ARG Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 28 SER Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 213 TYR Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 105 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 11 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 71 MET Chi-restraints excluded: chain 4 residue 90 THR Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 52 ASN Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 110 LYS Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 7 residue 89 LYS Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 92 LEU Chi-restraints excluded: chain 7 residue 101 ILE Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 22 THR Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain 9 residue 83 THR Chi-restraints excluded: chain 9 residue 92 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 74 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 20 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain J residue 86 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 595 optimal weight: 8.9990 chunk 958 optimal weight: 0.9990 chunk 584 optimal weight: 7.9990 chunk 454 optimal weight: 8.9990 chunk 666 optimal weight: 10.0000 chunk 1005 optimal weight: 10.0000 chunk 925 optimal weight: 1.9990 chunk 800 optimal weight: 0.3980 chunk 83 optimal weight: 10.0000 chunk 618 optimal weight: 10.0000 chunk 490 optimal weight: 10.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 154 ASN s 156 GLN Q 32 ASN Q 150 GLN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 GLN e 18 GLN i 49 ASN 1 15 HIS 1 178 ASN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 110 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN D 60 GLN E 40 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 156684 Z= 0.309 Angle : 0.628 12.226 234478 Z= 0.328 Chirality : 0.039 0.346 29976 Planarity : 0.005 0.114 12458 Dihedral : 23.289 179.098 78637 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.50 % Favored : 91.31 % Rotamer: Outliers : 4.19 % Allowed : 23.88 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.18 % 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: -1.21 (0.11), residues: 5614 helix: 0.63 (0.12), residues: 1822 sheet: -1.29 (0.16), residues: 1045 loop : -1.59 (0.11), residues: 2747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP P 213 HIS 0.010 0.001 HIS C 12 PHE 0.019 0.002 PHE 1 69 TYR 0.023 0.002 TYR 7 128 ARG 0.010 0.001 ARG 4 93 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11228 Ramachandran restraints generated. 5614 Oldfield, 0 Emsley, 5614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1223 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1027 time to evaluate : 6.199 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 125 LYS cc_start: 0.8863 (ptpt) cc_final: 0.8571 (mttt) REVERT: P 199 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8562 (pm20) REVERT: P 203 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8133 (ptt180) REVERT: P 236 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7548 (mt-10) REVERT: P 239 ASN cc_start: 0.8209 (OUTLIER) cc_final: 0.7927 (m110) REVERT: P 251 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7931 (tt0) REVERT: P 252 THR cc_start: 0.8130 (OUTLIER) cc_final: 0.7852 (p) REVERT: P 270 ARG cc_start: 0.8759 (mmm160) cc_final: 0.7384 (ttt-90) REVERT: Q 104 VAL cc_start: 0.8325 (m) cc_final: 0.8120 (t) REVERT: Q 199 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8326 (p) REVERT: R 22 ASP cc_start: 0.8826 (OUTLIER) cc_final: 0.8385 (p0) REVERT: R 77 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8273 (pt) REVERT: R 122 GLU cc_start: 0.9131 (tp30) cc_final: 0.8792 (pt0) REVERT: R 139 LYS cc_start: 0.9236 (tptp) cc_final: 0.8957 (ttpp) REVERT: R 144 GLU cc_start: 0.9002 (tt0) cc_final: 0.8670 (pm20) REVERT: R 145 ASP cc_start: 0.8953 (t0) cc_final: 0.8753 (OUTLIER) REVERT: R 155 GLU cc_start: 0.8471 (tp30) cc_final: 0.8183 (tm-30) REVERT: R 171 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8623 (m-30) REVERT: R 184 ASP cc_start: 0.8901 (m-30) cc_final: 0.8669 (t0) REVERT: R 197 GLU cc_start: 0.8345 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: S 11 GLU cc_start: 0.8982 (mt-10) cc_final: 0.8735 (tp30) REVERT: S 19 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8572 (tm-30) REVERT: S 23 ASN cc_start: 0.9111 (m110) cc_final: 0.8835 (m110) REVERT: S 30 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7617 (ptp-110) REVERT: S 78 LYS cc_start: 0.9031 (mttt) cc_final: 0.8773 (mttm) REVERT: S 113 ASP cc_start: 0.8068 (m-30) cc_final: 0.7804 (t0) REVERT: S 120 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8713 (mtpp) REVERT: S 142 ASP cc_start: 0.8175 (t0) cc_final: 0.7892 (t70) REVERT: S 143 TYR cc_start: 0.8077 (t80) cc_final: 0.7833 (t80) REVERT: T 3 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7804 (ttm170) REVERT: T 99 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7500 (ttpp) REVERT: T 106 SER cc_start: 0.9155 (m) cc_final: 0.8891 (t) REVERT: U 35 LYS cc_start: 0.8781 (mttt) cc_final: 0.8436 (mtpp) REVERT: V 117 MET cc_start: 0.1396 (mmm) cc_final: 0.1164 (mmm) REVERT: V 136 MET cc_start: 0.2070 (mtm) cc_final: 0.1810 (ptt) REVERT: W 1 MET cc_start: 0.8321 (ptp) cc_final: 0.7831 (pp-130) REVERT: W 111 LYS cc_start: 0.8224 (pttt) cc_final: 0.7943 (mmtm) REVERT: X 53 LYS cc_start: 0.9152 (pttp) cc_final: 0.8662 (mmtp) REVERT: X 106 GLU cc_start: 0.8629 (mp0) cc_final: 0.8206 (mp0) REVERT: Y 55 MET cc_start: 0.8673 (tpt) cc_final: 0.8397 (tpt) REVERT: Y 91 ASP cc_start: 0.8591 (t0) cc_final: 0.8235 (p0) REVERT: Z 6 ARG cc_start: 0.8919 (ttp80) cc_final: 0.8343 (tmt-80) REVERT: Z 55 ARG cc_start: 0.8515 (tpp80) cc_final: 0.8209 (ttm110) REVERT: Z 60 GLN cc_start: 0.8401 (pt0) cc_final: 0.8112 (pp30) REVERT: Z 127 LYS cc_start: 0.8704 (mtpp) cc_final: 0.8123 (tptt) REVERT: b 46 GLU cc_start: 0.8610 (tt0) cc_final: 0.8333 (mt-10) REVERT: b 56 LYS cc_start: 0.8935 (pmtt) cc_final: 0.8591 (tppt) REVERT: b 80 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8316 (mm-30) REVERT: b 102 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.8015 (ptt90) REVERT: c 7 GLN cc_start: 0.8938 (tt0) cc_final: 0.8314 (tp-100) REVERT: c 10 GLN cc_start: 0.8607 (pt0) cc_final: 0.8351 (mt0) REVERT: d 11 ARG cc_start: 0.8390 (tpt170) cc_final: 0.7571 (ttm170) REVERT: d 84 LYS cc_start: 0.8623 (ttpp) cc_final: 0.8311 (mttt) REVERT: e 72 VAL cc_start: 0.8634 (OUTLIER) cc_final: 0.8329 (m) REVERT: e 79 ARG cc_start: 0.8830 (OUTLIER) cc_final: 0.8277 (ptp-170) REVERT: f 4 ILE cc_start: 0.9117 (mp) cc_final: 0.8905 (mp) REVERT: g 76 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8418 (ttp80) REVERT: h 45 HIS cc_start: 0.8337 (OUTLIER) cc_final: 0.6819 (p90) REVERT: h 79 LYS cc_start: 0.8856 (mttm) cc_final: 0.8510 (mtpp) REVERT: i 1 MET cc_start: 0.7799 (ppp) cc_final: 0.7534 (pmm) REVERT: i 55 GLU cc_start: 0.9178 (mp0) cc_final: 0.8869 (pm20) REVERT: k 43 GLU cc_start: 0.8085 (tt0) cc_final: 0.7666 (tm-30) REVERT: l 1 MET cc_start: 0.7980 (mtm) cc_final: 0.7507 (ptp) REVERT: m 5 ILE cc_start: 0.8314 (tt) cc_final: 0.8003 (pt) REVERT: m 31 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8020 (ptp-170) REVERT: n 12 LYS cc_start: 0.8817 (tptt) cc_final: 0.8353 (mmtt) REVERT: n 15 MET cc_start: 0.8873 (mtt) cc_final: 0.8570 (mtp) REVERT: n 28 LEU cc_start: 0.8866 (OUTLIER) cc_final: 0.8454 (pp) REVERT: o 35 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8548 (pt0) REVERT: p 14 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8454 (mtt180) REVERT: p 25 LYS cc_start: 0.8766 (tptt) cc_final: 0.8286 (ttpp) REVERT: p 28 ARG cc_start: 0.9110 (mtp180) cc_final: 0.8781 (mtt90) REVERT: r 15 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8499 (tttp) REVERT: L 25 ARG cc_start: 0.8249 (mtm-85) cc_final: 0.7810 (mtp85) REVERT: 1 74 ARG cc_start: 0.7239 (mtm-85) cc_final: 0.7020 (mtm110) REVERT: 1 78 GLU cc_start: 0.8542 (pt0) cc_final: 0.7752 (pp20) REVERT: 1 82 ASP cc_start: 0.9407 (OUTLIER) cc_final: 0.9129 (m-30) REVERT: 1 165 ASP cc_start: 0.8465 (t70) cc_final: 0.8044 (t0) REVERT: 1 167 ASP cc_start: 0.8483 (p0) cc_final: 0.8057 (m-30) REVERT: 1 188 ASP cc_start: 0.8538 (t0) cc_final: 0.8337 (m-30) REVERT: 1 192 ASP cc_start: 0.8810 (t0) cc_final: 0.8578 (t0) REVERT: 1 199 VAL cc_start: 0.9051 (OUTLIER) cc_final: 0.8799 (t) REVERT: 2 28 GLU cc_start: 0.8432 (pm20) cc_final: 0.7951 (pm20) REVERT: 2 86 LYS cc_start: 0.8455 (ttpp) cc_final: 0.8103 (tptm) REVERT: 2 105 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8107 (pm20) REVERT: 2 107 ARG cc_start: 0.8157 (ptp-110) cc_final: 0.7502 (mmm-85) REVERT: 3 44 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7476 (mtp180) REVERT: 3 128 ARG cc_start: 0.8350 (mtp180) cc_final: 0.7796 (mtp-110) REVERT: 3 147 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8626 (mp0) REVERT: 3 172 GLU cc_start: 0.8945 (tp30) cc_final: 0.8480 (mm-30) REVERT: 3 177 LYS cc_start: 0.8253 (mtmt) cc_final: 0.7357 (tptt) REVERT: 3 179 GLU cc_start: 0.8807 (pt0) cc_final: 0.8492 (pp20) REVERT: 4 12 GLN cc_start: 0.8642 (tp40) cc_final: 0.8289 (tt0) REVERT: 4 29 ARG cc_start: 0.8687 (mtt-85) cc_final: 0.8442 (mtm-85) REVERT: 4 61 GLN cc_start: 0.9090 (tt0) cc_final: 0.8716 (tp-100) REVERT: 4 152 MET cc_start: 0.8988 (mmt) cc_final: 0.8761 (mtp) REVERT: 4 157 ARG cc_start: 0.9331 (OUTLIER) cc_final: 0.7776 (ptm-80) REVERT: 5 79 ARG cc_start: 0.7867 (mmt-90) cc_final: 0.7417 (ttp-170) REVERT: 6 48 GLU cc_start: 0.8457 (tt0) cc_final: 0.8077 (mp0) REVERT: 6 74 GLU cc_start: 0.8214 (pt0) cc_final: 0.7740 (pm20) REVERT: 6 90 GLU cc_start: 0.8693 (mp0) cc_final: 0.8437 (pp20) REVERT: 6 92 ARG cc_start: 0.8272 (mmm160) cc_final: 0.7975 (mtp180) REVERT: 6 99 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8585 (mt) REVERT: 6 136 LYS cc_start: 0.8890 (tttm) cc_final: 0.8517 (tppt) REVERT: 6 144 MET cc_start: 0.8526 (tpp) cc_final: 0.8274 (tpp) REVERT: 6 148 ASN cc_start: 0.9022 (m110) cc_final: 0.8814 (m-40) REVERT: 7 31 LYS cc_start: 0.8967 (mmmt) cc_final: 0.8642 (mtpm) REVERT: 7 50 LYS cc_start: 0.8836 (OUTLIER) cc_final: 0.8616 (ptmm) REVERT: 7 56 LYS cc_start: 0.8496 (mtmt) cc_final: 0.8233 (mttt) REVERT: 7 58 GLU cc_start: 0.8701 (mm-30) cc_final: 0.8340 (tt0) REVERT: 7 80 ARG cc_start: 0.9159 (OUTLIER) cc_final: 0.8619 (ptm-80) REVERT: 7 92 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8209 (mp) REVERT: 7 118 GLN cc_start: 0.8803 (tt0) cc_final: 0.8363 (mp10) REVERT: 8 22 LYS cc_start: 0.8272 (mtmt) cc_final: 0.7642 (mtpp) REVERT: 8 45 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7653 (tpp80) REVERT: 8 61 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8135 (mp) REVERT: 8 88 MET cc_start: 0.7570 (ptt) cc_final: 0.7170 (mmp) REVERT: 8 120 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.7603 (ptmm) REVERT: 8 127 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7987 (p90) REVERT: 9 7 ARG cc_start: 0.8057 (mtt-85) cc_final: 0.7479 (mpt-90) REVERT: 9 45 ARG cc_start: 0.7855 (tpp-160) cc_final: 0.6051 (ttp-170) REVERT: A 127 ARG cc_start: 0.8224 (mmm160) cc_final: 0.7972 (mmm160) REVERT: B 54 ARG cc_start: 0.8065 (ttp-170) cc_final: 0.7520 (tpt170) REVERT: B 56 ARG cc_start: 0.8931 (tpp-160) cc_final: 0.8577 (ttp80) REVERT: B 70 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7702 (mp0) REVERT: C 31 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8466 (mtmp) REVERT: C 109 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7903 (tpt-90) REVERT: C 113 ARG cc_start: 0.7792 (OUTLIER) cc_final: 0.6140 (ptp90) REVERT: D 4 GLN cc_start: 0.8628 (mm110) cc_final: 0.8381 (tp40) REVERT: E 58 ARG cc_start: 0.8531 (ttt-90) cc_final: 0.8117 (ttm110) REVERT: E 77 ARG cc_start: 0.8817 (mtp180) cc_final: 0.8475 (mtp180) REVERT: E 83 GLU cc_start: 0.9079 (mm-30) cc_final: 0.8806 (pp20) REVERT: F 77 GLU cc_start: 0.8849 (tt0) cc_final: 0.8074 (mp0) REVERT: G 48 ASP cc_start: 0.8506 (p0) cc_final: 0.8172 (p0) REVERT: G 65 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8327 (ptt180) REVERT: I 21 LYS cc_start: 0.8350 (mttt) cc_final: 0.8001 (mppt) REVERT: I 81 ARG cc_start: 0.8654 (tpp80) cc_final: 0.6795 (pmt-80) REVERT: J 33 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8208 (ttmt) REVERT: K 33 ARG cc_start: 0.7831 (ttt180) cc_final: 0.7553 (ttp-170) REVERT: K 34 ARG cc_start: 0.7264 (ttt-90) cc_final: 0.6102 (mmp80) outliers start: 196 outliers final: 131 residues processed: 1124 average time/residue: 2.2053 time to fit residues: 3519.7010 Evaluate side-chains 1176 residues out of total 4681 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1009 time to evaluate : 6.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 130 THR Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 165 VAL Chi-restraints excluded: chain P residue 183 LYS Chi-restraints excluded: chain P residue 203 ARG Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 251 GLN Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 255 LYS Chi-restraints excluded: chain Q residue 96 ILE Chi-restraints excluded: chain Q residue 105 LYS Chi-restraints excluded: chain Q residue 139 SER Chi-restraints excluded: chain Q residue 177 VAL Chi-restraints excluded: chain Q residue 199 SER Chi-restraints excluded: chain R residue 22 ASP Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 77 ILE Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain R residue 171 ASP Chi-restraints excluded: chain R residue 197 GLU Chi-restraints excluded: chain S residue 24 SER Chi-restraints excluded: chain S residue 30 ARG Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain S residue 68 THR Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 101 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 120 LYS Chi-restraints excluded: chain S residue 153 ASP Chi-restraints excluded: chain T residue 99 LYS Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain W residue 131 ASN Chi-restraints excluded: chain X residue 20 MET Chi-restraints excluded: chain X residue 97 THR Chi-restraints excluded: chain Y residue 14 LYS Chi-restraints excluded: chain Z residue 27 SER Chi-restraints excluded: chain a residue 36 THR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 19 GLN Chi-restraints excluded: chain b residue 20 GLU Chi-restraints excluded: chain b residue 45 SER Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 52 SER Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 102 ARG Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 73 VAL Chi-restraints excluded: chain c residue 85 SER Chi-restraints excluded: chain c residue 110 ILE Chi-restraints excluded: chain e residue 72 VAL Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 96 ILE Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 32 LEU Chi-restraints excluded: chain g residue 50 LEU Chi-restraints excluded: chain g residue 70 HIS Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 28 VAL Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain h residue 81 ASP Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 25 LYS Chi-restraints excluded: chain i residue 40 ILE Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 43 THR Chi-restraints excluded: chain j residue 62 LYS Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 81 SER Chi-restraints excluded: chain k residue 14 THR Chi-restraints excluded: chain k residue 33 LEU Chi-restraints excluded: chain k residue 35 SER Chi-restraints excluded: chain k residue 59 ILE Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain m residue 31 ARG Chi-restraints excluded: chain n residue 25 VAL Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 42 LEU Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain L residue 27 THR Chi-restraints excluded: chain 1 residue 31 ILE Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 82 ASP Chi-restraints excluded: chain 1 residue 87 CYS Chi-restraints excluded: chain 1 residue 157 LEU Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 213 TYR Chi-restraints excluded: chain 1 residue 221 VAL Chi-restraints excluded: chain 2 residue 94 ILE Chi-restraints excluded: chain 2 residue 105 GLU Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 29 ASP Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 71 MET Chi-restraints excluded: chain 4 residue 90 THR Chi-restraints excluded: chain 4 residue 114 VAL Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 54 LEU Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 89 VAL Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 99 LEU Chi-restraints excluded: chain 6 residue 110 LYS Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 7 residue 51 VAL Chi-restraints excluded: chain 7 residue 61 LEU Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 7 residue 89 LYS Chi-restraints excluded: chain 7 residue 90 ASP Chi-restraints excluded: chain 7 residue 92 LEU Chi-restraints excluded: chain 8 residue 45 ARG Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 111 VAL Chi-restraints excluded: chain 8 residue 118 LEU Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 22 THR Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain 9 residue 83 THR Chi-restraints excluded: chain 9 residue 92 LEU Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 41 THR Chi-restraints excluded: chain B residue 109 ASP Chi-restraints excluded: chain B residue 115 SER Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 25 VAL Chi-restraints excluded: chain C residue 31 LYS Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 109 ARG Chi-restraints excluded: chain C residue 113 ARG Chi-restraints excluded: chain D residue 20 TYR Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain F residue 19 VAL Chi-restraints excluded: chain F residue 42 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain G residue 51 ASN Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain J residue 33 LYS Chi-restraints excluded: chain J residue 54 MET Chi-restraints excluded: chain J residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1009 random chunks: chunk 635 optimal weight: 10.0000 chunk 852 optimal weight: 0.9980 chunk 245 optimal weight: 6.9990 chunk 738 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 222 optimal weight: 7.9990 chunk 801 optimal weight: 9.9990 chunk 335 optimal weight: 10.0000 chunk 823 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 147 optimal weight: 0.7980 overall best weight: 4.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 154 ASN s 156 GLN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN e 18 GLN i 49 ASN 4 77 ASN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 110 GLN ** A 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 105 ASN D 60 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.131236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.097005 restraints weight = 190798.714| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.93 r_work: 0.2977 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2851 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2851 r_free = 0.2851 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 156684 Z= 0.314 Angle : 0.630 11.669 234478 Z= 0.329 Chirality : 0.040 0.351 29976 Planarity : 0.005 0.114 12458 Dihedral : 23.281 179.210 78637 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.20 % Allowed : 8.07 % Favored : 91.73 % Rotamer: Outliers : 4.15 % Allowed : 24.13 % Favored : 71.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.52 % Twisted General : 0.16 % 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: -1.18 (0.11), residues: 5614 helix: 0.68 (0.12), residues: 1817 sheet: -1.25 (0.15), residues: 1067 loop : -1.59 (0.12), residues: 2730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP P 213 HIS 0.008 0.001 HIS h 45 PHE 0.026 0.002 PHE 6 62 TYR 0.021 0.002 TYR 7 128 ARG 0.010 0.001 ARG 4 93 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 51655.45 seconds wall clock time: 893 minutes 35.11 seconds (53615.11 seconds total)