Starting phenix.real_space_refine on Mon Mar 25 05:10:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgn_13956/03_2024/7qgn_13956.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgn_13956/03_2024/7qgn_13956.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.37 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgn_13956/03_2024/7qgn_13956.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgn_13956/03_2024/7qgn_13956.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgn_13956/03_2024/7qgn_13956.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgn_13956/03_2024/7qgn_13956.pdb" } resolution = 3.37 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= 0.020 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1561 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 4696 5.49 5 Mg 2 5.21 5 S 154 5.16 5 C 74102 2.51 5 N 27425 2.21 5 O 40926 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 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 GLU 53": "OE1" <-> "OE2" Residue "U GLU 127": "OE1" <-> "OE2" Residue "V TYR 8": "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 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 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 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 "j PHE 45": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k ARG 11": "NH1" <-> "NH2" Residue "k ARG 18": "NH1" <-> "NH2" 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 "C ARG 7": "NH1" <-> "NH2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C ARG 162": "NH1" <-> "NH2" Residue "2 PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 131": "NH1" <-> "NH2" Residue "8 PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 ARG 124": "NH1" <-> "NH2" Residue "E ARG 56": "NH1" <-> "NH2" Residue "I PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 28": "NH1" <-> "NH2" Residue "I PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 38": "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: 147306 Number of models: 1 Model: "" Number of chains: 59 Chain: "A" Number of atoms: 1561 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1561 Classifications: {'RNA': 73} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59} Chain: "B" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 194 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 131 Unresolved non-hydrogen angles: 159 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 2, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 61 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: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} 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': 213, 'rna2p_pyr': 118, 'rna3p_pur': 1459, 'rna3p_pyr': 1107} Link IDs: {'rna2p': 331, 'rna3p': 2565} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 2897, 62195 Classifications: {'RNA': 2897} Modifications used: {'rna2p_pur': 213, 'rna2p_pyr': 117, 'rna3p_pur': 1459, 'rna3p_pyr': 1108} Link IDs: {'rna2p': 330, 'rna3p': 2566} Chain breaks: 1 bond proxies already assigned to first conformer: 69636 Chain: "L" Number of atoms: 419 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 419 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "C" Number of atoms: 1027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1027 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 131} Chain breaks: 1 Chain: "0" Number of atoms: 32873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1532, 32873 Classifications: {'RNA': 1532} Modifications used: {'rna2p_pur': 87, 'rna2p_pyr': 60, 'rna3p_pur': 786, 'rna3p_pyr': 599} Link IDs: {'rna2p': 147, 'rna3p': 1384} 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: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} Chain breaks: 1 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "t" 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: "u" 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: "v" 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: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' K': 1, ' MG': 2} Classifications: {'undetermined': 3, 'water': 9} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A U N2506 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U N2506 " occ=0.50 residue: pdb=" O HOH A 203 " occ=0.00 Time building chain proxies: 78.52, per 1000 atoms: 0.53 Number of scatterers: 147306 At special positions: 0 Unit cell: (270.045, 273.222, 271.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 154 16.00 P 4696 15.00 Mg 2 11.99 O 40926 8.00 N 27425 7.00 C 74102 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 Atom "ATOM 72473 O4' A N1876 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 60.42 Conformation dependent library (CDL) restraints added in 7.5 seconds 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10986 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 77 sheets defined 33.9% alpha, 17.8% beta 1617 base pairs and 2611 stacking pairs defined. Time for finding SS restraints: 66.49 Creating SS restraints... Processing helix chain 'B' and resid 8 through 19 Processing helix chain 's' and resid 121 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: 3.615A 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: 3.643A 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 41 through 72 removed outlier: 3.663A pdb=" N ARG U 50 " --> pdb=" O PHE U 46 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG U 51 " --> pdb=" O PHE U 47 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA U 56 " --> pdb=" O ALA U 52 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 103 removed outlier: 3.759A pdb=" N ILE U 99 " --> pdb=" O GLY U 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP U 101 " --> pdb=" O ARG U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 113 No H-bonds generated for 'chain 'U' and resid 111 through 113' Processing helix chain 'V' and resid 24 through 29 Processing helix chain 'V' and resid 35 through 39 removed outlier: 3.678A 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: 3.951A 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: 3.702A 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: 4.299A 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: 4.881A 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: 4.991A pdb=" N ARG b 13 " --> pdb=" O ARG b 9 " (cutoff:3.500A) removed outlier: 5.234A 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: 4.481A pdb=" N GLN d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) removed outlier: 4.498A 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: 3.984A 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: 3.689A 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: 4.160A 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: 3.641A 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 'C' and resid 5 through 13 Processing helix chain 'C' and resid 22 through 30 removed outlier: 5.030A pdb=" N ALA C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 58 Processing helix chain 'C' and resid 181 through 197 removed outlier: 4.060A pdb=" N ASN C 188 " --> pdb=" O LYS C 184 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) 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: 3.830A 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: 3.627A pdb=" N ARG 1 222 " --> pdb=" O ALA 1 218 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 12 removed outlier: 3.710A 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: 3.594A 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: 3.988A pdb=" N LEU 3 11 " --> pdb=" O PRO 3 7 " (cutoff:3.500A) removed outlier: 3.506A 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: 4.039A 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: 3.816A 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: 3.646A 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: 3.667A 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: 3.804A 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: 3.758A 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 'D' and resid 59 through 72 Processing helix chain 'D' and resid 74 through 78 removed outlier: 3.642A pdb=" N GLY D 78 " --> pdb=" O LYS D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 101 Processing helix chain 'E' and resid 3 through 10 Processing helix chain 'E' and resid 23 through 27 removed outlier: 3.849A pdb=" N CYS E 27 " --> pdb=" O LEU E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.527A pdb=" N LYS E 116 " --> pdb=" O ALA E 113 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY E 118 " --> pdb=" O SER E 115 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 19 Processing helix chain 'F' and resid 20 through 22 No H-bonds generated for 'chain 'F' and resid 20 through 22' Processing helix chain 'F' and resid 27 through 37 Processing helix chain 'F' and resid 49 through 61 Processing helix chain 'F' and resid 65 through 84 Processing helix chain 'F' and resid 85 through 94 removed outlier: 3.586A pdb=" N GLY F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 20 removed outlier: 3.713A pdb=" N LYS G 7 " --> pdb=" O LYS G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 31 removed outlier: 4.343A pdb=" N LYS G 28 " --> pdb=" O ARG G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 43 through 48 Processing helix chain 'G' and resid 56 through 60 removed outlier: 3.947A pdb=" N GLN G 60 " --> pdb=" O PRO G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 91 Processing helix chain 'H' and resid 4 through 16 Processing helix chain 'H' and resid 24 through 45 removed outlier: 4.089A pdb=" N GLU H 45 " --> pdb=" O GLY H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 72 Processing helix chain 'H' and resid 74 through 86 Processing helix chain 'I' and resid 53 through 64 Processing helix chain 'I' and resid 68 through 76 Processing helix chain 'J' and resid 49 through 52 removed outlier: 4.553A pdb=" N GLU J 52 " --> pdb=" O GLU J 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 49 through 52' Processing helix chain 'K' and resid 25 through 32 Processing helix chain 'K' and resid 41 through 46 Processing helix chain 'K' and resid 48 through 65 Processing helix chain 't' and resid 12 through 25 Processing helix chain 't' and resid 41 through 45 removed outlier: 3.574A pdb=" N ILE t 45 " --> pdb=" O PRO t 42 " (cutoff:3.500A) Processing helix chain 't' and resid 63 through 67 removed outlier: 3.955A pdb=" N VAL t 67 " --> pdb=" O ASP t 64 " (cutoff:3.500A) Processing helix chain 't' and resid 71 through 75 Processing helix chain 'u' and resid 6 through 39 removed outlier: 3.654A pdb=" N ARG u 10 " --> pdb=" O SER u 6 " (cutoff:3.500A) Processing helix chain 'u' and resid 43 through 65 removed outlier: 3.710A pdb=" N ALA u 47 " --> pdb=" O ASP u 43 " (cutoff:3.500A) Proline residue: u 56 - end of helix removed outlier: 3.517A pdb=" N GLY u 65 " --> pdb=" O GLN u 61 " (cutoff:3.500A) Processing helix chain 'u' and resid 69 through 87 Processing helix chain 'v' and resid 27 through 32 removed outlier: 3.771A pdb=" N VAL v 32 " --> pdb=" O VAL v 28 " (cutoff:3.500A) Processing helix chain 'v' 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: 5.599A 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: 6.195A pdb=" N THR P 173 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 6.553A 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: 6.540A pdb=" N GLU Q 28 " --> pdb=" O LYS Q 8 " (cutoff:3.500A) removed outlier: 3.609A 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: 6.594A pdb=" N ALA Q 47 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N VAL Q 37 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) removed outlier: 6.494A 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 'U' and resid 77 through 82 removed outlier: 7.207A pdb=" N VAL U 78 " --> pdb=" O ASN U 145 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL U 147 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE U 80 " --> pdb=" O VAL U 147 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL U 142 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL U 130 " --> pdb=" O VAL U 142 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER U 131 " --> pdb=" O ARG U 116 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'V' and resid 99 through 102 removed outlier: 6.726A pdb=" N GLY V 99 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N GLU V 141 " --> pdb=" O GLY V 99 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ILE V 101 " --> pdb=" O GLU V 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, 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: 6.361A pdb=" N VAL W 18 " --> pdb=" O LEU W 57 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'W' and resid 73 through 77 Processing sheet with id=AC4, first strand: chain 'X' and resid 7 through 10 removed outlier: 3.994A pdb=" N VAL X 10 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 6.523A 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: 5.724A pdb=" N VAL X 24 " --> pdb=" O ILE X 38 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ILE X 38 " --> pdb=" O VAL X 24 " (cutoff:3.500A) removed outlier: 5.591A pdb=" N VAL X 62 " --> pdb=" O VAL X 85 " (cutoff:3.500A) removed outlier: 6.310A 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: 6.542A pdb=" N ASN X 9 " --> pdb=" O CYS X 84 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 9.054A 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: 5.578A pdb=" N ILE c 84 " --> pdb=" O LYS c 29 " (cutoff:3.500A) removed outlier: 7.936A 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=AC6, 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=AC7, first strand: chain 'Z' and resid 62 through 65 removed outlier: 6.459A 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: 6.673A pdb=" N PHE Z 31 " --> pdb=" O GLU Z 104 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Z' and resid 40 through 42 removed outlier: 5.499A 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=AC9, first strand: chain 'a' and resid 33 through 37 removed outlier: 5.887A pdb=" N MET a 110 " --> pdb=" O CYS a 100 " (cutoff:3.500A) Processing sheet with id=AD1, 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: 4.567A 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: 4.697A pdb=" N SER b 52 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE b 35 " --> pdb=" O SER b 52 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'c' and resid 90 through 91 removed outlier: 4.217A pdb=" N LYS c 111 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing sheet with id=AD3, 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: 6.024A pdb=" N VAL e 4 " --> pdb=" O LEU e 39 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'e' and resid 19 through 23 removed outlier: 6.669A pdb=" N PHE e 93 " --> pdb=" O HIS e 66 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N HIS e 66 " --> pdb=" O PHE e 93 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP e 95 " --> pdb=" O VAL e 64 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS e 60 " --> pdb=" O THR e 99 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE e 101 " --> pdb=" O VAL e 58 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL e 58 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'e' and resid 72 through 78 removed outlier: 4.301A pdb=" N TYR e 83 " --> pdb=" O ARG e 78 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'f' and resid 3 through 10 removed outlier: 5.733A pdb=" N SER f 101 " --> pdb=" O HIS f 9 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N HIS f 102 " --> pdb=" O VAL f 76 " (cutoff:3.500A) removed outlier: 4.302A 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=AD7, first strand: chain 'f' and resid 82 through 87 Processing sheet with id=AD8, first strand: chain 'g' and resid 11 through 14 removed outlier: 6.688A 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=AD9, first strand: chain 'g' and resid 67 through 70 Processing sheet with id=AE1, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AE2, first strand: chain 'h' and resid 41 through 45 Processing sheet with id=AE3, first strand: chain 'h' and resid 83 through 88 Processing sheet with id=AE4, first strand: chain 'i' and resid 3 through 8 removed outlier: 7.797A pdb=" N ASN i 5 " --> pdb=" O ASP i 43 " (cutoff:3.500A) removed outlier: 4.582A 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: 6.317A pdb=" N ILE i 29 " --> pdb=" O PHE i 91 " (cutoff:3.500A) removed outlier: 7.239A 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: 6.626A pdb=" N GLN i 78 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 4.674A 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: 6.453A pdb=" N PHE i 91 " --> pdb=" O ALA i 74 " (cutoff:3.500A) removed outlier: 6.669A 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: 6.135A pdb=" N VAL i 72 " --> pdb=" O ARG i 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'j' and resid 22 through 23 removed outlier: 6.799A pdb=" N LEU j 59 " --> pdb=" O ILE j 37 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'j' and resid 30 through 31 Processing sheet with id=AE7, first strand: chain 'k' and resid 13 through 17 Processing sheet with id=AE8, first strand: chain 'k' and resid 34 through 40 Processing sheet with id=AE9, first strand: chain 'm' and resid 36 through 38 Processing sheet with id=AF1, first strand: chain 'n' and resid 29 through 30 Processing sheet with id=AF2, first strand: chain 'n' and resid 48 through 49 Processing sheet with id=AF3, first strand: chain 'o' and resid 20 through 25 Processing sheet with id=AF4, first strand: chain 'q' and resid 14 through 16 Processing sheet with id=AF5, 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=AF6, 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: 6.792A pdb=" N THR L 13 " --> pdb=" O LEU L 32 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'C' and resid 20 through 21 removed outlier: 7.917A pdb=" N TYR C 21 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA C 223 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 212 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 211 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N VAL C 42 " --> pdb=" O ILE C 175 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ILE C 175 " --> pdb=" O VAL C 42 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N THR C 173 " --> pdb=" O VAL C 44 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N VAL C 46 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AF9, 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: 8.125A 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: 6.791A pdb=" N VAL 1 183 " --> pdb=" O PHE 1 198 " (cutoff:3.500A) removed outlier: 7.456A 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=AG1, first strand: chain '2' and resid 52 through 56 removed outlier: 6.731A pdb=" N HIS 2 69 " --> pdb=" O SER 2 53 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ILE 2 55 " --> pdb=" O THR 2 67 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N THR 2 67 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain '2' and resid 167 through 171 Processing sheet with id=AG3, first strand: chain '3' and resid 128 through 129 Processing sheet with id=AG4, first strand: chain '4' and resid 13 through 15 Processing sheet with id=AG5, first strand: chain '4' and resid 19 through 22 Processing sheet with id=AG6, first strand: chain '4' and resid 85 through 89 Processing sheet with id=AG7, 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: 6.995A pdb=" N LEU 5 61 " --> pdb=" O ASP 5 41 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLY 5 43 " --> pdb=" O TYR 5 59 " (cutoff:3.500A) Processing sheet with id=AG8, 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: 6.995A pdb=" N LEU 5 61 " --> pdb=" O ASP 5 41 " (cutoff:3.500A) removed outlier: 4.136A 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=AG9, first strand: chain '6' and resid 73 through 74 Processing sheet with id=AH1, first strand: chain '7' and resid 24 through 28 removed outlier: 6.222A pdb=" N GLU 7 58 " --> pdb=" O VAL 7 51 " (cutoff:3.500A) removed outlier: 4.451A 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: 4.144A pdb=" N PHE 7 49 " --> pdb=" O GLU 7 60 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR 7 62 " --> pdb=" O GLU 7 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '7' and resid 75 through 77 Processing sheet with id=AH3, 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=AH4, 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: 7.462A pdb=" N VAL 8 67 " --> pdb=" O VAL 8 29 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain '9' and resid 45 through 52 Processing sheet with id=AH6, first strand: chain '9' and resid 45 through 52 Processing sheet with id=AH7, first strand: chain 'D' and resid 41 through 46 removed outlier: 6.717A pdb=" N ALA D 41 " --> pdb=" O ASP D 36 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ASP D 36 " --> pdb=" O ALA D 41 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU D 82 " --> pdb=" O ILE D 107 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN D 109 " --> pdb=" O LEU D 82 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'E' and resid 30 through 32 Processing sheet with id=AH9, first strand: chain 'E' and resid 36 through 40 removed outlier: 4.278A pdb=" N TYR E 95 " --> pdb=" O THR E 64 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 73 through 74 removed outlier: 3.566A pdb=" N LEU G 79 " --> pdb=" O LEU G 74 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'I' and resid 34 through 35 Processing sheet with id=AI3, first strand: chain 'I' and resid 37 through 39 removed outlier: 3.730A pdb=" N ARG I 51 " --> pdb=" O PHE I 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'J' and resid 8 through 14 removed outlier: 7.815A pdb=" N GLN J 9 " --> pdb=" O GLU J 26 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU J 26 " --> pdb=" O GLN J 9 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL J 22 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N TRP J 73 " --> pdb=" O HIS J 45 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N GLU J 60 " --> pdb=" O VAL J 76 " (cutoff:3.500A) removed outlier: 5.207A pdb=" N VAL J 78 " --> pdb=" O VAL J 58 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N VAL J 58 " --> pdb=" O VAL J 78 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 't' and resid 31 through 33 1859 hydrogen bonds defined for protein. 5166 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4065 hydrogen bonds 6360 hydrogen bond angles 0 basepair planarities 1617 basepair parallelities 2611 stacking parallelities Total time for adding SS restraints: 296.32 Time building geometry restraints manager: 65.42 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: 10279 1.25 - 1.41: 57658 1.41 - 1.57: 83897 1.57 - 1.74: 7894 1.74 - 1.90: 276 Bond restraints: 160004 Sorted by residual: bond pdb=" P G N2502 " pdb=" OP2 G N2502 " ideal model delta sigma weight residual 1.485 1.768 -0.283 2.00e-02 2.50e+03 2.00e+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 1.68e+02 bond pdb=" P G N1333 " pdb=" OP2 G N1333 " ideal model delta sigma weight residual 1.485 1.703 -0.218 2.00e-02 2.50e+03 1.19e+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 1.17e+02 bond pdb=" C ALA 4 127 " pdb=" O ALA 4 127 " ideal model delta sigma weight residual 1.234 1.104 0.130 1.22e-02 6.72e+03 1.13e+02 ... (remaining 159999 not shown) Histogram of bond angle deviations from ideal: 80.73 - 93.22: 9 93.22 - 105.70: 27736 105.70 - 118.19: 125672 118.19 - 130.67: 84232 130.67 - 143.16: 1636 Bond angle restraints: 239285 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 104.00 131.26 -27.26 1.50e+00 4.44e-01 3.30e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" O5' C N2507 " ideal model delta sigma weight residual 104.00 80.73 23.27 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 119.47 134.26 -14.79 1.16e+00 7.43e-01 1.63e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" OP1 C N2507 " ideal model delta sigma weight residual 108.00 142.97 -34.97 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 96.42 16.58 1.50e+00 4.44e-01 1.22e+02 ... (remaining 239280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.85: 90728 35.85 - 71.70: 10779 71.70 - 107.55: 942 107.55 - 143.40: 25 143.40 - 179.26: 37 Dihedral angle restraints: 102511 sinusoidal: 85490 harmonic: 17021 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 -48.37 -131.63 0 5.00e+00 4.00e-02 6.93e+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 -115.13 -64.87 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" CA LYS D 125 " pdb=" C LYS D 125 " pdb=" N LYS D 126 " pdb=" CA LYS D 126 " ideal model delta harmonic sigma weight residual -180.00 -115.40 -64.60 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 102508 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 29033 0.215 - 0.430: 1455 0.430 - 0.645: 98 0.645 - 0.860: 11 0.860 - 1.075: 5 Chirality restraints: 30602 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 1.44 1.07 2.00e-01 2.50e+01 2.89e+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 -0.89 2.00e-01 2.50e+01 1.97e+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 1.94e+01 ... (remaining 30599 not shown) Planarity restraints: 12840 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A N2765 " -0.012 2.00e-02 2.50e+03 8.71e-02 2.08e+02 pdb=" N9 A N2765 " 0.010 2.00e-02 2.50e+03 pdb=" C8 A N2765 " -0.063 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 7.16e-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 " 0.069 2.00e-02 2.50e+03 pdb=" C6 A N1802 " 0.000 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 " 0.091 2.00e-02 2.50e+03 pdb=" C4 A N1802 " 0.135 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 12837 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.64: 26 1.64 - 2.52: 810 2.52 - 3.39: 176514 3.39 - 4.27: 593483 4.27 - 5.14: 847346 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1618179 Sorted by model distance: nonbonded pdb=" O4' C A 56 " pdb=" N1 A N 896 " model vdw 0.771 3.120 nonbonded pdb=" CB THR D 108 " pdb=" OE2 GLU v 8 " model vdw 0.874 3.470 nonbonded pdb=" O4' C A 56 " pdb=" C2 A N 896 " model vdw 0.978 3.340 nonbonded pdb=" O2' C M 55 " pdb=" CA ALA S 75 " model vdw 1.028 3.470 nonbonded pdb=" C1' C A 56 " pdb=" N1 A N 896 " model vdw 1.132 3.550 ... (remaining 1618174 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=0.00 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: 6.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.680 Construct map_model_manager: 0.150 Extract box with map and model: 23.600 Check model and map are aligned: 1.560 Set scattering table: 1.090 Process input model: 613.020 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 652.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4495 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 0.283 160004 Z= 0.978 Angle : 1.622 34.968 239285 Z= 0.966 Chirality : 0.112 1.075 30602 Planarity : 0.015 0.113 12840 Dihedral : 22.927 179.256 91522 Min Nonbonded Distance : 0.771 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.60 % Favored : 90.40 % Rotamer: Outliers : 1.61 % Allowed : 5.07 % Favored : 93.32 % Cbeta Deviations : 1.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.02 % Twisted General : 0.61 % 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: -3.93 (0.09), residues: 5863 helix: -2.71 (0.09), residues: 1867 sheet: -2.34 (0.14), residues: 1065 loop : -2.59 (0.10), residues: 2931 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 0.059 0.005 ARG R 40 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1066 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 988 time to evaluate : 6.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 144 VAL cc_start: 0.3850 (t) cc_final: 0.3569 (t) REVERT: S 56 ASP cc_start: 0.7408 (m-30) cc_final: 0.6730 (t70) REVERT: V 6 GLN cc_start: 0.8163 (tt0) cc_final: 0.7893 (tm-30) REVERT: V 136 MET cc_start: 0.1579 (mtm) cc_final: 0.0869 (mtm) REVERT: g 2 ILE cc_start: 0.6131 (mp) cc_final: 0.5710 (mp) REVERT: i 48 MET cc_start: 0.4278 (tpt) cc_final: 0.3814 (tpt) REVERT: m 18 PRO cc_start: 0.1442 (Cg_exo) cc_final: 0.1240 (Cg_endo) REVERT: n 34 SER cc_start: 0.6188 (t) cc_final: 0.5425 (p) REVERT: L 31 ASP cc_start: 0.3054 (p0) cc_final: 0.2538 (m-30) REVERT: 4 123 VAL cc_start: 0.7356 (OUTLIER) cc_final: 0.6968 (m) REVERT: 5 49 TYR cc_start: 0.4414 (p90) cc_final: 0.3673 (p90) REVERT: 5 80 PHE cc_start: 0.8514 (t80) cc_final: 0.8124 (p90) REVERT: 9 14 ASP cc_start: 0.7360 (t70) cc_final: 0.7122 (t70) REVERT: 9 19 ASP cc_start: 0.7483 (p0) cc_final: 0.6398 (m-30) REVERT: 9 77 VAL cc_start: 0.7267 (t) cc_final: 0.6523 (t) REVERT: G 34 VAL cc_start: 0.8871 (t) cc_final: 0.8304 (t) REVERT: I 21 VAL cc_start: 0.3939 (t) cc_final: 0.3300 (p) REVERT: K 21 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.4579 (pt) REVERT: t 16 LEU cc_start: 0.8469 (tp) cc_final: 0.8168 (tt) REVERT: t 49 ILE cc_start: 0.6223 (OUTLIER) cc_final: 0.5715 (pt) REVERT: v 4 ILE cc_start: 0.7035 (OUTLIER) cc_final: 0.6655 (mt) REVERT: v 35 ARG cc_start: 0.5810 (ttt180) cc_final: 0.5530 (ttp-170) outliers start: 78 outliers final: 8 residues processed: 1048 average time/residue: 1.3517 time to fit residues: 2429.7151 Evaluate side-chains 439 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 427 time to evaluate : 6.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 218 PRO Chi-restraints excluded: chain U residue 27 ARG Chi-restraints excluded: chain h residue 68 SER Chi-restraints excluded: chain j residue 41 ARG Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 4 residue 123 VAL Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 20 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 878 optimal weight: 9.9990 chunk 788 optimal weight: 30.0000 chunk 437 optimal weight: 6.9990 chunk 269 optimal weight: 5.9990 chunk 531 optimal weight: 5.9990 chunk 421 optimal weight: 6.9990 chunk 815 optimal weight: 0.1980 chunk 315 optimal weight: 20.0000 chunk 495 optimal weight: 50.0000 chunk 606 optimal weight: 6.9990 chunk 944 optimal weight: 1.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 126 HIS P 86 ASN ** P 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 260 ASN Q 32 ASN Q 49 GLN Q 150 GLN ** Q 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 163 ASN R 165 HIS T 22 GLN T 73 ASN T 88 GLN T 115 HIS T 143 GLN U 11 ASN ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN ** U 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN V 43 ASN V 94 ASN W 40 HIS W 80 HIS a 3 HIS a 62 ASN b 38 GLN ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 GLN d 44 GLN e 18 GLN f 15 GLN j 57 HIS l 58 ASN m 20 HIS n 6 ASN n 38 HIS o 19 HIS o 26 ASN L 20 ASN ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 HIS 1 15 HIS ** 1 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 152 GLN 4 12 GLN 4 89 HIS 5 11 HIS ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 81 HIS 9 56 HIS ** D 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 77 HIS F 8 ASN ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN H 40 GLN I 63 GLN J 31 HIS K 52 GLN t 57 HIS u 61 GLN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4885 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 160004 Z= 0.195 Angle : 0.679 13.400 239285 Z= 0.352 Chirality : 0.038 0.337 30602 Planarity : 0.006 0.133 12840 Dihedral : 23.468 178.883 79914 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.20 % Allowed : 7.25 % Favored : 92.55 % Rotamer: Outliers : 3.55 % Allowed : 12.25 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.37 % 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: -2.47 (0.10), residues: 5863 helix: -0.70 (0.11), residues: 1845 sheet: -1.82 (0.15), residues: 1036 loop : -2.19 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP 2 22 HIS 0.015 0.001 HIS D 22 PHE 0.034 0.002 PHE R 23 TYR 0.020 0.002 TYR u 36 ARG 0.021 0.001 ARG t 37 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 533 time to evaluate : 6.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 149 MET cc_start: 0.6231 (mmp) cc_final: 0.5958 (mmp) REVERT: S 17 MET cc_start: 0.6797 (OUTLIER) cc_final: 0.6275 (tpt) REVERT: S 56 ASP cc_start: 0.7260 (m-30) cc_final: 0.6926 (t0) REVERT: U 149 GLU cc_start: 0.2878 (pt0) cc_final: 0.2524 (pm20) REVERT: V 6 GLN cc_start: 0.8195 (tt0) cc_final: 0.7855 (tm-30) REVERT: V 136 MET cc_start: 0.0114 (mtm) cc_final: -0.0724 (mtp) REVERT: Z 20 LEU cc_start: 0.4923 (mt) cc_final: 0.4718 (pt) REVERT: a 20 MET cc_start: 0.3961 (ptm) cc_final: 0.3520 (ttp) REVERT: a 112 TYR cc_start: 0.4280 (m-80) cc_final: 0.3655 (m-10) REVERT: L 31 ASP cc_start: 0.3265 (p0) cc_final: 0.1946 (m-30) REVERT: C 217 THR cc_start: 0.0366 (m) cc_final: 0.0147 (m) REVERT: 4 122 ASN cc_start: 0.4880 (OUTLIER) cc_final: 0.4667 (p0) REVERT: 5 1 MET cc_start: 0.5450 (ttt) cc_final: 0.4862 (tpt) REVERT: 8 21 ILE cc_start: 0.2764 (mt) cc_final: 0.2356 (mt) REVERT: D 52 PHE cc_start: 0.5462 (OUTLIER) cc_final: 0.4439 (p90) REVERT: I 42 ILE cc_start: 0.2244 (OUTLIER) cc_final: 0.2008 (mm) REVERT: I 46 LYS cc_start: 0.3930 (mttm) cc_final: 0.3414 (mtmm) REVERT: K 35 GLU cc_start: 0.9122 (tp30) cc_final: 0.8868 (tp30) REVERT: t 16 LEU cc_start: 0.8315 (tp) cc_final: 0.8079 (tt) REVERT: v 18 ARG cc_start: 0.7782 (mmp-170) cc_final: 0.7289 (mmm160) outliers start: 172 outliers final: 74 residues processed: 661 average time/residue: 1.2491 time to fit residues: 1457.3219 Evaluate side-chains 478 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 400 time to evaluate : 6.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 200 HIS Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 165 GLU Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 53 GLU Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 121 VAL Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain V residue 55 ILE Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain Y residue 91 ASP Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 92 VAL Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain e residue 2 TYR Chi-restraints excluded: chain e residue 15 SER Chi-restraints excluded: chain e residue 21 ARG Chi-restraints excluded: chain g residue 60 THR Chi-restraints excluded: chain h residue 31 SER Chi-restraints excluded: chain i residue 3 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain l residue 5 GLU Chi-restraints excluded: chain m residue 53 PHE Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain o residue 26 ASN Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 102 THR Chi-restraints excluded: chain 1 residue 142 GLU Chi-restraints excluded: chain 1 residue 220 THR Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 4 residue 46 VAL Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 122 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 85 ILE Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 8 residue 57 MET Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 9 residue 10 LEU Chi-restraints excluded: chain 9 residue 44 THR Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 97 ILE Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 95 LEU Chi-restraints excluded: chain F residue 98 ARG Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 67 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 32 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 524 optimal weight: 20.0000 chunk 293 optimal weight: 50.0000 chunk 786 optimal weight: 30.0000 chunk 643 optimal weight: 50.0000 chunk 260 optimal weight: 0.3980 chunk 946 optimal weight: 7.9990 chunk 1022 optimal weight: 10.0000 chunk 842 optimal weight: 8.9990 chunk 938 optimal weight: 8.9990 chunk 322 optimal weight: 6.9990 chunk 759 optimal weight: 30.0000 overall best weight: 6.6788 ------------------------------------------------------------------------------- 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 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 GLN R 92 HIS ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 163 ASN T 128 GLN U 2 GLN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 ASN ** e 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN g 15 HIS ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN l 20 ASN l 27 ASN p 29 GLN q 28 ASN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS ** 1 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 177 ASN 6 122 ASN 7 67 GLN 8 32 GLN ** 9 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 91 HIS ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN I 29 ASN K 52 GLN ** K 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 70 ASN u 75 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5576 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 160004 Z= 0.254 Angle : 0.751 21.324 239285 Z= 0.384 Chirality : 0.039 0.393 30602 Planarity : 0.007 0.144 12840 Dihedral : 23.712 175.504 79889 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.19 % Allowed : 8.14 % Favored : 91.68 % Rotamer: Outliers : 4.60 % Allowed : 12.87 % Favored : 82.53 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % 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: -2.17 (0.10), residues: 5863 helix: -0.38 (0.11), residues: 1855 sheet: -1.50 (0.15), residues: 1029 loop : -2.13 (0.10), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP t 34 HIS 0.017 0.002 HIS h 45 PHE 0.041 0.003 PHE t 41 TYR 0.050 0.003 TYR a 112 ARG 0.037 0.001 ARG h 7 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 762 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 223 poor density : 539 time to evaluate : 6.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 17 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6774 (tpp) REVERT: S 56 ASP cc_start: 0.7353 (m-30) cc_final: 0.7018 (t70) REVERT: U 149 GLU cc_start: 0.4232 (pt0) cc_final: 0.3788 (pm20) REVERT: V 6 GLN cc_start: 0.8241 (tt0) cc_final: 0.7879 (tm-30) REVERT: V 86 ILE cc_start: 0.1561 (OUTLIER) cc_final: 0.1313 (tp) REVERT: V 125 MET cc_start: 0.1267 (tpp) cc_final: 0.0873 (tpp) REVERT: V 127 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7592 (mmm160) REVERT: V 136 MET cc_start: 0.1200 (mtm) cc_final: 0.0771 (mtp) REVERT: W 1 MET cc_start: 0.5037 (ptp) cc_final: 0.4707 (mmt) REVERT: e 1 MET cc_start: 0.5626 (ttt) cc_final: 0.5298 (ptt) REVERT: f 86 MET cc_start: 0.7184 (tpp) cc_final: 0.6946 (tpt) REVERT: m 5 ILE cc_start: 0.5121 (OUTLIER) cc_final: 0.4736 (mt) REVERT: p 44 VAL cc_start: 0.6201 (OUTLIER) cc_final: 0.5921 (m) REVERT: 2 34 ASP cc_start: 0.8788 (p0) cc_final: 0.8455 (p0) REVERT: 5 1 MET cc_start: 0.6773 (ttt) cc_final: 0.5544 (tpt) REVERT: 5 17 GLN cc_start: 0.8334 (mp10) cc_final: 0.7998 (mp10) REVERT: 6 50 LEU cc_start: 0.6459 (tp) cc_final: 0.6032 (tp) REVERT: 6 142 HIS cc_start: 0.6474 (OUTLIER) cc_final: 0.6069 (t-90) REVERT: 8 27 LYS cc_start: 0.4852 (ptpt) cc_final: 0.3993 (tptt) REVERT: 8 63 LEU cc_start: 0.8016 (OUTLIER) cc_final: 0.7800 (mp) REVERT: 9 30 LYS cc_start: 0.6118 (pttp) cc_final: 0.5772 (mmtt) REVERT: F 33 ILE cc_start: 0.7157 (mt) cc_final: 0.6890 (mm) REVERT: I 46 LYS cc_start: 0.4017 (mttm) cc_final: 0.3742 (mttm) REVERT: t 16 LEU cc_start: 0.8272 (tp) cc_final: 0.8047 (tt) REVERT: v 18 ARG cc_start: 0.7456 (mmp-170) cc_final: 0.6497 (mmm160) outliers start: 223 outliers final: 78 residues processed: 696 average time/residue: 1.3523 time to fit residues: 1690.0007 Evaluate side-chains 467 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 383 time to evaluate : 6.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 162 VAL Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain Q residue 13 ARG Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain R residue 163 ASN Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain T residue 128 GLN Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain V residue 86 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 91 ASP Chi-restraints excluded: chain Z residue 108 VAL Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain d residue 90 ILE Chi-restraints excluded: chain e residue 2 TYR Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain i residue 77 VAL Chi-restraints excluded: chain m residue 5 ILE Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain o residue 5 ILE Chi-restraints excluded: chain o residue 26 ASN Chi-restraints excluded: chain o residue 27 LYS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain 1 residue 18 HIS Chi-restraints excluded: chain 1 residue 32 PHE Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 68 LEU Chi-restraints excluded: chain 1 residue 129 LEU Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 143 VAL Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 76 THR Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 46 ILE Chi-restraints excluded: chain 8 residue 46 MET Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 61 LEU Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 9 residue 8 ILE Chi-restraints excluded: chain 9 residue 89 ARG Chi-restraints excluded: chain 9 residue 92 LEU Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 48 LEU Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain t residue 60 VAL Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 14 SER Chi-restraints excluded: chain u residue 32 ILE Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 28 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 934 optimal weight: 7.9990 chunk 711 optimal weight: 40.0000 chunk 491 optimal weight: 40.0000 chunk 104 optimal weight: 2.9990 chunk 451 optimal weight: 50.0000 chunk 635 optimal weight: 50.0000 chunk 949 optimal weight: 10.0000 chunk 1005 optimal weight: 20.0000 chunk 496 optimal weight: 50.0000 chunk 899 optimal weight: 10.0000 chunk 270 optimal weight: 40.0000 overall best weight: 10.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 133 HIS ** s 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN S 127 ASN T 48 ASN ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 94 ASN W 130 HIS e 82 HIS j 50 ASN k 16 ASN ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 29 GLN r 13 ASN ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 HIS ** 1 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 74 ASN 5 63 ASN 6 68 ASN 9 58 ASN ** D 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 8 ASN F 91 HIS ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN I 29 ASN K 52 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.8678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.150 160004 Z= 0.270 Angle : 0.724 16.788 239285 Z= 0.373 Chirality : 0.039 0.552 30602 Planarity : 0.007 0.263 12840 Dihedral : 23.746 179.514 79883 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 22.73 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.76 % Favored : 92.09 % Rotamer: Outliers : 4.06 % Allowed : 15.53 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % 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: -1.99 (0.10), residues: 5863 helix: -0.25 (0.11), residues: 1845 sheet: -1.38 (0.15), residues: 1065 loop : -2.01 (0.10), residues: 2953 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP t 34 HIS 0.012 0.002 HIS 5 3 PHE 0.047 0.003 PHE t 41 TYR 0.024 0.002 TYR f 38 ARG 0.017 0.001 ARG v 17 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 197 poor density : 501 time to evaluate : 6.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 17 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.7005 (tpp) REVERT: S 56 ASP cc_start: 0.7838 (m-30) cc_final: 0.7505 (t0) REVERT: T 139 GLN cc_start: 0.3805 (OUTLIER) cc_final: 0.3206 (pt0) REVERT: U 11 ASN cc_start: 0.7355 (t0) cc_final: 0.7152 (t0) REVERT: U 149 GLU cc_start: 0.3469 (pt0) cc_final: 0.3052 (pm20) REVERT: V 6 GLN cc_start: 0.8195 (tt0) cc_final: 0.7847 (tm-30) REVERT: V 125 MET cc_start: 0.1528 (tpp) cc_final: 0.1052 (tpp) REVERT: V 127 ARG cc_start: 0.7923 (mmm160) cc_final: 0.6809 (mpp80) REVERT: V 136 MET cc_start: 0.1099 (mtm) cc_final: 0.0650 (mtp) REVERT: i 48 MET cc_start: 0.5883 (mmm) cc_final: 0.5583 (mmm) REVERT: p 44 VAL cc_start: 0.6054 (OUTLIER) cc_final: 0.5730 (m) REVERT: C 217 THR cc_start: 0.1814 (m) cc_final: 0.1561 (m) REVERT: 1 100 MET cc_start: 0.6645 (ppp) cc_final: 0.6395 (ptp) REVERT: 3 174 ASP cc_start: 0.6183 (OUTLIER) cc_final: 0.5862 (m-30) REVERT: 4 152 MET cc_start: 0.8410 (mmm) cc_final: 0.7968 (mtt) REVERT: 5 1 MET cc_start: 0.7003 (ttt) cc_final: 0.6125 (tpt) REVERT: 5 11 HIS cc_start: 0.8063 (t-90) cc_final: 0.7759 (t-90) REVERT: 6 22 LEU cc_start: 0.8670 (pp) cc_final: 0.8197 (mm) REVERT: 6 116 MET cc_start: 0.6951 (ptt) cc_final: 0.6424 (ptt) REVERT: 8 27 LYS cc_start: 0.6039 (ptpt) cc_final: 0.5815 (tptp) REVERT: 8 64 TYR cc_start: 0.5592 (OUTLIER) cc_final: 0.5004 (m-10) REVERT: 9 30 LYS cc_start: 0.6759 (pttp) cc_final: 0.6089 (mmtt) REVERT: D 18 ASP cc_start: 0.8248 (p0) cc_final: 0.8031 (p0) REVERT: D 112 ASP cc_start: 0.8415 (t70) cc_final: 0.8184 (t0) REVERT: F 11 ASP cc_start: 0.5885 (t0) cc_final: 0.5464 (t70) REVERT: F 33 ILE cc_start: 0.7359 (mt) cc_final: 0.7075 (mm) REVERT: H 78 TYR cc_start: 0.7244 (t80) cc_final: 0.6949 (t80) REVERT: I 36 VAL cc_start: 0.6988 (OUTLIER) cc_final: 0.6585 (p) REVERT: J 17 MET cc_start: 0.3670 (mpp) cc_final: 0.2382 (ptp) REVERT: K 25 ASP cc_start: 0.8701 (m-30) cc_final: 0.8408 (t0) REVERT: t 16 LEU cc_start: 0.8155 (tp) cc_final: 0.7891 (tt) outliers start: 197 outliers final: 103 residues processed: 640 average time/residue: 1.1676 time to fit residues: 1326.0657 Evaluate side-chains 508 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 399 time to evaluate : 6.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain Q residue 181 ASP Chi-restraints excluded: chain R residue 14 VAL Chi-restraints excluded: chain R residue 115 GLN Chi-restraints excluded: chain S residue 17 MET Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain T residue 139 GLN Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain W residue 62 VAL Chi-restraints excluded: chain X residue 62 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 90 ASN Chi-restraints excluded: chain Y residue 77 ILE Chi-restraints excluded: chain Y residue 81 ASP Chi-restraints excluded: chain Y residue 91 ASP Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 76 VAL Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 102 ASP Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain e residue 74 ILE Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain f residue 23 LEU Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 45 HIS Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain C residue 218 MET Chi-restraints excluded: chain 1 residue 44 GLU Chi-restraints excluded: chain 1 residue 46 THR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 80 VAL Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 183 VAL Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 142 MET Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 174 ASP Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 124 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 47 LEU Chi-restraints excluded: chain 5 residue 53 LYS Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 76 THR Chi-restraints excluded: chain 5 residue 85 ILE Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 137 LYS Chi-restraints excluded: chain 7 residue 36 ILE Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 8 residue 93 SER Chi-restraints excluded: chain 8 residue 98 LEU Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain 9 residue 77 VAL Chi-restraints excluded: chain 9 residue 89 ARG Chi-restraints excluded: chain D residue 33 THR Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 48 LEU Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 29 LEU Chi-restraints excluded: chain v residue 47 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 837 optimal weight: 40.0000 chunk 570 optimal weight: 50.0000 chunk 14 optimal weight: 50.0000 chunk 748 optimal weight: 20.0000 chunk 414 optimal weight: 50.0000 chunk 857 optimal weight: 30.0000 chunk 694 optimal weight: 30.0000 chunk 1 optimal weight: 50.0000 chunk 513 optimal weight: 50.0000 chunk 902 optimal weight: 30.0000 chunk 253 optimal weight: 50.0000 overall best weight: 30.0000 ------------------------------------------------------------------------------- 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 53 HIS ** P 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS P 243 HIS ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 130 GLN ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 GLN ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 23 ASN b 38 GLN ** c 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 72 ASN e 6 GLN e 18 GLN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 6 ASN ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 139 GLN 4 121 HIS ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 5 GLN 8 32 GLN 8 50 GLN 8 75 GLN ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 70 HIS ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN K 52 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 61 GLN ** u 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 78 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6318 moved from start: 1.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.160 160004 Z= 0.628 Angle : 1.180 21.340 239285 Z= 0.586 Chirality : 0.058 0.493 30602 Planarity : 0.010 0.169 12840 Dihedral : 24.912 179.846 79883 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 45.33 Ramachandran Plot: Outliers : 0.38 % Allowed : 11.89 % Favored : 87.74 % Rotamer: Outliers : 5.57 % Allowed : 17.43 % Favored : 77.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.31 % 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: -3.07 (0.10), residues: 5863 helix: -1.37 (0.11), residues: 1823 sheet: -1.85 (0.15), residues: 1020 loop : -2.57 (0.10), residues: 3020 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP 3 170 HIS 0.055 0.004 HIS Z 13 PHE 0.074 0.005 PHE S 138 TYR 0.060 0.005 TYR 8 64 ARG 0.033 0.002 ARG 5 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 270 poor density : 435 time to evaluate : 6.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 188 CYS cc_start: 0.6541 (m) cc_final: 0.5781 (m) REVERT: S 175 PHE cc_start: 0.0682 (OUTLIER) cc_final: 0.0058 (m-80) REVERT: U 123 ARG cc_start: 0.0297 (mtt180) cc_final: 0.0093 (mmt180) REVERT: U 149 GLU cc_start: 0.4753 (pt0) cc_final: 0.3950 (pm20) REVERT: V 6 GLN cc_start: 0.8356 (tt0) cc_final: 0.7764 (tm-30) REVERT: V 125 MET cc_start: 0.1331 (tpp) cc_final: 0.0966 (tpp) REVERT: V 127 ARG cc_start: 0.8127 (mmm160) cc_final: 0.7312 (mmp80) REVERT: X 106 GLU cc_start: 0.6193 (mt-10) cc_final: 0.5954 (mp0) REVERT: Y 82 LEU cc_start: 0.5040 (OUTLIER) cc_final: 0.4681 (tt) REVERT: Y 91 ASP cc_start: 0.5335 (OUTLIER) cc_final: 0.5062 (m-30) REVERT: b 98 GLN cc_start: 0.4446 (mm110) cc_final: 0.4229 (mm110) REVERT: e 101 ILE cc_start: 0.6803 (OUTLIER) cc_final: 0.6467 (tp) REVERT: i 1 MET cc_start: 0.2052 (OUTLIER) cc_final: 0.1118 (mmt) REVERT: i 48 MET cc_start: 0.6773 (mmm) cc_final: 0.6458 (mmm) REVERT: k 65 ASP cc_start: 0.8300 (m-30) cc_final: 0.8021 (p0) REVERT: p 22 MET cc_start: 0.6273 (ppp) cc_final: 0.5470 (ppp) REVERT: p 44 VAL cc_start: 0.5995 (OUTLIER) cc_final: 0.5733 (m) REVERT: 3 154 ARG cc_start: 0.1902 (mtm180) cc_final: 0.1199 (mmp80) REVERT: 3 174 ASP cc_start: 0.8238 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: 5 56 LYS cc_start: 0.8255 (mtpt) cc_final: 0.8051 (ptmm) REVERT: 8 27 LYS cc_start: 0.7240 (ptpt) cc_final: 0.6907 (tptt) REVERT: D 52 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7958 (p90) REVERT: t 16 LEU cc_start: 0.8426 (tp) cc_final: 0.8212 (tt) REVERT: t 44 MET cc_start: 0.8420 (OUTLIER) cc_final: 0.6940 (ppp) REVERT: v 35 ARG cc_start: 0.7264 (ttt180) cc_final: 0.6756 (ttt180) outliers start: 270 outliers final: 132 residues processed: 646 average time/residue: 1.2289 time to fit residues: 1409.5144 Evaluate side-chains 501 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 360 time to evaluate : 5.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 54 ILE Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain Q residue 82 PHE Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 132 VAL Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 175 PHE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 46 PHE Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 98 ASP Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain W residue 14 ASP Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 90 ASN Chi-restraints excluded: chain Y residue 81 ASP Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 91 ASP Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain c residue 21 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain d residue 18 LEU Chi-restraints excluded: chain d residue 102 ASP Chi-restraints excluded: chain e residue 101 ILE Chi-restraints excluded: chain g residue 61 LEU Chi-restraints excluded: chain h residue 35 ILE Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain i residue 35 GLU Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 31 VAL Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 41 THR Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain n residue 54 VAL Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain q residue 32 ILE Chi-restraints excluded: chain r residue 36 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain 1 residue 22 TYR Chi-restraints excluded: chain 1 residue 41 ILE Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 80 VAL Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 187 VAL Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 212 LEU Chi-restraints excluded: chain 2 residue 52 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 167 LYS Chi-restraints excluded: chain 3 residue 174 ASP Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 47 LEU Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 76 THR Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 5 residue 97 THR Chi-restraints excluded: chain 6 residue 49 THR Chi-restraints excluded: chain 6 residue 59 LEU Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 7 residue 36 ILE Chi-restraints excluded: chain 7 residue 46 ILE Chi-restraints excluded: chain 7 residue 47 GLU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 8 residue 46 MET Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 8 residue 93 SER Chi-restraints excluded: chain 8 residue 98 LEU Chi-restraints excluded: chain 8 residue 103 PHE Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain 9 residue 77 VAL Chi-restraints excluded: chain 9 residue 88 MET Chi-restraints excluded: chain 9 residue 89 ARG Chi-restraints excluded: chain 9 residue 90 LEU Chi-restraints excluded: chain 9 residue 97 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 86 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain E residue 74 LEU Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 104 CYS Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 19 LEU Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 50 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 82 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 38 PHE Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain t residue 12 ASP Chi-restraints excluded: chain t residue 44 MET Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain u residue 8 LYS Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 19 PHE Chi-restraints excluded: chain v residue 28 VAL Chi-restraints excluded: chain v residue 33 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 338 optimal weight: 50.0000 chunk 905 optimal weight: 8.9990 chunk 198 optimal weight: 30.0000 chunk 590 optimal weight: 40.0000 chunk 248 optimal weight: 3.9990 chunk 1006 optimal weight: 5.9990 chunk 835 optimal weight: 5.9990 chunk 465 optimal weight: 50.0000 chunk 83 optimal weight: 0.4980 chunk 332 optimal weight: 9.9990 chunk 528 optimal weight: 30.0000 overall best weight: 5.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 138 HIS ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 173 GLN R 24 ASN ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 ASN T 64 GLN T 88 GLN ** T 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 ASN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 34 HIS e 6 GLN e 86 GLN j 76 ASN ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN ** 2 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 54 GLN ** 5 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 68 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 43 ASN ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6081 moved from start: 1.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 160004 Z= 0.180 Angle : 0.667 14.991 239285 Z= 0.344 Chirality : 0.038 0.378 30602 Planarity : 0.005 0.122 12840 Dihedral : 24.064 179.608 79883 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.73 % Favored : 92.17 % Rotamer: Outliers : 2.56 % Allowed : 20.24 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.17 % 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: -2.12 (0.10), residues: 5863 helix: -0.27 (0.11), residues: 1852 sheet: -1.44 (0.15), residues: 1038 loop : -2.16 (0.10), residues: 2973 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP t 34 HIS 0.017 0.002 HIS F 14 PHE 0.029 0.002 PHE 5 80 TYR 0.034 0.002 TYR 1 213 ARG 0.012 0.001 ARG S 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 461 time to evaluate : 6.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: P 121 ASP cc_start: 0.8377 (p0) cc_final: 0.8064 (p0) REVERT: S 38 MET cc_start: 0.3716 (OUTLIER) cc_final: 0.2683 (tpt) REVERT: T 58 TYR cc_start: 0.6474 (m-10) cc_final: 0.6254 (m-10) REVERT: V 125 MET cc_start: 0.1072 (tpp) cc_final: 0.0627 (tpp) REVERT: V 127 ARG cc_start: 0.8043 (mmm160) cc_final: 0.7519 (mmp80) REVERT: V 136 MET cc_start: 0.0522 (mtp) cc_final: 0.0319 (mtp) REVERT: X 20 MET cc_start: 0.5988 (tpp) cc_final: 0.5618 (mmp) REVERT: X 106 GLU cc_start: 0.6229 (mt-10) cc_final: 0.5841 (mp0) REVERT: Y 82 LEU cc_start: 0.5627 (OUTLIER) cc_final: 0.5377 (tp) REVERT: i 1 MET cc_start: 0.2221 (mmt) cc_final: 0.1768 (mpp) REVERT: p 44 VAL cc_start: 0.5860 (OUTLIER) cc_final: 0.5555 (m) REVERT: q 49 MET cc_start: 0.4192 (mmm) cc_final: 0.3440 (mmt) REVERT: L 20 ASN cc_start: 0.5911 (m110) cc_final: 0.5709 (m110) REVERT: 2 34 ASP cc_start: 0.8293 (p0) cc_final: 0.8065 (p0) REVERT: 3 159 LEU cc_start: 0.4280 (mt) cc_final: 0.4049 (mt) REVERT: 3 174 ASP cc_start: 0.7660 (p0) cc_final: 0.7109 (m-30) REVERT: 3 188 ARG cc_start: 0.4072 (tpt90) cc_final: 0.2868 (mtt180) REVERT: 6 22 LEU cc_start: 0.9102 (pp) cc_final: 0.8865 (mm) REVERT: 9 75 ASP cc_start: 0.5401 (t0) cc_final: 0.5178 (t0) REVERT: G 89 MET cc_start: 0.6596 (ptp) cc_final: 0.6254 (ptp) REVERT: I 1 MET cc_start: 0.5164 (tpp) cc_final: 0.4814 (tpp) REVERT: K 73 ARG cc_start: 0.8902 (tpm170) cc_final: 0.8423 (mtm-85) REVERT: t 16 LEU cc_start: 0.8163 (tp) cc_final: 0.7928 (tt) REVERT: v 20 LYS cc_start: 0.7993 (mptt) cc_final: 0.7665 (mptt) outliers start: 124 outliers final: 71 residues processed: 553 average time/residue: 1.2635 time to fit residues: 1238.9813 Evaluate side-chains 456 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 382 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 186 LEU Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 77 PHE Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain l residue 7 ARG Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain 1 residue 22 TYR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 159 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 2 residue 76 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 76 TYR Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 124 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 97 THR Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 8 residue 93 SER Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain 9 residue 97 ASP Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 121 CYS Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 20 THR Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain J residue 53 CYS Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain v residue 6 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 970 optimal weight: 30.0000 chunk 113 optimal weight: 8.9990 chunk 573 optimal weight: 50.0000 chunk 734 optimal weight: 20.0000 chunk 569 optimal weight: 50.0000 chunk 847 optimal weight: 20.0000 chunk 561 optimal weight: 40.0000 chunk 1002 optimal weight: 20.0000 chunk 627 optimal weight: 50.0000 chunk 611 optimal weight: 40.0000 chunk 462 optimal weight: 50.0000 overall best weight: 19.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 153 GLN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN R 30 GLN ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 64 GLN T 73 ASN T 88 GLN ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN b 38 GLN d 59 GLN ** d 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 131 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 70 HIS D 118 HIS ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 78 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6295 moved from start: 1.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.146 160004 Z= 0.405 Angle : 0.890 18.316 239285 Z= 0.450 Chirality : 0.046 0.391 30602 Planarity : 0.007 0.123 12840 Dihedral : 24.441 179.137 79883 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 35.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 11.56 % Favored : 88.30 % Rotamer: Outliers : 3.86 % Allowed : 20.13 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.23 % 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: -2.52 (0.10), residues: 5863 helix: -0.70 (0.11), residues: 1845 sheet: -1.67 (0.15), residues: 1015 loop : -2.32 (0.10), residues: 3003 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP S 97 HIS 0.018 0.002 HIS W 77 PHE 0.042 0.003 PHE v 12 TYR 0.042 0.003 TYR V 8 ARG 0.012 0.001 ARG F 29 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 387 time to evaluate : 6.588 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: V 127 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7529 (mmp80) REVERT: X 13 ASN cc_start: 0.6842 (p0) cc_final: 0.6636 (p0) REVERT: X 20 MET cc_start: 0.6378 (tpp) cc_final: 0.6041 (mmp) REVERT: X 106 GLU cc_start: 0.6636 (mt-10) cc_final: 0.6406 (mp0) REVERT: c 43 PHE cc_start: 0.4552 (t80) cc_final: 0.4303 (t80) REVERT: h 9 ASP cc_start: 0.8362 (OUTLIER) cc_final: 0.8158 (t70) REVERT: i 1 MET cc_start: 0.2184 (OUTLIER) cc_final: 0.1959 (mpp) REVERT: p 44 VAL cc_start: 0.6223 (OUTLIER) cc_final: 0.5894 (m) REVERT: 3 174 ASP cc_start: 0.7715 (OUTLIER) cc_final: 0.7297 (m-30) REVERT: 5 63 ASN cc_start: 0.8266 (t0) cc_final: 0.8046 (t0) REVERT: 5 90 MET cc_start: 0.8909 (mmm) cc_final: 0.8653 (mmm) REVERT: 9 75 ASP cc_start: 0.5574 (t0) cc_final: 0.5329 (t0) REVERT: t 16 LEU cc_start: 0.8316 (tp) cc_final: 0.8086 (tt) REVERT: v 21 ARG cc_start: 0.9148 (tmt-80) cc_final: 0.8793 (tmm160) outliers start: 187 outliers final: 120 residues processed: 532 average time/residue: 1.2619 time to fit residues: 1202.2515 Evaluate side-chains 488 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 364 time to evaluate : 5.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 120 VAL Chi-restraints excluded: chain P residue 171 TYR Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 77 PHE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 46 PHE Chi-restraints excluded: chain U residue 68 ARG Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain W residue 77 HIS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain W residue 138 GLN Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 34 ILE Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 97 ILE Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain c residue 27 GLU Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain d residue 102 ASP Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain h residue 9 ASP Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain i residue 1 MET Chi-restraints excluded: chain k residue 58 VAL Chi-restraints excluded: chain l residue 7 ARG Chi-restraints excluded: chain l residue 9 LYS Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain q residue 57 LEU Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 22 TYR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 159 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 173 ILE Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 187 VAL Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 220 THR Chi-restraints excluded: chain 2 residue 52 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 76 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 20 PHE Chi-restraints excluded: chain 3 residue 174 ASP Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 15 SER Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 5 residue 97 THR Chi-restraints excluded: chain 6 residue 15 ASP Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 64 VAL Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 43 GLU Chi-restraints excluded: chain 7 residue 55 THR Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 8 residue 35 LEU Chi-restraints excluded: chain 8 residue 37 GLN Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 8 residue 104 VAL Chi-restraints excluded: chain 9 residue 44 THR Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain F residue 39 ILE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 5 SER Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 11 ILE Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain J residue 46 VAL Chi-restraints excluded: chain J residue 57 ASP Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 71 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 MET Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 19 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 620 optimal weight: 50.0000 chunk 400 optimal weight: 50.0000 chunk 598 optimal weight: 30.0000 chunk 301 optimal weight: 7.9990 chunk 196 optimal weight: 0.0020 chunk 194 optimal weight: 0.9980 chunk 637 optimal weight: 40.0000 chunk 682 optimal weight: 50.0000 chunk 495 optimal weight: 50.0000 chunk 93 optimal weight: 10.0000 chunk 787 optimal weight: 30.0000 overall best weight: 9.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN R 115 GLN ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN ** T 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 28 ASN ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 38 GLN ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN 3 131 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 25 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6195 moved from start: 1.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 160004 Z= 0.225 Angle : 0.682 14.951 239285 Z= 0.351 Chirality : 0.038 0.402 30602 Planarity : 0.005 0.121 12840 Dihedral : 24.138 179.987 79883 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 24.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.28 % Favored : 90.62 % Rotamer: Outliers : 3.05 % Allowed : 21.00 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.21 % 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: -2.16 (0.10), residues: 5863 helix: -0.29 (0.12), residues: 1859 sheet: -1.47 (0.16), residues: 1022 loop : -2.20 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP S 97 HIS 0.011 0.001 HIS F 91 PHE 0.037 0.002 PHE v 12 TYR 0.031 0.002 TYR 1 213 ARG 0.008 0.001 ARG 5 45 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 391 time to evaluate : 6.082 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: T 56 ASP cc_start: 0.6280 (p0) cc_final: 0.6020 (p0) REVERT: V 127 ARG cc_start: 0.8046 (mmm160) cc_final: 0.7495 (mmp80) REVERT: X 20 MET cc_start: 0.6251 (tpp) cc_final: 0.5921 (mmp) REVERT: a 24 MET cc_start: 0.6208 (ptt) cc_final: 0.5939 (ptt) REVERT: i 48 MET cc_start: 0.7035 (mmm) cc_final: 0.6685 (tpp) REVERT: i 50 MET cc_start: 0.6991 (ppp) cc_final: 0.6601 (ppp) REVERT: p 44 VAL cc_start: 0.5919 (OUTLIER) cc_final: 0.5600 (m) REVERT: L 22 MET cc_start: 0.4823 (tpp) cc_final: 0.4586 (tpt) REVERT: 2 34 ASP cc_start: 0.8361 (p0) cc_final: 0.8137 (p0) REVERT: 3 105 MET cc_start: 0.3196 (mmm) cc_final: 0.2984 (mmt) REVERT: 3 174 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7208 (m-30) REVERT: 7 113 ASP cc_start: 0.7486 (OUTLIER) cc_final: 0.7219 (p0) REVERT: 9 75 ASP cc_start: 0.5373 (t0) cc_final: 0.5155 (t0) REVERT: D 93 ARG cc_start: 0.7125 (OUTLIER) cc_final: 0.6014 (pmm-80) REVERT: K 72 ASP cc_start: 0.7986 (p0) cc_final: 0.7775 (p0) REVERT: t 16 LEU cc_start: 0.8228 (tp) cc_final: 0.8011 (tt) REVERT: v 18 ARG cc_start: 0.7602 (mmm160) cc_final: 0.7295 (mmp80) REVERT: v 21 ARG cc_start: 0.9066 (tmt-80) cc_final: 0.8701 (tmm160) REVERT: v 35 ARG cc_start: 0.7333 (ttt180) cc_final: 0.6821 (ttt180) outliers start: 148 outliers final: 112 residues processed: 499 average time/residue: 1.1834 time to fit residues: 1060.4266 Evaluate side-chains 479 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 363 time to evaluate : 6.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 171 TYR Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain W residue 77 HIS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain X residue 92 GLU Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain g residue 61 LEU Chi-restraints excluded: chain h residue 72 ILE Chi-restraints excluded: chain h residue 87 PHE Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain l residue 7 ARG Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain L residue 40 CYS Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 22 TYR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 159 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 220 THR Chi-restraints excluded: chain 2 residue 52 VAL Chi-restraints excluded: chain 2 residue 64 ILE Chi-restraints excluded: chain 2 residue 76 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 174 ASP Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 124 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 7 VAL Chi-restraints excluded: chain 5 residue 9 MET Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 70 VAL Chi-restraints excluded: chain 5 residue 84 VAL Chi-restraints excluded: chain 5 residue 97 THR Chi-restraints excluded: chain 6 residue 15 ASP Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 7 residue 113 ASP Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 63 LEU Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 8 residue 93 SER Chi-restraints excluded: chain 8 residue 104 VAL Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 39 LEU Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 65 LEU Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 MET Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 19 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 911 optimal weight: 10.0000 chunk 960 optimal weight: 4.9990 chunk 876 optimal weight: 20.0000 chunk 934 optimal weight: 40.0000 chunk 562 optimal weight: 40.0000 chunk 406 optimal weight: 50.0000 chunk 733 optimal weight: 20.0000 chunk 286 optimal weight: 50.0000 chunk 844 optimal weight: 10.0000 chunk 883 optimal weight: 7.9990 chunk 930 optimal weight: 1.9990 overall best weight: 6.9994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 24 ASN R 163 ASN S 5 HIS ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 52 ASN ** S 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 111 HIS U 2 GLN W 138 GLN b 38 GLN ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 55 HIS 5 63 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6144 moved from start: 1.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 160004 Z= 0.183 Angle : 0.626 14.670 239285 Z= 0.322 Chirality : 0.035 0.404 30602 Planarity : 0.005 0.114 12840 Dihedral : 23.942 179.814 79883 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 21.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.35 % Favored : 90.53 % Rotamer: Outliers : 2.64 % Allowed : 21.80 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.14 % 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: -1.84 (0.11), residues: 5863 helix: 0.12 (0.12), residues: 1848 sheet: -1.30 (0.16), residues: 1033 loop : -2.11 (0.11), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP S 97 HIS 0.007 0.001 HIS W 77 PHE 0.049 0.002 PHE 3 182 TYR 0.033 0.002 TYR 1 213 ARG 0.008 0.001 ARG 5 45 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 531 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 403 time to evaluate : 6.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 100 MET cc_start: 0.4689 (mpp) cc_final: 0.4365 (mmp) REVERT: S 38 MET cc_start: 0.4067 (OUTLIER) cc_final: 0.3083 (tpt) REVERT: T 56 ASP cc_start: 0.5925 (p0) cc_final: 0.5658 (p0) REVERT: V 127 ARG cc_start: 0.8013 (mmm160) cc_final: 0.6624 (mpp80) REVERT: a 24 MET cc_start: 0.6079 (ptt) cc_final: 0.5793 (ptt) REVERT: a 110 MET cc_start: 0.6578 (tpp) cc_final: 0.6291 (tpt) REVERT: i 50 MET cc_start: 0.7057 (ppp) cc_final: 0.6758 (ppp) REVERT: l 9 LYS cc_start: 0.6131 (pttt) cc_final: 0.5521 (mmtm) REVERT: n 55 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7229 (tp) REVERT: p 44 VAL cc_start: 0.6058 (OUTLIER) cc_final: 0.5751 (m) REVERT: q 49 MET cc_start: 0.3962 (mmm) cc_final: 0.3727 (mmt) REVERT: L 22 MET cc_start: 0.4820 (tpp) cc_final: 0.4572 (tpt) REVERT: 2 34 ASP cc_start: 0.8305 (p0) cc_final: 0.8102 (p0) REVERT: 3 35 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: 3 105 MET cc_start: 0.2902 (mmm) cc_final: 0.2324 (mmt) REVERT: 3 159 LEU cc_start: 0.4996 (mt) cc_final: 0.4752 (mt) REVERT: 3 174 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6930 (m-30) REVERT: D 93 ARG cc_start: 0.6962 (OUTLIER) cc_final: 0.6075 (pmm-80) REVERT: I 1 MET cc_start: 0.6417 (tpp) cc_final: 0.5806 (tpp) REVERT: K 72 ASP cc_start: 0.7951 (p0) cc_final: 0.7740 (p0) REVERT: t 16 LEU cc_start: 0.8174 (tp) cc_final: 0.7967 (tt) REVERT: v 21 ARG cc_start: 0.8977 (tmt-80) cc_final: 0.8662 (tmm160) outliers start: 128 outliers final: 98 residues processed: 498 average time/residue: 1.2383 time to fit residues: 1107.1329 Evaluate side-chains 475 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 371 time to evaluate : 6.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain W residue 77 HIS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain g residue 61 LEU Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain k residue 58 VAL Chi-restraints excluded: chain l residue 26 PHE Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain 1 residue 22 TYR Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 159 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 187 VAL Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 76 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 99 ASP Chi-restraints excluded: chain 3 residue 174 ASP Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 124 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 63 ASN Chi-restraints excluded: chain 5 residue 70 VAL Chi-restraints excluded: chain 5 residue 97 THR Chi-restraints excluded: chain 6 residue 15 ASP Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 7 residue 113 ASP Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 56 ASP Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 84 VAL Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 29 GLN Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 49 ILE Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain v residue 6 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 613 optimal weight: 30.0000 chunk 987 optimal weight: 9.9990 chunk 602 optimal weight: 50.0000 chunk 468 optimal weight: 50.0000 chunk 686 optimal weight: 30.0000 chunk 1036 optimal weight: 0.0010 chunk 953 optimal weight: 5.9990 chunk 825 optimal weight: 20.0000 chunk 85 optimal weight: 20.0000 chunk 637 optimal weight: 50.0000 chunk 505 optimal weight: 50.0000 overall best weight: 11.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN ** V 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 53 ASN ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 HIS K 52 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6212 moved from start: 1.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 160004 Z= 0.249 Angle : 0.682 14.357 239285 Z= 0.350 Chirality : 0.037 0.410 30602 Planarity : 0.005 0.114 12840 Dihedral : 24.053 179.704 79883 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 25.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.17 % Favored : 89.73 % Rotamer: Outliers : 2.50 % Allowed : 22.05 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.12 % 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: 5863 helix: -0.01 (0.12), residues: 1856 sheet: -1.32 (0.16), residues: 1033 loop : -2.11 (0.11), residues: 2974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP S 97 HIS 0.055 0.002 HIS S 5 PHE 0.044 0.002 PHE v 12 TYR 0.044 0.002 TYR S 7 ARG 0.012 0.001 ARG R 114 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11726 Ramachandran restraints generated. 5863 Oldfield, 0 Emsley, 5863 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 500 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 379 time to evaluate : 6.628 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: S 38 MET cc_start: 0.4244 (OUTLIER) cc_final: 0.3020 (tpt) REVERT: S 99 PHE cc_start: 0.5607 (t80) cc_final: 0.5329 (t80) REVERT: V 127 ARG cc_start: 0.8073 (mmm160) cc_final: 0.6783 (mtm180) REVERT: a 24 MET cc_start: 0.6413 (ptt) cc_final: 0.6134 (ptt) REVERT: a 110 MET cc_start: 0.6758 (tpp) cc_final: 0.6541 (tpt) REVERT: g 1 MET cc_start: 0.1556 (mmm) cc_final: 0.1305 (mmp) REVERT: i 50 MET cc_start: 0.7125 (ppp) cc_final: 0.6861 (ppp) REVERT: n 55 ILE cc_start: 0.7531 (OUTLIER) cc_final: 0.7304 (tp) REVERT: p 44 VAL cc_start: 0.6186 (OUTLIER) cc_final: 0.5832 (m) REVERT: q 49 MET cc_start: 0.3895 (mmm) cc_final: 0.3580 (mmt) REVERT: 2 34 ASP cc_start: 0.8305 (p0) cc_final: 0.8088 (p0) REVERT: 3 105 MET cc_start: 0.3335 (mmm) cc_final: 0.2870 (mmt) REVERT: 3 159 LEU cc_start: 0.4993 (mt) cc_final: 0.4587 (mt) REVERT: 3 174 ASP cc_start: 0.7542 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: 9 100 ILE cc_start: 0.8950 (mm) cc_final: 0.8738 (tp) REVERT: D 93 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6191 (pmm-80) REVERT: t 53 ASN cc_start: 0.6488 (OUTLIER) cc_final: 0.6274 (p0) REVERT: v 21 ARG cc_start: 0.8994 (tmt-80) cc_final: 0.8659 (tmm160) outliers start: 121 outliers final: 105 residues processed: 470 average time/residue: 1.2371 time to fit residues: 1048.4414 Evaluate side-chains 480 residues out of total 4887 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 369 time to evaluate : 6.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 64 ILE Chi-restraints excluded: chain P residue 116 ILE Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 9 VAL Chi-restraints excluded: chain Q residue 121 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain S residue 5 HIS Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 141 ILE Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 11 VAL Chi-restraints excluded: chain T residue 166 ASP Chi-restraints excluded: chain U residue 20 ASN Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 80 ILE Chi-restraints excluded: chain U residue 134 VAL Chi-restraints excluded: chain V residue 17 MET Chi-restraints excluded: chain W residue 77 HIS Chi-restraints excluded: chain W residue 81 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 84 CYS Chi-restraints excluded: chain Y residue 82 LEU Chi-restraints excluded: chain Y residue 117 THR Chi-restraints excluded: chain Z residue 93 VAL Chi-restraints excluded: chain Z residue 129 THR Chi-restraints excluded: chain a residue 37 THR Chi-restraints excluded: chain a residue 98 LEU Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain c residue 102 GLU Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 53 PHE Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain g residue 61 LEU Chi-restraints excluded: chain h residue 96 PHE Chi-restraints excluded: chain h residue 102 THR Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain j residue 67 VAL Chi-restraints excluded: chain k residue 58 VAL Chi-restraints excluded: chain m residue 37 GLU Chi-restraints excluded: chain m residue 54 MET Chi-restraints excluded: chain n residue 55 ILE Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 12 ILE Chi-restraints excluded: chain L residue 25 ARG Chi-restraints excluded: chain L residue 35 ASP Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain 1 residue 47 VAL Chi-restraints excluded: chain 1 residue 62 SER Chi-restraints excluded: chain 1 residue 159 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 186 ILE Chi-restraints excluded: chain 1 residue 187 VAL Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 1 residue 220 THR Chi-restraints excluded: chain 2 residue 76 VAL Chi-restraints excluded: chain 2 residue 106 VAL Chi-restraints excluded: chain 2 residue 200 VAL Chi-restraints excluded: chain 3 residue 35 GLU Chi-restraints excluded: chain 3 residue 174 ASP Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 117 VAL Chi-restraints excluded: chain 4 residue 124 LEU Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 36 ILE Chi-restraints excluded: chain 5 residue 58 HIS Chi-restraints excluded: chain 5 residue 70 VAL Chi-restraints excluded: chain 5 residue 97 THR Chi-restraints excluded: chain 6 residue 15 ASP Chi-restraints excluded: chain 6 residue 32 VAL Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 125 SER Chi-restraints excluded: chain 6 residue 126 ASP Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 59 LEU Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 7 residue 113 ASP Chi-restraints excluded: chain 7 residue 121 LEU Chi-restraints excluded: chain 8 residue 21 ILE Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 64 TYR Chi-restraints excluded: chain 9 residue 56 HIS Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain E residue 78 SER Chi-restraints excluded: chain E residue 81 LEU Chi-restraints excluded: chain F residue 47 GLU Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 21 PHE Chi-restraints excluded: chain G residue 34 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 2 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain K residue 21 ILE Chi-restraints excluded: chain K residue 40 VAL Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain K residue 73 ARG Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 53 ASN Chi-restraints excluded: chain u residue 39 ILE Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 33 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1040 random chunks: chunk 655 optimal weight: 40.0000 chunk 878 optimal weight: 20.0000 chunk 252 optimal weight: 20.0000 chunk 760 optimal weight: 20.0000 chunk 121 optimal weight: 6.9990 chunk 229 optimal weight: 40.0000 chunk 826 optimal weight: 1.9990 chunk 345 optimal weight: 50.0000 chunk 848 optimal weight: 6.9990 chunk 104 optimal weight: 50.0000 chunk 152 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 63 ASN ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN ** E 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.040439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.034046 restraints weight = 1952256.063| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 3.24 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3463 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3463 r_free = 0.3463 target_work(ls_wunit_k1) = 0.032 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3463 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 1.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 160004 Z= 0.199 Angle : 0.634 15.438 239285 Z= 0.325 Chirality : 0.036 0.413 30602 Planarity : 0.005 0.113 12840 Dihedral : 23.951 179.489 79883 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 21.93 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.43 % Rotamer: Outliers : 2.64 % Allowed : 22.22 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.14 % 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: -1.76 (0.11), residues: 5863 helix: 0.16 (0.12), residues: 1864 sheet: -1.22 (0.16), residues: 1020 loop : -2.06 (0.11), residues: 2979 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP S 97 HIS 0.019 0.001 HIS S 5 PHE 0.033 0.002 PHE R 124 TYR 0.032 0.002 TYR 1 213 ARG 0.010 0.001 ARG 8 45 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 27174.02 seconds wall clock time: 483 minutes 43.35 seconds (29023.35 seconds total)