Starting phenix.real_space_refine on Mon Mar 25 01:10:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg8_13952/03_2024/7qg8_13952.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg8_13952/03_2024/7qg8_13952.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg8_13952/03_2024/7qg8_13952.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg8_13952/03_2024/7qg8_13952.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg8_13952/03_2024/7qg8_13952.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qg8_13952/03_2024/7qg8_13952.pdb" } resolution = 3.97 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= -0.008 sd= 0.148 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 73984 2.51 5 N 27386 2.21 5 O 40885 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" Residue "v PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147108 Number of models: 1 Model: "" Number of chains: 58 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: "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: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 48} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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: 77.67, per 1000 atoms: 0.53 Number of scatterers: 147108 At special positions: 0 Unit cell: (233.26, 277.95, 274.68, 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 40885 8.00 N 27386 7.00 C 73984 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 72279 O4' A N1876 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.91 Conformation dependent library (CDL) restraints added in 7.0 seconds 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10910 Finding SS restraints... Secondary structure from input PDB file: 180 helices and 77 sheets defined 33.9% alpha, 18.0% beta 1618 base pairs and 2610 stacking pairs defined. Time for finding SS restraints: 66.23 Creating SS restraints... Processing helix chain 's' and resid 120 through 127 Processing helix chain 's' and resid 139 through 143 Processing helix chain 's' and resid 147 through 156 Processing helix chain 'P' and resid 30 through 32 No H-bonds generated for 'chain 'P' and resid 30 through 32' Processing helix chain 'P' and resid 197 through 203 removed outlier: 3.616A pdb=" N ARG P 203 " --> pdb=" O HIS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.998A pdb=" N ALA P 211 " --> pdb=" O LYS P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 225 Processing helix chain 'Q' and resid 61 through 72 Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 120 through 125 Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 24 through 39 Processing helix chain 'R' and resid 97 through 115 Processing helix chain 'R' and resid 130 through 141 Processing helix chain 'R' and resid 154 through 161 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.559A 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: 5.073A 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: 3.662A pdb=" N ARG U 50 " --> pdb=" O PHE U 46 " (cutoff:3.500A) removed outlier: 3.685A 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: 3.760A 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: 3.952A 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: 3.559A 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: 4.882A 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: 3.513A 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: 3.524A pdb=" N ARG c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 20 removed outlier: 3.561A 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: 4.465A 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: 3.643A 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: 3.642A 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: 3.656A 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: 3.535A 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: 3.679A pdb=" N VAL 8 48 " --> pdb=" O ARG 8 45 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN 8 50 " --> pdb=" O VAL 8 47 " (cutoff:3.500A) Proline residue: 8 51 - end of helix Processing helix chain '8' and resid 72 through 86 Processing helix chain '8' and resid 93 through 101 removed outlier: 4.091A 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: 3.850A pdb=" N CYS E 27 " --> pdb=" O LEU E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 118 removed outlier: 3.526A 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: 3.587A pdb=" N GLY F 94 " --> pdb=" O ARG F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 20 removed outlier: 3.714A 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: 3.948A 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: 3.956A 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: 3.770A 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: 6.204A pdb=" N LEU P 95 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 5.598A 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: 6.554A pdb=" N MET P 181 " --> pdb=" O VAL P 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 144 through 145 removed outlier: 5.978A 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: 7.138A 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: 5.805A 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: 6.810A 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: 6.429A 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: 7.961A 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: 4.179A 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: 6.727A pdb=" N GLY V 99 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU V 141 " --> pdb=" O GLY V 99 " (cutoff:3.500A) removed outlier: 6.980A 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: 6.424A 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: 7.597A 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: 6.524A pdb=" N ARG X 17 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA X 16 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 6.239A 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: 8.263A 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: 6.536A 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: 5.309A pdb=" N VAL c 86 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 7.100A 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: 7.937A pdb=" N TRP c 31 " --> pdb=" O ASP c 82 " (cutoff:3.500A) removed outlier: 7.420A 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: 5.826A 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: 6.460A pdb=" N LEU Z 33 " --> pdb=" O LEU Z 102 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU Z 104 " --> pdb=" O PHE Z 31 " (cutoff:3.500A) removed outlier: 6.674A 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: 6.947A 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: 4.216A 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: 6.710A pdb=" N TYR e 2 " --> pdb=" O ILE e 41 " (cutoff:3.500A) removed outlier: 4.466A 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: 6.710A 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: 6.706A 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: 4.302A 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: 5.737A pdb=" N HIS f 102 " --> pdb=" O VAL f 76 " (cutoff:3.500A) removed outlier: 4.303A 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: 4.675A pdb=" N ILE i 89 " --> pdb=" O ASP i 76 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N ASP i 76 " --> pdb=" O ILE i 89 " (cutoff:3.500A) removed outlier: 6.453A 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: 6.800A 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: 6.531A 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: 9.295A 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: 6.364A 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: 7.214A 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: 6.639A 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: 8.124A pdb=" N ILE 1 186 " --> pdb=" O LEU 1 161 " (cutoff:3.500A) removed outlier: 7.606A 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: 6.730A 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: 5.987A 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: 5.038A 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: 6.560A 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: 7.463A 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: 6.412A 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: 4.162A 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: 7.814A 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: 7.266A pdb=" N VAL J 22 " --> pdb=" O VAL J 13 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N TRP J 73 " --> pdb=" O HIS J 45 " (cutoff:3.500A) removed outlier: 6.954A 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 1852 hydrogen bonds defined for protein. 5145 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4067 hydrogen bonds 6360 hydrogen bond angles 0 basepair planarities 1618 basepair parallelities 2610 stacking parallelities Total time for adding SS restraints: 280.99 Time building geometry restraints manager: 68.23 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: 10335 1.25 - 1.41: 57932 1.41 - 1.57: 83437 1.57 - 1.74: 7827 1.74 - 1.90: 276 Bond restraints: 159807 Sorted by residual: bond pdb=" P G N2502 " pdb=" OP2 G N2502 " ideal model delta sigma weight residual 1.485 1.767 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" P A N1156 " pdb=" OP2 A N1156 " ideal model delta sigma weight residual 1.485 1.744 -0.259 2.00e-02 2.50e+03 1.67e+02 bond pdb=" P G N1333 " pdb=" OP2 G N1333 " ideal model delta sigma weight residual 1.485 1.703 -0.218 2.00e-02 2.50e+03 1.18e+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 1.105 0.129 1.22e-02 6.72e+03 1.12e+02 ... (remaining 159802 not shown) Histogram of bond angle deviations from ideal: 80.74 - 93.23: 9 93.23 - 105.72: 27892 105.72 - 118.20: 125471 118.20 - 130.69: 84000 130.69 - 143.17: 1640 Bond angle restraints: 239012 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 104.00 131.23 -27.23 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 80.74 23.26 1.50e+00 4.44e-01 2.40e+02 angle pdb=" C THR Q 151 " pdb=" N PRO Q 152 " pdb=" CA PRO Q 152 " ideal model delta sigma weight residual 119.47 134.27 -14.80 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 239007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 90612 35.84 - 71.69: 10772 71.69 - 107.53: 948 107.53 - 143.37: 25 143.37 - 179.22: 37 Dihedral angle restraints: 102394 sinusoidal: 85487 harmonic: 16907 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 -48.41 -131.59 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 -115.18 -64.82 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 -115.35 -64.65 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 102391 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 28988 0.215 - 0.430: 1461 0.430 - 0.644: 99 0.644 - 0.859: 11 0.859 - 1.074: 5 Chirality restraints: 30564 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 2.88e+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 1.93e+01 ... (remaining 30561 not shown) Planarity restraints: 12801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A N2765 " -0.013 2.00e-02 2.50e+03 8.71e-02 2.09e+02 pdb=" N9 A N2765 " 0.011 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 " -0.040 2.00e-02 2.50e+03 pdb=" N7 A N1802 " -0.000 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 7.72e-02 1.34e+02 pdb=" N1 U N2522 " -0.046 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 " 0.049 2.00e-02 2.50e+03 pdb=" C6 U N2522 " -0.002 2.00e-02 2.50e+03 ... (remaining 12798 not shown) Histogram of nonbonded interaction distances: 0.77 - 1.64: 17 1.64 - 2.52: 796 2.52 - 3.39: 176091 3.39 - 4.27: 593006 4.27 - 5.14: 846915 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1616825 Sorted by model distance: nonbonded pdb=" O4' C A 56 " pdb=" N1 A N 896 " model vdw 0.770 3.120 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 nonbonded pdb=" O2' C M 55 " pdb=" CB ALA S 75 " model vdw 1.135 3.460 ... (remaining 1616820 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 group one per residue 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: 17.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.620 Construct map_model_manager: 0.180 Extract box with map and model: 41.090 Check model and map are aligned: 1.400 Set scattering table: 0.940 Process input model: 602.000 Find NCS groups from input model: 2.950 Set up NCS constraints: 0.420 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:2.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 669.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3979 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 0.282 159807 Z= 0.984 Angle : 1.623 34.973 239012 Z= 0.966 Chirality : 0.112 1.074 30564 Planarity : 0.015 0.113 12801 Dihedral : 22.932 179.217 91481 Min Nonbonded Distance : 0.770 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.63 % Favored : 90.35 % Rotamer: Outliers : 1.61 % Allowed : 5.03 % Favored : 93.36 % Cbeta Deviations : 1.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.03 % Twisted General : 0.62 % 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: -3.97 (0.09), residues: 5826 helix: -2.75 (0.09), residues: 1849 sheet: -2.34 (0.14), residues: 1065 loop : -2.64 (0.10), residues: 2912 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) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1173 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1095 time to evaluate : 6.408 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: 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: 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: s 151 VAL cc_start: 0.6494 (t) cc_final: 0.6267 (t) REVERT: P 201 MET cc_start: 0.1155 (ptt) cc_final: 0.0590 (ppp) REVERT: S 31 VAL cc_start: 0.3935 (OUTLIER) cc_final: 0.3690 (p) REVERT: T 141 ILE cc_start: 0.6765 (pt) cc_final: 0.6154 (pt) REVERT: U 3 VAL cc_start: 0.7435 (m) cc_final: 0.7186 (m) REVERT: V 68 THR cc_start: 0.6487 (p) cc_final: 0.6152 (p) REVERT: W 16 TYR cc_start: 0.5551 (m-10) cc_final: 0.4260 (m-10) REVERT: C 48 LEU cc_start: 0.6281 (mt) cc_final: 0.5912 (tp) REVERT: C 170 ILE cc_start: 0.4780 (mp) cc_final: 0.3805 (mt) REVERT: 1 93 ASN cc_start: 0.4639 (p0) cc_final: 0.3368 (p0) REVERT: 1 138 THR cc_start: 0.7461 (p) cc_final: 0.6564 (p) REVERT: 2 122 SER cc_start: 0.8389 (m) cc_final: 0.8018 (p) REVERT: 3 105 MET cc_start: 0.0049 (mtt) cc_final: -0.0364 (mtt) REVERT: 6 94 VAL cc_start: 0.6981 (t) cc_final: 0.6677 (p) REVERT: J 17 MET cc_start: -0.4188 (ptp) cc_final: -0.4407 (ttp) REVERT: t 49 ILE cc_start: 0.2774 (OUTLIER) cc_final: 0.2459 (pt) outliers start: 78 outliers final: 11 residues processed: 1160 average time/residue: 1.4246 time to fit residues: 2750.3147 Evaluate side-chains 527 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 514 time to evaluate : 6.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 205 PRO Chi-restraints excluded: chain S residue 31 VAL Chi-restraints excluded: chain U residue 50 ARG Chi-restraints excluded: chain U residue 55 GLU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 53 ARG Chi-restraints excluded: chain d residue 16 LYS Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain j residue 41 ARG Chi-restraints excluded: chain 4 residue 157 ARG Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain t residue 49 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 875 optimal weight: 7.9990 chunk 785 optimal weight: 20.0000 chunk 436 optimal weight: 10.0000 chunk 268 optimal weight: 8.9990 chunk 530 optimal weight: 6.9990 chunk 419 optimal weight: 5.9990 chunk 812 optimal weight: 50.0000 chunk 314 optimal weight: 7.9990 chunk 494 optimal weight: 1.9990 chunk 604 optimal weight: 9.9990 chunk 941 optimal weight: 40.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 126 HIS ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 86 ASN P 134 ASN P 260 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 150 GLN Q 173 GLN Q 185 ASN R 92 HIS S 52 ASN T 22 GLN T 88 GLN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 143 GLN ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 40 HIS W 80 HIS ** W 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 35 HIS ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 HIS b 38 GLN c 41 GLN ** d 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 82 HIS f 15 GLN g 15 HIS ** h 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 6 GLN l 25 GLN l 38 GLN n 6 ASN p 13 ASN ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 48 GLN C 47 ASN C 58 ASN C 172 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN 1 42 ASN 1 51 ASN 1 109 GLN ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN ** 7 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 56 HIS D 64 GLN ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 GLN ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS I 63 GLN J 31 HIS K 31 ASN K 52 GLN ** u 20 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 70 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4478 moved from start: 0.3765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 159807 Z= 0.255 Angle : 0.778 13.139 239012 Z= 0.395 Chirality : 0.040 0.332 30564 Planarity : 0.007 0.131 12801 Dihedral : 23.806 179.712 79878 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.52 % Favored : 92.24 % Rotamer: Outliers : 3.96 % Allowed : 13.60 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.03 % Twisted General : 0.33 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.54 (0.10), residues: 5826 helix: -0.97 (0.11), residues: 1849 sheet: -1.67 (0.15), residues: 1055 loop : -2.16 (0.10), residues: 2922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP 6 103 HIS 0.016 0.002 HIS n 19 PHE 0.030 0.003 PHE D 61 TYR 0.036 0.003 TYR K 64 ARG 0.016 0.001 ARG 7 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 833 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 641 time to evaluate : 6.535 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: 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: symmetry clash REVERT: P 201 MET cc_start: 0.0736 (ptt) cc_final: 0.0397 (ppp) REVERT: P 243 HIS cc_start: 0.4646 (OUTLIER) cc_final: 0.3655 (t-90) REVERT: S 173 PHE cc_start: 0.5113 (m-10) cc_final: 0.4401 (m-10) REVERT: S 174 ASP cc_start: 0.7428 (m-30) cc_final: 0.7203 (t0) REVERT: S 177 PHE cc_start: 0.5572 (OUTLIER) cc_final: 0.4750 (m-80) REVERT: T 44 LYS cc_start: 0.8150 (mmtt) cc_final: 0.7811 (mmtm) REVERT: U 2 GLN cc_start: 0.7440 (mm-40) cc_final: 0.6636 (tp-100) REVERT: V 125 MET cc_start: 0.4010 (tpt) cc_final: 0.3271 (mmp) REVERT: X 1 MET cc_start: 0.1924 (mtt) cc_final: 0.1564 (ttm) REVERT: a 110 MET cc_start: 0.3717 (mmm) cc_final: 0.2860 (mmm) REVERT: i 34 LYS cc_start: 0.8312 (mmtt) cc_final: 0.8059 (mmpt) REVERT: m 40 ASP cc_start: 0.6337 (t0) cc_final: 0.6004 (t70) REVERT: m 58 GLU cc_start: 0.6079 (pm20) cc_final: 0.5805 (pm20) REVERT: n 55 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6701 (mm) REVERT: p 1 MET cc_start: 0.1918 (tpt) cc_final: 0.1463 (tpp) REVERT: C 47 ASN cc_start: 0.7826 (OUTLIER) cc_final: 0.6005 (m-40) REVERT: 1 133 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7863 (pp20) REVERT: 5 6 ILE cc_start: 0.5550 (OUTLIER) cc_final: 0.5338 (mp) REVERT: 5 18 VAL cc_start: 0.7179 (t) cc_final: 0.6947 (p) REVERT: 8 6 TYR cc_start: 0.4928 (m-80) cc_final: 0.3879 (m-80) outliers start: 192 outliers final: 69 residues processed: 781 average time/residue: 1.4493 time to fit residues: 1917.5405 Evaluate side-chains 533 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 458 time to evaluate : 6.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 243 HIS Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain T residue 131 ILE Chi-restraints excluded: chain U residue 22 LYS Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain V residue 8 TYR Chi-restraints excluded: chain V residue 36 MET Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain X residue 86 LEU Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 62 ASP Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 85 VAL Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 25 GLN Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain n residue 28 LEU 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 16 ILE Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain C residue 47 ASN Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 109 GLN Chi-restraints excluded: chain 1 residue 128 LYS Chi-restraints excluded: chain 1 residue 133 GLU Chi-restraints excluded: chain 1 residue 141 LEU Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 197 ASP Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 70 THR Chi-restraints excluded: chain 2 residue 75 ILE Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 120 VAL Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 5 residue 6 ILE Chi-restraints excluded: chain 5 residue 37 HIS Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 9 residue 24 GLU Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain u residue 36 TYR Chi-restraints excluded: chain v residue 4 ILE Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 29 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 523 optimal weight: 20.0000 chunk 292 optimal weight: 6.9990 chunk 783 optimal weight: 30.0000 chunk 641 optimal weight: 10.0000 chunk 259 optimal weight: 20.0000 chunk 943 optimal weight: 5.9990 chunk 1019 optimal weight: 0.9990 chunk 840 optimal weight: 0.0670 chunk 935 optimal weight: 20.0000 chunk 321 optimal weight: 40.0000 chunk 756 optimal weight: 30.0000 overall best weight: 4.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 127 ASN P 25 HIS P 117 GLN ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 126 ASN R 97 ASN T 20 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN U 66 ASN ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 12 GLN c 52 ASN d 37 GLN d 72 ASN ** h 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 58 ASN ** m 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 28 ASN ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 109 GLN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 140 ASN ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 ASN 7 18 GLN 7 67 GLN 9 58 ASN D 64 GLN ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4653 moved from start: 0.5214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 159807 Z= 0.204 Angle : 0.650 15.815 239012 Z= 0.334 Chirality : 0.036 0.317 30564 Planarity : 0.006 0.080 12801 Dihedral : 23.995 178.836 79846 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.42 % Favored : 92.36 % Rotamer: Outliers : 3.63 % Allowed : 16.01 % Favored : 80.36 % Cbeta Deviations : 0.00 % 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: -1.94 (0.10), residues: 5826 helix: -0.26 (0.12), residues: 1873 sheet: -1.30 (0.15), residues: 1069 loop : -1.98 (0.11), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP R 60 HIS 0.011 0.001 HIS c 77 PHE 0.029 0.002 PHE a 21 TYR 0.027 0.002 TYR 5 59 ARG 0.018 0.001 ARG 3 111 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 713 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 537 time to evaluate : 6.427 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: 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 181 MET cc_start: -0.0238 (mmm) cc_final: -0.0517 (mmm) REVERT: Q 30 GLU cc_start: 0.4057 (OUTLIER) cc_final: 0.3094 (pp20) REVERT: S 173 PHE cc_start: 0.4415 (m-10) cc_final: 0.4132 (m-10) REVERT: T 42 GLU cc_start: 0.7736 (pm20) cc_final: 0.7431 (pm20) REVERT: T 44 LYS cc_start: 0.8301 (mmtt) cc_final: 0.7907 (mmtm) REVERT: U 44 ILE cc_start: 0.5605 (OUTLIER) cc_final: 0.2851 (tt) REVERT: V 17 MET cc_start: 0.4302 (ppp) cc_final: 0.4055 (ppp) REVERT: V 49 ILE cc_start: 0.4173 (OUTLIER) cc_final: 0.3904 (tp) REVERT: V 125 MET cc_start: 0.4513 (tpt) cc_final: 0.3769 (mmp) REVERT: W 141 ASP cc_start: 0.8282 (t0) cc_final: 0.7983 (m-30) REVERT: X 53 LYS cc_start: 0.2454 (OUTLIER) cc_final: 0.2105 (mmtm) REVERT: f 1 MET cc_start: 0.6080 (pmm) cc_final: 0.5787 (ppp) REVERT: g 54 GLU cc_start: 0.4389 (OUTLIER) cc_final: 0.4173 (pm20) REVERT: m 40 ASP cc_start: 0.6366 (t0) cc_final: 0.6120 (t0) REVERT: C 196 LEU cc_start: 0.7340 (OUTLIER) cc_final: 0.6982 (pp) REVERT: 6 56 LYS cc_start: 0.6544 (OUTLIER) cc_final: 0.6333 (pttt) REVERT: 6 58 GLU cc_start: 0.5711 (OUTLIER) cc_final: 0.5483 (tm-30) REVERT: 8 68 LYS cc_start: -0.3413 (OUTLIER) cc_final: -0.3673 (pttt) REVERT: 9 19 ASP cc_start: 0.8301 (p0) cc_final: 0.8029 (p0) REVERT: F 23 TYR cc_start: 0.5578 (OUTLIER) cc_final: 0.5037 (m-80) REVERT: J 25 ILE cc_start: 0.6828 (mm) cc_final: 0.6228 (mm) REVERT: J 27 ARG cc_start: 0.5452 (ptp-170) cc_final: 0.4777 (ptp-170) REVERT: J 28 PHE cc_start: 0.5585 (m-10) cc_final: 0.4580 (t80) outliers start: 176 outliers final: 87 residues processed: 670 average time/residue: 1.3932 time to fit residues: 1597.2592 Evaluate side-chains 530 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 433 time to evaluate : 5.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain Q residue 12 THR Chi-restraints excluded: chain Q residue 30 GLU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain V residue 8 TYR Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 68 THR Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 142 ILE Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 19 VAL Chi-restraints excluded: chain X residue 53 LYS Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 79 LEU Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 84 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain d residue 57 PHE Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain f residue 22 ASP Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 59 GLU Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 54 GLU Chi-restraints excluded: chain g residue 74 ILE Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 38 VAL Chi-restraints excluded: chain 1 residue 56 GLU Chi-restraints excluded: chain 1 residue 109 GLN Chi-restraints excluded: chain 1 residue 127 ASP Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 187 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 56 VAL Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 105 ILE Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 151 GLU Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 37 HIS Chi-restraints excluded: chain 6 residue 56 LYS Chi-restraints excluded: chain 6 residue 58 GLU Chi-restraints excluded: chain 7 residue 48 ASP Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 68 LYS Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain t residue 66 MET Chi-restraints excluded: chain u residue 36 TYR Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 6 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 932 optimal weight: 4.9990 chunk 709 optimal weight: 40.0000 chunk 489 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 450 optimal weight: 40.0000 chunk 633 optimal weight: 30.0000 chunk 946 optimal weight: 0.9990 chunk 1002 optimal weight: 40.0000 chunk 494 optimal weight: 20.0000 chunk 897 optimal weight: 4.9990 chunk 270 optimal weight: 3.9990 overall best weight: 6.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: s 123 ASN s 128 GLN ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 115 GLN ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 47 HIS ** W 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 ASN d 59 GLN ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN h 74 ASN k 16 ASN k 20 HIS l 20 ASN ** l 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 103 ASN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 100 ASN 3 152 GLN ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 51 ASN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5040 moved from start: 0.7724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.155 159807 Z= 0.270 Angle : 0.751 13.321 239012 Z= 0.379 Chirality : 0.038 0.380 30564 Planarity : 0.007 0.110 12801 Dihedral : 24.351 179.846 79846 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 35.43 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.19 % Favored : 91.64 % Rotamer: Outliers : 4.15 % Allowed : 17.52 % Favored : 78.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.19 % 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: -1.97 (0.10), residues: 5826 helix: -0.40 (0.11), residues: 1881 sheet: -1.29 (0.15), residues: 1066 loop : -1.92 (0.11), residues: 2879 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP 6 103 HIS 0.020 0.002 HIS 5 58 PHE 0.052 0.003 PHE v 19 TYR 0.051 0.003 TYR J 34 ARG 0.019 0.001 ARG U 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 719 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 518 time to evaluate : 6.451 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: 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: 0.6550 (pmm) cc_final: 0.6019 (pmm) REVERT: S 173 PHE cc_start: 0.4494 (m-10) cc_final: 0.3404 (m-10) REVERT: V 36 MET cc_start: 0.9348 (ppp) cc_final: 0.8583 (ppp) REVERT: V 49 ILE cc_start: 0.4516 (OUTLIER) cc_final: 0.4300 (tp) REVERT: V 117 MET cc_start: 0.6819 (tpt) cc_final: 0.6529 (tpt) REVERT: V 125 MET cc_start: 0.4470 (OUTLIER) cc_final: 0.3840 (mmp) REVERT: X 53 LYS cc_start: 0.4784 (tptp) cc_final: 0.4057 (mmtm) REVERT: Y 78 ARG cc_start: 0.1978 (mtp-110) cc_final: 0.0329 (mmt180) REVERT: Z 31 PHE cc_start: 0.4135 (OUTLIER) cc_final: 0.3804 (m-80) REVERT: Z 136 MET cc_start: 0.7478 (ptm) cc_final: 0.7218 (ppp) REVERT: e 1 MET cc_start: 0.4948 (tpt) cc_final: 0.4443 (tmm) REVERT: i 50 MET cc_start: 0.7419 (ptt) cc_final: 0.5963 (ptp) REVERT: k 56 MET cc_start: 0.5943 (OUTLIER) cc_final: 0.5714 (pmm) REVERT: m 40 ASP cc_start: 0.6104 (t0) cc_final: 0.5807 (t70) REVERT: L 22 MET cc_start: 0.6822 (pmm) cc_final: 0.6377 (pmm) REVERT: C 48 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6596 (mm) REVERT: 3 194 ASP cc_start: 0.6287 (p0) cc_final: 0.6040 (p0) REVERT: 4 39 VAL cc_start: 0.5400 (OUTLIER) cc_final: 0.5160 (m) REVERT: 6 103 TRP cc_start: 0.4988 (m-10) cc_final: 0.4718 (m-10) REVERT: 7 111 MET cc_start: 0.5690 (pmm) cc_final: 0.5363 (pmm) REVERT: 8 32 GLN cc_start: 0.7927 (mp10) cc_final: 0.7696 (pp30) REVERT: 8 68 LYS cc_start: -0.2712 (OUTLIER) cc_final: -0.3507 (pttt) REVERT: F 23 TYR cc_start: 0.6080 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: G 49 GLN cc_start: 0.0130 (OUTLIER) cc_final: -0.1492 (pm20) REVERT: H 36 ILE cc_start: 0.0782 (mt) cc_final: 0.0241 (mm) REVERT: I 1 MET cc_start: 0.5815 (tpp) cc_final: 0.3019 (mtm) REVERT: J 17 MET cc_start: -0.2588 (ttp) cc_final: -0.4502 (mtm) outliers start: 201 outliers final: 118 residues processed: 666 average time/residue: 1.3007 time to fit residues: 1498.2277 Evaluate side-chains 555 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 428 time to evaluate : 6.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 267 ILE Chi-restraints excluded: chain Q residue 11 MET Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 127 PHE Chi-restraints excluded: chain Q residue 165 MET Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 20 ASN Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain V residue 8 TYR Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 49 ILE Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 125 MET Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 17 ARG Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 43 ILE Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 31 PHE Chi-restraints excluded: chain Z residue 88 ASN Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 116 VAL Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 84 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain e residue 40 MET Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain f residue 22 ASP Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 56 MET Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain m residue 11 ARG Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 3 VAL Chi-restraints excluded: chain r residue 16 ILE Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 56 GLU Chi-restraints excluded: chain 1 residue 93 ASN Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 56 VAL Chi-restraints excluded: chain 2 residue 67 THR Chi-restraints excluded: chain 2 residue 84 VAL Chi-restraints excluded: chain 2 residue 128 VAL Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 39 VAL Chi-restraints excluded: chain 4 residue 46 VAL Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 6 residue 56 LYS Chi-restraints excluded: chain 7 residue 80 ARG Chi-restraints excluded: chain 8 residue 58 VAL Chi-restraints excluded: chain 8 residue 68 LYS Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 85 MET Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 62 ASN Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 20 ASN Chi-restraints excluded: chain H residue 88 ARG Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 42 ILE Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 29 VAL Chi-restraints excluded: chain K residue 51 TYR Chi-restraints excluded: chain t residue 47 LEU Chi-restraints excluded: chain t residue 81 ARG Chi-restraints excluded: chain u residue 36 TYR Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 29 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 834 optimal weight: 9.9990 chunk 569 optimal weight: 50.0000 chunk 14 optimal weight: 40.0000 chunk 746 optimal weight: 30.0000 chunk 413 optimal weight: 20.0000 chunk 855 optimal weight: 0.3980 chunk 692 optimal weight: 30.0000 chunk 1 optimal weight: 50.0000 chunk 511 optimal weight: 30.0000 chunk 899 optimal weight: 9.9990 chunk 252 optimal weight: 6.9990 overall best weight: 9.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 81 ASN ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 20 ASN ** l 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 13 ASN ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 89 HIS ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 68 ASN 6 142 HIS 8 25 ASN 8 31 ASN ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN F 8 ASN ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 54 GLN t 14 HIS ** u 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5336 moved from start: 1.0622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.165 159807 Z= 0.328 Angle : 0.834 17.889 239012 Z= 0.423 Chirality : 0.042 0.372 30564 Planarity : 0.008 0.160 12801 Dihedral : 25.051 178.683 79846 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 40.85 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.17 % Favored : 90.59 % Rotamer: Outliers : 5.18 % Allowed : 18.80 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.10), residues: 5826 helix: -0.70 (0.11), residues: 1874 sheet: -1.43 (0.15), residues: 1031 loop : -2.11 (0.11), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.005 TRP 6 103 HIS 0.047 0.003 HIS 2 6 PHE 0.072 0.005 PHE a 102 TYR 0.052 0.004 TYR P 171 ARG 0.064 0.001 ARG S 178 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 530 time to evaluate : 6.463 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: s 149 MET cc_start: 0.7503 (pmm) cc_final: 0.7020 (pmm) REVERT: Q 30 GLU cc_start: 0.4407 (OUTLIER) cc_final: 0.4200 (pt0) REVERT: S 173 PHE cc_start: 0.2929 (m-10) cc_final: 0.2649 (m-10) REVERT: S 177 PHE cc_start: 0.5476 (OUTLIER) cc_final: 0.4606 (m-80) REVERT: T 83 PHE cc_start: 0.5633 (OUTLIER) cc_final: 0.5235 (t80) REVERT: V 36 MET cc_start: 0.9183 (ppp) cc_final: 0.8597 (ppp) REVERT: V 117 MET cc_start: 0.7006 (tpt) cc_final: 0.6517 (tpt) REVERT: V 136 MET cc_start: 0.5782 (OUTLIER) cc_final: 0.5153 (mmm) REVERT: X 1 MET cc_start: 0.2705 (OUTLIER) cc_final: 0.1343 (ppp) REVERT: X 53 LYS cc_start: 0.6104 (tptp) cc_final: 0.5828 (mmtm) REVERT: a 24 MET cc_start: 0.3160 (mmt) cc_final: 0.2958 (mmt) REVERT: e 1 MET cc_start: 0.5556 (tpt) cc_final: 0.5288 (tpt) REVERT: f 110 ARG cc_start: 0.7025 (OUTLIER) cc_final: 0.6795 (ptt90) REVERT: l 19 LEU cc_start: 0.8634 (pp) cc_final: 0.8355 (mm) REVERT: m 40 ASP cc_start: 0.5709 (t0) cc_final: 0.5349 (t0) REVERT: L 22 MET cc_start: 0.6506 (pmm) cc_final: 0.6009 (pmm) REVERT: C 48 LEU cc_start: 0.7943 (mp) cc_final: 0.7529 (mm) REVERT: C 166 ASP cc_start: 0.4618 (OUTLIER) cc_final: 0.3796 (p0) REVERT: 1 214 LEU cc_start: 0.7912 (mp) cc_final: 0.7677 (tp) REVERT: 2 47 LEU cc_start: 0.7661 (mt) cc_final: 0.7232 (mt) REVERT: 2 122 SER cc_start: 0.8465 (m) cc_final: 0.8173 (p) REVERT: 4 71 MET cc_start: 0.6235 (mmm) cc_final: 0.5590 (mmm) REVERT: 5 42 TRP cc_start: 0.4738 (OUTLIER) cc_final: 0.4512 (t60) REVERT: 5 59 TYR cc_start: 0.2963 (OUTLIER) cc_final: 0.2205 (m-10) REVERT: 8 68 LYS cc_start: -0.2464 (OUTLIER) cc_final: -0.3131 (pttt) REVERT: 9 15 HIS cc_start: 0.7719 (OUTLIER) cc_final: 0.7136 (p-80) REVERT: F 23 TYR cc_start: 0.6214 (OUTLIER) cc_final: 0.5732 (m-80) REVERT: I 1 MET cc_start: 0.5363 (tpp) cc_final: 0.2674 (mtm) REVERT: J 17 MET cc_start: -0.0735 (ttp) cc_final: -0.2484 (mpp) outliers start: 251 outliers final: 134 residues processed: 718 average time/residue: 1.2974 time to fit residues: 1618.1913 Evaluate side-chains 582 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 436 time to evaluate : 6.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 134 ASN Chi-restraints excluded: chain P residue 172 VAL Chi-restraints excluded: chain P residue 243 HIS Chi-restraints excluded: chain P residue 261 LYS Chi-restraints excluded: chain Q residue 30 GLU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain Q residue 185 ASN Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain R residue 116 ASP Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain T residue 103 ILE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 35 LYS Chi-restraints excluded: chain U residue 44 ILE Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain V residue 8 TYR Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 2 ARG Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain a residue 90 ARG Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 54 VAL Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 84 GLU Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain d residue 53 ARG Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 13 ARG Chi-restraints excluded: chain e residue 32 THR Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 110 ARG Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain i residue 5 ASN Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 50 MET Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 26 PHE Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain C residue 166 ASP Chi-restraints excluded: chain C residue 168 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 85 LEU Chi-restraints excluded: chain 1 residue 110 SER Chi-restraints excluded: chain 1 residue 127 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 35 SER Chi-restraints excluded: chain 2 residue 55 ILE Chi-restraints excluded: chain 2 residue 56 VAL Chi-restraints excluded: chain 2 residue 67 THR Chi-restraints excluded: chain 2 residue 157 LEU Chi-restraints excluded: chain 2 residue 165 THR Chi-restraints excluded: chain 2 residue 191 THR Chi-restraints excluded: chain 3 residue 145 ILE Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 105 ILE Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 26 THR Chi-restraints excluded: chain 5 residue 42 TRP Chi-restraints excluded: chain 5 residue 59 TYR Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 93 LYS Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 7 residue 83 LEU Chi-restraints excluded: chain 8 residue 39 PHE Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 50 GLN Chi-restraints excluded: chain 8 residue 68 LYS Chi-restraints excluded: chain 8 residue 127 PHE Chi-restraints excluded: chain 9 residue 15 HIS Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain E residue 8 VAL Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 53 ILE Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 49 GLN Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 73 PHE Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 48 ASP Chi-restraints excluded: chain K residue 30 LYS Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain t residue 14 HIS Chi-restraints excluded: chain u residue 36 TYR Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 17 ARG Chi-restraints excluded: chain v residue 29 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 337 optimal weight: 8.9990 chunk 902 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 588 optimal weight: 30.0000 chunk 247 optimal weight: 10.0000 chunk 1003 optimal weight: 6.9990 chunk 832 optimal weight: 7.9990 chunk 464 optimal weight: 30.0000 chunk 83 optimal weight: 10.0000 chunk 331 optimal weight: 1.9990 chunk 526 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 ASN ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN T 20 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 43 ASN W 136 GLN ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN l 20 ASN ** l 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 38 GLN ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 168 HIS 3 89 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 68 GLN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 37 GLN D 64 GLN ** D 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 49 GLN ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 14 HIS ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 68 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5330 moved from start: 1.1261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 159807 Z= 0.225 Angle : 0.695 13.685 239012 Z= 0.351 Chirality : 0.037 0.315 30564 Planarity : 0.006 0.185 12801 Dihedral : 24.783 179.606 79846 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 35.55 Ramachandran Plot: Outliers : 0.14 % Allowed : 8.32 % Favored : 91.54 % Rotamer: Outliers : 3.98 % Allowed : 21.83 % Favored : 74.19 % 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: -1.95 (0.11), residues: 5826 helix: -0.29 (0.12), residues: 1870 sheet: -1.28 (0.15), residues: 1049 loop : -1.97 (0.11), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP t 34 HIS 0.017 0.002 HIS t 14 PHE 0.038 0.002 PHE 5 78 TYR 0.024 0.002 TYR H 78 ARG 0.010 0.001 ARG 9 37 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 673 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 480 time to evaluate : 6.483 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: symmetry clash REVERT: s 149 MET cc_start: 0.7490 (pmm) cc_final: 0.6992 (pmm) REVERT: Q 123 LYS cc_start: 0.5015 (OUTLIER) cc_final: 0.4607 (ptpt) REVERT: S 177 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5094 (m-80) REVERT: T 83 PHE cc_start: 0.5970 (OUTLIER) cc_final: 0.5450 (t80) REVERT: U 112 LYS cc_start: 0.2613 (ttpt) cc_final: 0.2027 (mmmm) REVERT: V 36 MET cc_start: 0.9218 (ppp) cc_final: 0.8626 (ppp) REVERT: V 117 MET cc_start: 0.5928 (tpt) cc_final: 0.4718 (tpp) REVERT: V 136 MET cc_start: 0.5931 (OUTLIER) cc_final: 0.5362 (mmm) REVERT: V 138 LEU cc_start: 0.0136 (OUTLIER) cc_final: -0.0126 (mt) REVERT: W 1 MET cc_start: 0.2972 (mtm) cc_final: 0.2578 (mtm) REVERT: X 1 MET cc_start: 0.2610 (OUTLIER) cc_final: 0.1505 (ppp) REVERT: X 53 LYS cc_start: 0.6581 (tptp) cc_final: 0.6201 (mmtm) REVERT: Y 78 ARG cc_start: 0.1615 (mtp-110) cc_final: -0.0347 (mmt180) REVERT: Y 93 ASN cc_start: 0.7942 (p0) cc_final: 0.7605 (t0) REVERT: Z 136 MET cc_start: 0.7474 (ppp) cc_final: 0.6971 (ppp) REVERT: a 24 MET cc_start: 0.3389 (mmt) cc_final: 0.3148 (mmt) REVERT: e 98 ILE cc_start: 0.6230 (mm) cc_final: 0.5895 (mm) REVERT: g 24 MET cc_start: 0.8103 (tpp) cc_final: 0.7889 (tpp) REVERT: i 5 ASN cc_start: 0.7940 (OUTLIER) cc_final: 0.7659 (t0) REVERT: p 46 LYS cc_start: 0.7935 (ptmt) cc_final: 0.7539 (tptt) REVERT: q 49 MET cc_start: 0.7362 (tpp) cc_final: 0.7084 (tpp) REVERT: L 22 MET cc_start: 0.6301 (pmm) cc_final: 0.5837 (pmm) REVERT: C 48 LEU cc_start: 0.8285 (mp) cc_final: 0.8080 (mm) REVERT: 5 21 MET cc_start: 0.8900 (ppp) cc_final: 0.8507 (ppp) REVERT: 6 116 MET cc_start: 0.1012 (ptt) cc_final: 0.0743 (ptt) REVERT: 7 66 PHE cc_start: 0.7838 (t80) cc_final: 0.7550 (t80) REVERT: 7 67 GLN cc_start: 0.7271 (mp10) cc_final: 0.7067 (mp10) REVERT: 8 31 ASN cc_start: 0.6767 (t0) cc_final: 0.6332 (t0) REVERT: 8 32 GLN cc_start: 0.7986 (mp10) cc_final: 0.7663 (pm20) REVERT: 8 46 MET cc_start: 0.6770 (ppp) cc_final: 0.6438 (ppp) REVERT: 8 68 LYS cc_start: -0.2281 (OUTLIER) cc_final: -0.3104 (pttt) REVERT: 9 15 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7195 (p-80) REVERT: H 36 ILE cc_start: 0.0934 (mt) cc_final: 0.0401 (mm) REVERT: I 1 MET cc_start: 0.5246 (tpp) cc_final: 0.3058 (mtm) REVERT: J 17 MET cc_start: -0.0953 (ttp) cc_final: -0.1163 (tpt) REVERT: J 27 ARG cc_start: 0.6047 (ptp-170) cc_final: 0.5846 (ptp-170) outliers start: 193 outliers final: 112 residues processed: 619 average time/residue: 1.3376 time to fit residues: 1441.3301 Evaluate side-chains 541 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 420 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain Q residue 30 GLU Chi-restraints excluded: chain Q residue 73 VAL Chi-restraints excluded: chain Q residue 79 LEU Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 123 LYS Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain R residue 124 PHE Chi-restraints excluded: chain R residue 191 ASP Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 35 LYS Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain V residue 8 TYR Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 107 LEU Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Z residue 7 THR Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 70 THR Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 84 GLU Chi-restraints excluded: chain c residue 16 ASP Chi-restraints excluded: chain c residue 19 SER Chi-restraints excluded: chain c residue 32 VAL Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 82 ASP Chi-restraints excluded: chain d residue 53 ARG Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain i residue 5 ASN Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 3 VAL Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 13 THR Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 2 residue 21 THR Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 67 THR Chi-restraints excluded: chain 2 residue 84 VAL Chi-restraints excluded: chain 3 residue 20 PHE Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 129 VAL Chi-restraints excluded: chain 3 residue 145 ILE Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 24 THR Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 68 GLN Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 68 LYS Chi-restraints excluded: chain 9 residue 15 HIS Chi-restraints excluded: chain 9 residue 73 LEU Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 129 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain F residue 91 HIS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain I residue 19 VAL Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 12 PHE Chi-restraints excluded: chain v residue 29 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 967 optimal weight: 30.0000 chunk 113 optimal weight: 50.0000 chunk 571 optimal weight: 30.0000 chunk 732 optimal weight: 30.0000 chunk 567 optimal weight: 50.0000 chunk 844 optimal weight: 10.0000 chunk 560 optimal weight: 30.0000 chunk 999 optimal weight: 30.0000 chunk 625 optimal weight: 20.0000 chunk 609 optimal weight: 30.0000 chunk 461 optimal weight: 40.0000 overall best weight: 24.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 127 ASN ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 3 GLN ** X 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 18 GLN ** b 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 15 GLN ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 72 ASN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 15 GLN f 40 ASN ** l 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 43 HIS ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 40 GLN 3 41 HIS ** 3 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 17 GLN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 75 GLN ** 8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 HIS ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 45 HIS ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 48 GLN ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5864 moved from start: 1.5135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.164 159807 Z= 0.624 Angle : 1.341 31.735 239012 Z= 0.660 Chirality : 0.062 0.614 30564 Planarity : 0.011 0.194 12801 Dihedral : 26.423 179.715 79846 Min Nonbonded Distance : 1.702 Molprobity Statistics. All-atom Clashscore : 89.86 Ramachandran Plot: Outliers : 0.34 % Allowed : 13.47 % Favored : 86.18 % Rotamer: Outliers : 5.69 % Allowed : 22.05 % Favored : 72.25 % 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: -3.45 (0.10), residues: 5826 helix: -1.83 (0.10), residues: 1806 sheet: -1.93 (0.15), residues: 974 loop : -2.74 (0.10), residues: 3046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.005 TRP t 34 HIS 0.023 0.004 HIS 6 142 PHE 0.053 0.005 PHE R 23 TYR 0.046 0.005 TYR F 23 ARG 0.023 0.002 ARG d 11 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 760 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 484 time to evaluate : 6.401 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: symmetry clash revert: symmetry clash REVERT: P 225 MET cc_start: 0.4212 (mmt) cc_final: 0.3615 (mmt) REVERT: Q 123 LYS cc_start: 0.6080 (OUTLIER) cc_final: 0.5278 (mtmt) REVERT: R 199 MET cc_start: 0.7291 (ptp) cc_final: 0.6409 (tpt) REVERT: U 42 LYS cc_start: 0.8805 (mtmt) cc_final: 0.8602 (tmtt) REVERT: U 112 LYS cc_start: 0.3449 (ttpt) cc_final: 0.2914 (mmmm) REVERT: V 136 MET cc_start: 0.6987 (OUTLIER) cc_final: 0.6590 (mmm) REVERT: V 138 LEU cc_start: 0.1249 (OUTLIER) cc_final: 0.1037 (mt) REVERT: X 1 MET cc_start: 0.2593 (OUTLIER) cc_final: 0.2152 (ppp) REVERT: Y 93 ASN cc_start: 0.8479 (p0) cc_final: 0.8037 (t0) REVERT: Z 105 MET cc_start: 0.2599 (OUTLIER) cc_final: 0.1978 (mmm) REVERT: Z 136 MET cc_start: 0.7827 (ppp) cc_final: 0.7302 (ppp) REVERT: a 69 ARG cc_start: 0.4913 (mtt90) cc_final: 0.4478 (mmp-170) REVERT: a 75 ILE cc_start: 0.6432 (mm) cc_final: 0.6134 (mm) REVERT: i 5 ASN cc_start: 0.7886 (OUTLIER) cc_final: 0.7646 (t0) REVERT: k 48 THR cc_start: 0.7896 (OUTLIER) cc_final: 0.7422 (p) REVERT: k 71 LEU cc_start: 0.8816 (mt) cc_final: 0.8598 (mt) REVERT: p 46 LYS cc_start: 0.7836 (ptmt) cc_final: 0.7539 (tptt) REVERT: q 49 MET cc_start: 0.6893 (tpp) cc_final: 0.6515 (tpp) REVERT: C 48 LEU cc_start: 0.8603 (mp) cc_final: 0.8067 (tp) REVERT: 1 184 PHE cc_start: 0.7289 (OUTLIER) cc_final: 0.6325 (m-80) REVERT: 2 79 LYS cc_start: 0.8002 (tppt) cc_final: 0.7714 (tppt) REVERT: 2 142 MET cc_start: 0.7989 (ppp) cc_final: 0.7523 (ptt) REVERT: 4 71 MET cc_start: 0.6905 (mmm) cc_final: 0.6569 (mmm) REVERT: 5 9 MET cc_start: 0.5918 (tpp) cc_final: 0.5165 (tpp) REVERT: 5 86 ARG cc_start: 0.5696 (mmm-85) cc_final: 0.3974 (mmt180) REVERT: 8 46 MET cc_start: 0.7192 (ppp) cc_final: 0.6838 (ppp) REVERT: 8 89 GLU cc_start: 0.6370 (tm-30) cc_final: 0.5902 (tm-30) REVERT: 8 90 TYR cc_start: 0.6462 (OUTLIER) cc_final: 0.6032 (m-80) REVERT: 8 93 SER cc_start: 0.8003 (t) cc_final: 0.7742 (p) REVERT: 9 15 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7639 (p-80) REVERT: 9 47 GLU cc_start: 0.5959 (mt-10) cc_final: 0.5572 (mm-30) REVERT: D 24 HIS cc_start: 0.5756 (OUTLIER) cc_final: 0.4837 (t-90) REVERT: I 1 MET cc_start: 0.6059 (tpp) cc_final: 0.3554 (mtm) REVERT: J 17 MET cc_start: 0.1035 (ttp) cc_final: 0.0710 (tpp) REVERT: t 81 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.2831 (ppt170) outliers start: 276 outliers final: 190 residues processed: 699 average time/residue: 1.4721 time to fit residues: 1798.3759 Evaluate side-chains 627 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 202 poor density : 425 time to evaluate : 6.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 147 ASN Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 94 VAL Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 134 ASN Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain P residue 255 LYS Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 33 ARG Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 123 LYS Chi-restraints excluded: chain Q residue 169 ARG Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain R residue 3 LEU Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain S residue 38 MET Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 138 PHE Chi-restraints excluded: chain S residue 158 THR Chi-restraints excluded: chain S residue 163 ASP Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 35 LYS Chi-restraints excluded: chain U residue 122 LEU Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain W residue 28 LEU Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain X residue 25 LEU Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 69 VAL Chi-restraints excluded: chain X residue 100 PHE Chi-restraints excluded: chain X residue 107 LEU Chi-restraints excluded: chain Y residue 10 GLU Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 116 VAL Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 123 ARG Chi-restraints excluded: chain Y residue 132 ARG Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 25 ASP Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 88 ASN Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain Z residue 105 MET Chi-restraints excluded: chain Z residue 132 THR Chi-restraints excluded: chain a residue 90 ARG Chi-restraints excluded: chain a residue 103 ARG Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 60 GLU Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 84 GLU Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain b residue 108 ASP Chi-restraints excluded: chain c residue 16 ASP Chi-restraints excluded: chain c residue 65 SER Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain d residue 53 ARG Chi-restraints excluded: chain e residue 45 GLU Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain f residue 30 SER Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 110 ARG Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 43 ILE Chi-restraints excluded: chain g residue 51 PHE Chi-restraints excluded: chain i residue 5 ASN Chi-restraints excluded: chain i residue 8 VAL Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 47 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 50 ARG Chi-restraints excluded: chain k residue 58 VAL Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 26 PHE Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain n residue 4 GLN Chi-restraints excluded: chain n residue 9 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 151 ILE Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 105 GLU Chi-restraints excluded: chain 3 residue 20 PHE Chi-restraints excluded: chain 3 residue 124 MET Chi-restraints excluded: chain 3 residue 145 ILE Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 194 ASP Chi-restraints excluded: chain 4 residue 15 LEU Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 142 ASP Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 5 residue 70 VAL Chi-restraints excluded: chain 6 residue 3 ARG Chi-restraints excluded: chain 6 residue 48 GLU Chi-restraints excluded: chain 6 residue 73 VAL Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 106 GLU Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 7 residue 10 MET Chi-restraints excluded: chain 7 residue 38 ASN Chi-restraints excluded: chain 7 residue 50 LYS Chi-restraints excluded: chain 7 residue 74 SER Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 8 residue 30 ILE Chi-restraints excluded: chain 8 residue 37 GLN Chi-restraints excluded: chain 8 residue 39 PHE Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 8 residue 50 GLN Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 8 residue 90 TYR Chi-restraints excluded: chain 8 residue 120 LYS Chi-restraints excluded: chain 9 residue 15 HIS Chi-restraints excluded: chain 9 residue 26 VAL Chi-restraints excluded: chain 9 residue 71 LEU Chi-restraints excluded: chain 9 residue 73 LEU Chi-restraints excluded: chain D residue 24 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 42 LEU Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 119 ASN Chi-restraints excluded: chain E residue 16 VAL Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain F residue 4 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 82 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 93 ILE Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 46 HIS Chi-restraints excluded: chain H residue 68 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 26 ILE Chi-restraints excluded: chain K residue 55 LEU Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 81 ARG Chi-restraints excluded: chain u residue 48 GLN Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain v residue 6 VAL Chi-restraints excluded: chain v residue 12 PHE Chi-restraints excluded: chain v residue 14 VAL Chi-restraints excluded: chain v residue 17 ARG Chi-restraints excluded: chain v residue 20 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 618 optimal weight: 10.0000 chunk 399 optimal weight: 20.0000 chunk 596 optimal weight: 20.0000 chunk 301 optimal weight: 7.9990 chunk 196 optimal weight: 30.0000 chunk 193 optimal weight: 9.9990 chunk 635 optimal weight: 9.9990 chunk 680 optimal weight: 30.0000 chunk 494 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 785 optimal weight: 20.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 ASN ** b 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 40 ASN h 74 ASN i 87 GLN ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 45 GLN ** n 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 58 ASN 1 177 ASN 2 19 ASN ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 74 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 ASN ** 5 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 40 GLN ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 48 GLN ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 1.5042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.110 159807 Z= 0.280 Angle : 0.829 16.010 239012 Z= 0.419 Chirality : 0.043 0.394 30564 Planarity : 0.007 0.192 12801 Dihedral : 25.772 179.743 79844 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 45.74 Ramachandran Plot: Outliers : 0.17 % Allowed : 10.01 % Favored : 89.82 % Rotamer: Outliers : 4.39 % Allowed : 25.15 % Favored : 70.46 % 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: -2.94 (0.10), residues: 5826 helix: -1.20 (0.11), residues: 1868 sheet: -1.78 (0.15), residues: 969 loop : -2.54 (0.10), residues: 2989 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP P 213 HIS 0.015 0.002 HIS D 22 PHE 0.047 0.003 PHE 8 127 TYR 0.040 0.003 TYR 1 213 ARG 0.015 0.001 ARG 5 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 701 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 213 poor density : 488 time to evaluate : 5.798 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: P 225 MET cc_start: 0.4032 (mmt) cc_final: 0.3680 (mmp) REVERT: Q 123 LYS cc_start: 0.5901 (OUTLIER) cc_final: 0.5249 (mtmt) REVERT: Q 185 ASN cc_start: 0.6108 (m-40) cc_final: 0.5733 (m-40) REVERT: R 106 LYS cc_start: 0.6123 (mttm) cc_final: 0.5785 (mttp) REVERT: R 199 MET cc_start: 0.7396 (ptp) cc_final: 0.6639 (tpt) REVERT: U 57 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8824 (pttp) REVERT: V 40 LYS cc_start: 0.7129 (OUTLIER) cc_final: 0.6734 (pptt) REVERT: V 125 MET cc_start: 0.5963 (mmt) cc_final: 0.5437 (mmp) REVERT: V 136 MET cc_start: 0.6680 (OUTLIER) cc_final: 0.6338 (mmm) REVERT: V 138 LEU cc_start: 0.0494 (OUTLIER) cc_final: 0.0291 (mt) REVERT: W 108 MET cc_start: 0.5506 (mmt) cc_final: 0.5225 (mmt) REVERT: X 1 MET cc_start: 0.2937 (OUTLIER) cc_final: 0.2736 (ppp) REVERT: X 116 ILE cc_start: 0.7804 (mt) cc_final: 0.7412 (tp) REVERT: Y 78 ARG cc_start: 0.2273 (mtp-110) cc_final: 0.0255 (mmt180) REVERT: Y 93 ASN cc_start: 0.8379 (p0) cc_final: 0.8158 (t0) REVERT: Z 136 MET cc_start: 0.7923 (ppp) cc_final: 0.7508 (ppp) REVERT: i 50 MET cc_start: 0.7563 (ptt) cc_final: 0.7092 (ptt) REVERT: k 48 THR cc_start: 0.7964 (m) cc_final: 0.7427 (p) REVERT: p 46 LYS cc_start: 0.7643 (ptmt) cc_final: 0.7255 (tptt) REVERT: q 49 MET cc_start: 0.6791 (tpp) cc_final: 0.6414 (tpp) REVERT: C 48 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.7847 (tp) REVERT: 1 184 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.6176 (m-80) REVERT: 2 79 LYS cc_start: 0.8004 (tppt) cc_final: 0.7742 (tppt) REVERT: 2 83 ASP cc_start: 0.6388 (t0) cc_final: 0.5321 (p0) REVERT: 2 129 MET cc_start: 0.7480 (tmm) cc_final: 0.7239 (tpt) REVERT: 5 9 MET cc_start: 0.5884 (tpp) cc_final: 0.5627 (mmm) REVERT: 6 116 MET cc_start: 0.1436 (ptt) cc_final: 0.0684 (ptt) REVERT: 8 46 MET cc_start: 0.7188 (ppp) cc_final: 0.6778 (ppp) REVERT: 8 93 SER cc_start: 0.7484 (t) cc_final: 0.6975 (p) REVERT: 9 6 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.7422 (pt) REVERT: 9 15 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.7338 (p-80) REVERT: H 36 ILE cc_start: 0.1728 (mt) cc_final: 0.1421 (mm) REVERT: I 1 MET cc_start: 0.5223 (tpp) cc_final: 0.3275 (mtm) REVERT: J 8 LEU cc_start: 0.7135 (tp) cc_final: 0.6913 (tt) REVERT: J 17 MET cc_start: 0.0861 (ttp) cc_final: 0.0530 (tpp) REVERT: t 79 THR cc_start: 0.7114 (OUTLIER) cc_final: 0.6392 (t) REVERT: t 81 ARG cc_start: 0.5789 (OUTLIER) cc_final: 0.2622 (ppt170) REVERT: v 36 GLU cc_start: 0.6552 (tm-30) cc_final: 0.6166 (tm-30) outliers start: 213 outliers final: 136 residues processed: 646 average time/residue: 1.3376 time to fit residues: 1490.4950 Evaluate side-chains 581 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 148 poor density : 433 time to evaluate : 5.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain s residue 149 MET Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 134 ASN Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 221 ARG Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain Q residue 30 GLU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 123 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 169 ARG Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain Q residue 175 LEU Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 138 PHE Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 74 SER Chi-restraints excluded: chain T residue 83 PHE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 57 LYS Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain W residue 5 THR Chi-restraints excluded: chain X residue 1 MET Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 22 ILE Chi-restraints excluded: chain X residue 61 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain X residue 88 ASN Chi-restraints excluded: chain X residue 107 LEU Chi-restraints excluded: chain Y residue 89 VAL Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 123 ARG Chi-restraints excluded: chain Y residue 132 ARG Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 42 THR Chi-restraints excluded: chain Z residue 54 THR Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 90 ARG Chi-restraints excluded: chain a residue 103 ARG Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain c residue 16 ASP Chi-restraints excluded: chain c residue 76 THR Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain d residue 9 ILE Chi-restraints excluded: chain d residue 53 ARG Chi-restraints excluded: chain d residue 57 PHE Chi-restraints excluded: chain d residue 100 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 99 THR Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 50 ARG Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain n residue 9 THR Chi-restraints excluded: chain n residue 28 LEU Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain C residue 48 LEU Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 105 GLU Chi-restraints excluded: chain 3 residue 20 PHE Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 151 LYS Chi-restraints excluded: chain 3 residue 194 ASP Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 5 residue 64 VAL Chi-restraints excluded: chain 6 residue 73 VAL Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 74 SER Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 8 residue 37 GLN Chi-restraints excluded: chain 8 residue 47 VAL Chi-restraints excluded: chain 9 residue 6 ILE Chi-restraints excluded: chain 9 residue 15 HIS Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 71 HIS Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 81 ARG Chi-restraints excluded: chain u residue 58 VAL Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain v residue 12 PHE Chi-restraints excluded: chain v residue 17 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 909 optimal weight: 8.9990 chunk 957 optimal weight: 10.0000 chunk 873 optimal weight: 40.0000 chunk 931 optimal weight: 40.0000 chunk 560 optimal weight: 30.0000 chunk 405 optimal weight: 30.0000 chunk 731 optimal weight: 30.0000 chunk 285 optimal weight: 8.9990 chunk 841 optimal weight: 3.9990 chunk 880 optimal weight: 30.0000 chunk 928 optimal weight: 20.0000 overall best weight: 10.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN Q 185 ASN ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 119 ASN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 52 ASN ** d 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 72 ASN f 40 ASN ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 GLN ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 19 HIS ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 37 GLN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 1.5881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 159807 Z= 0.311 Angle : 0.843 15.810 239012 Z= 0.424 Chirality : 0.043 0.363 30564 Planarity : 0.007 0.194 12801 Dihedral : 25.690 179.651 79844 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 52.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 12.15 % Favored : 87.73 % Rotamer: Outliers : 4.13 % Allowed : 26.16 % Favored : 69.71 % 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: -2.85 (0.10), residues: 5826 helix: -1.09 (0.11), residues: 1849 sheet: -1.74 (0.15), residues: 963 loop : -2.49 (0.10), residues: 3014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.003 TRP t 34 HIS 0.027 0.002 HIS Y 35 PHE 0.031 0.003 PHE S 100 TYR 0.036 0.003 TYR u 36 ARG 0.025 0.001 ARG U 51 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 682 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 482 time to evaluate : 6.502 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: P 225 MET cc_start: 0.4175 (mmt) cc_final: 0.3842 (mmp) REVERT: P 239 ASN cc_start: 0.3342 (OUTLIER) cc_final: 0.3098 (t0) REVERT: Q 123 LYS cc_start: 0.5822 (OUTLIER) cc_final: 0.5050 (mtmt) REVERT: R 19 PHE cc_start: 0.6522 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: R 199 MET cc_start: 0.7260 (ptp) cc_final: 0.6609 (tpt) REVERT: S 108 VAL cc_start: 0.7647 (OUTLIER) cc_final: 0.7422 (t) REVERT: V 36 MET cc_start: 0.8801 (ppp) cc_final: 0.7936 (ppp) REVERT: V 125 MET cc_start: 0.5869 (mmt) cc_final: 0.5323 (mmp) REVERT: V 136 MET cc_start: 0.6350 (OUTLIER) cc_final: 0.6031 (mmm) REVERT: V 138 LEU cc_start: 0.0536 (OUTLIER) cc_final: 0.0324 (mt) REVERT: X 44 LYS cc_start: 0.6580 (mtmm) cc_final: 0.6215 (mtmm) REVERT: Z 136 MET cc_start: 0.7980 (ppp) cc_final: 0.7553 (ppp) REVERT: e 79 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.5176 (pmt-80) REVERT: g 40 LYS cc_start: 0.6666 (OUTLIER) cc_final: 0.5663 (mttt) REVERT: k 48 THR cc_start: 0.7688 (m) cc_final: 0.7141 (p) REVERT: m 3 LYS cc_start: 0.7197 (pttm) cc_final: 0.6972 (pttp) REVERT: p 46 LYS cc_start: 0.7354 (ptmt) cc_final: 0.7015 (tptt) REVERT: q 49 MET cc_start: 0.7153 (tpp) cc_final: 0.6782 (tpp) REVERT: C 48 LEU cc_start: 0.8605 (mp) cc_final: 0.7871 (tp) REVERT: 1 184 PHE cc_start: 0.6899 (OUTLIER) cc_final: 0.5792 (m-80) REVERT: 2 79 LYS cc_start: 0.8347 (tppt) cc_final: 0.8144 (tppt) REVERT: 2 83 ASP cc_start: 0.6631 (t0) cc_final: 0.5692 (p0) REVERT: 2 129 MET cc_start: 0.7751 (tmm) cc_final: 0.7381 (tpt) REVERT: 4 71 MET cc_start: 0.6493 (mmm) cc_final: 0.5991 (mmp) REVERT: 5 13 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7933 (p0) REVERT: 5 88 MET cc_start: 0.4589 (tpp) cc_final: 0.4140 (tpp) REVERT: 6 40 GLU cc_start: 0.4589 (OUTLIER) cc_final: 0.4269 (pt0) REVERT: 6 116 MET cc_start: 0.1315 (ptt) cc_final: 0.0714 (mtt) REVERT: 8 93 SER cc_start: 0.7822 (t) cc_final: 0.7320 (p) REVERT: 9 15 HIS cc_start: 0.7870 (OUTLIER) cc_final: 0.7431 (p-80) REVERT: G 50 THR cc_start: 0.7012 (OUTLIER) cc_final: 0.6689 (p) REVERT: I 1 MET cc_start: 0.5819 (tpp) cc_final: 0.3528 (mtm) REVERT: J 8 LEU cc_start: 0.7348 (tp) cc_final: 0.7132 (tt) REVERT: t 79 THR cc_start: 0.7150 (OUTLIER) cc_final: 0.6416 (t) REVERT: t 81 ARG cc_start: 0.6113 (OUTLIER) cc_final: 0.3320 (ppt170) REVERT: v 36 GLU cc_start: 0.6724 (tm-30) cc_final: 0.6224 (tm-30) outliers start: 200 outliers final: 135 residues processed: 632 average time/residue: 1.3163 time to fit residues: 1444.7662 Evaluate side-chains 593 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 443 time to evaluate : 6.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 134 ASN Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 243 HIS Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain Q residue 30 GLU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 123 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 169 ARG Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 4 VAL Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain R residue 69 ARG Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 111 ILE Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 138 PHE Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain V residue 138 LEU Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 70 LYS Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 110 VAL Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Y residue 123 ARG Chi-restraints excluded: chain Y residue 132 ARG Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain Z residue 126 ILE Chi-restraints excluded: chain a residue 90 ARG Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 65 THR Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain b residue 88 LYS Chi-restraints excluded: chain c residue 16 ASP Chi-restraints excluded: chain d residue 9 ILE Chi-restraints excluded: chain d residue 53 ARG Chi-restraints excluded: chain d residue 57 PHE Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 79 ARG Chi-restraints excluded: chain e residue 84 ARG Chi-restraints excluded: chain e residue 98 ILE Chi-restraints excluded: chain e residue 99 THR Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain f residue 110 ARG Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain g residue 40 LYS Chi-restraints excluded: chain i residue 58 SER Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 50 ARG Chi-restraints excluded: chain k residue 60 ASP Chi-restraints excluded: chain l residue 20 ASN Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain l residue 42 LEU Chi-restraints excluded: chain l residue 52 ARG Chi-restraints excluded: chain n residue 4 GLN Chi-restraints excluded: chain n residue 23 THR Chi-restraints excluded: chain q residue 4 ILE Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 37 GLN Chi-restraints excluded: chain L residue 8 LYS Chi-restraints excluded: chain L residue 20 ASN Chi-restraints excluded: chain C residue 56 ASP Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 127 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 31 ASP Chi-restraints excluded: chain 2 residue 33 LEU Chi-restraints excluded: chain 2 residue 105 GLU Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 3 residue 194 ASP Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 13 ASP Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 6 residue 40 GLU Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 113 ASP Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 10 MET Chi-restraints excluded: chain 7 residue 74 SER Chi-restraints excluded: chain 7 residue 104 VAL Chi-restraints excluded: chain 7 residue 112 THR Chi-restraints excluded: chain 8 residue 37 GLN Chi-restraints excluded: chain 8 residue 52 LEU Chi-restraints excluded: chain 9 residue 15 HIS Chi-restraints excluded: chain D residue 22 HIS Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain F residue 7 ILE Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain F residue 85 CYS Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain K residue 42 SER Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 62 VAL Chi-restraints excluded: chain t residue 79 THR Chi-restraints excluded: chain t residue 81 ARG Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 66 LEU Chi-restraints excluded: chain v residue 17 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 611 optimal weight: 20.0000 chunk 984 optimal weight: 0.0570 chunk 601 optimal weight: 40.0000 chunk 467 optimal weight: 20.0000 chunk 684 optimal weight: 20.0000 chunk 1033 optimal weight: 0.0270 chunk 950 optimal weight: 6.9990 chunk 822 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 635 optimal weight: 20.0000 chunk 504 optimal weight: 40.0000 overall best weight: 5.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 97 ASN ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 GLN T 48 ASN ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 40 ASN ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 38 HIS ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN 3 71 GLN 3 89 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 135 ASN ** 5 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 81 ASN ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN ** E 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 105 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 GLN ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 26 ASN ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5560 moved from start: 1.5880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 159807 Z= 0.198 Angle : 0.720 21.571 239012 Z= 0.364 Chirality : 0.038 0.344 30564 Planarity : 0.006 0.172 12801 Dihedral : 25.349 179.196 79844 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 35.10 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.25 % Favored : 90.63 % Rotamer: Outliers : 2.70 % Allowed : 27.93 % Favored : 69.36 % 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: -2.46 (0.10), residues: 5826 helix: -0.68 (0.11), residues: 1853 sheet: -1.58 (0.15), residues: 983 loop : -2.30 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP P 213 HIS 0.014 0.001 HIS 1 18 PHE 0.084 0.003 PHE P 240 TYR 0.025 0.002 TYR 5 59 ARG 0.018 0.001 ARG m 11 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11652 Ramachandran restraints generated. 5826 Oldfield, 0 Emsley, 5826 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 622 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 491 time to evaluate : 6.411 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: P 239 ASN cc_start: 0.2079 (OUTLIER) cc_final: 0.1858 (t0) REVERT: Q 123 LYS cc_start: 0.5554 (OUTLIER) cc_final: 0.5249 (mtmm) REVERT: R 19 PHE cc_start: 0.6487 (OUTLIER) cc_final: 0.6123 (m-80) REVERT: V 125 MET cc_start: 0.5264 (mmt) cc_final: 0.4760 (mmp) REVERT: V 136 MET cc_start: 0.6406 (OUTLIER) cc_final: 0.6162 (mmm) REVERT: X 1 MET cc_start: 0.3119 (ppp) cc_final: 0.2226 (ppp) REVERT: X 44 LYS cc_start: 0.5824 (mtmm) cc_final: 0.5563 (mtmm) REVERT: Z 136 MET cc_start: 0.8016 (ppp) cc_final: 0.7631 (ppp) REVERT: c 40 LEU cc_start: 0.4680 (tt) cc_final: 0.4343 (tp) REVERT: g 1 MET cc_start: 0.1058 (OUTLIER) cc_final: 0.0815 (pmm) REVERT: k 48 THR cc_start: 0.7662 (m) cc_final: 0.7153 (p) REVERT: l 37 LEU cc_start: 0.6542 (tt) cc_final: 0.6269 (tp) REVERT: p 46 LYS cc_start: 0.7541 (ptmt) cc_final: 0.7055 (tptt) REVERT: q 49 MET cc_start: 0.7161 (tpp) cc_final: 0.6880 (tpp) REVERT: C 48 LEU cc_start: 0.8498 (mp) cc_final: 0.7867 (tp) REVERT: 1 184 PHE cc_start: 0.7016 (OUTLIER) cc_final: 0.6257 (m-80) REVERT: 2 83 ASP cc_start: 0.6625 (t0) cc_final: 0.5713 (p0) REVERT: 5 88 MET cc_start: 0.4307 (tpp) cc_final: 0.3643 (tpp) REVERT: 6 116 MET cc_start: 0.2067 (ptt) cc_final: 0.1233 (mtt) REVERT: 9 15 HIS cc_start: 0.7925 (OUTLIER) cc_final: 0.7649 (p-80) REVERT: G 50 THR cc_start: 0.7016 (OUTLIER) cc_final: 0.6765 (p) REVERT: I 1 MET cc_start: 0.5594 (tpp) cc_final: 0.3553 (mtm) REVERT: J 8 LEU cc_start: 0.7262 (tp) cc_final: 0.7029 (tt) REVERT: t 81 ARG cc_start: 0.6043 (OUTLIER) cc_final: 0.3314 (ppt170) outliers start: 131 outliers final: 101 residues processed: 588 average time/residue: 1.3973 time to fit residues: 1440.0084 Evaluate side-chains 560 residues out of total 4851 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 450 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain P residue 34 LEU Chi-restraints excluded: chain P residue 74 ILE Chi-restraints excluded: chain P residue 130 LEU Chi-restraints excluded: chain P residue 187 ASP Chi-restraints excluded: chain P residue 239 ASN Chi-restraints excluded: chain P residue 252 THR Chi-restraints excluded: chain Q residue 30 GLU Chi-restraints excluded: chain Q residue 52 THR Chi-restraints excluded: chain Q residue 60 VAL Chi-restraints excluded: chain Q residue 91 THR Chi-restraints excluded: chain Q residue 98 VAL Chi-restraints excluded: chain Q residue 123 LYS Chi-restraints excluded: chain Q residue 126 ASN Chi-restraints excluded: chain Q residue 169 ARG Chi-restraints excluded: chain Q residue 170 VAL Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain R residue 7 ASP Chi-restraints excluded: chain R residue 19 PHE Chi-restraints excluded: chain R residue 23 PHE Chi-restraints excluded: chain R residue 146 VAL Chi-restraints excluded: chain R residue 175 ILE Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 108 VAL Chi-restraints excluded: chain S residue 134 GLU Chi-restraints excluded: chain S residue 177 PHE Chi-restraints excluded: chain U residue 5 LEU Chi-restraints excluded: chain U residue 8 LYS Chi-restraints excluded: chain U residue 94 ILE Chi-restraints excluded: chain U residue 99 ILE Chi-restraints excluded: chain V residue 8 TYR Chi-restraints excluded: chain V residue 24 VAL Chi-restraints excluded: chain V residue 40 LYS Chi-restraints excluded: chain V residue 95 LYS Chi-restraints excluded: chain V residue 121 ASP Chi-restraints excluded: chain V residue 136 MET Chi-restraints excluded: chain X residue 12 ASP Chi-restraints excluded: chain X residue 63 VAL Chi-restraints excluded: chain X residue 65 THR Chi-restraints excluded: chain Y residue 103 ILE Chi-restraints excluded: chain Y residue 122 VAL Chi-restraints excluded: chain Z residue 10 ARG Chi-restraints excluded: chain Z residue 102 LEU Chi-restraints excluded: chain a residue 90 ARG Chi-restraints excluded: chain b residue 26 LEU Chi-restraints excluded: chain b residue 47 VAL Chi-restraints excluded: chain b residue 53 THR Chi-restraints excluded: chain b residue 69 ASP Chi-restraints excluded: chain c residue 16 ASP Chi-restraints excluded: chain c residue 83 SER Chi-restraints excluded: chain d residue 9 ILE Chi-restraints excluded: chain d residue 53 ARG Chi-restraints excluded: chain d residue 57 PHE Chi-restraints excluded: chain d residue 104 VAL Chi-restraints excluded: chain e residue 49 ILE Chi-restraints excluded: chain e residue 84 ARG Chi-restraints excluded: chain f residue 66 ILE Chi-restraints excluded: chain g residue 1 MET Chi-restraints excluded: chain g residue 3 ARG Chi-restraints excluded: chain g residue 16 VAL Chi-restraints excluded: chain j residue 17 GLU Chi-restraints excluded: chain k residue 50 ARG Chi-restraints excluded: chain l residue 34 SER Chi-restraints excluded: chain n residue 9 THR Chi-restraints excluded: chain o residue 23 THR Chi-restraints excluded: chain q residue 7 VAL Chi-restraints excluded: chain r residue 1 MET Chi-restraints excluded: chain r residue 3 VAL Chi-restraints excluded: chain C residue 222 VAL Chi-restraints excluded: chain 1 residue 30 PHE Chi-restraints excluded: chain 1 residue 127 ASP Chi-restraints excluded: chain 1 residue 163 VAL Chi-restraints excluded: chain 1 residue 171 ILE Chi-restraints excluded: chain 1 residue 184 PHE Chi-restraints excluded: chain 1 residue 199 VAL Chi-restraints excluded: chain 2 residue 105 GLU Chi-restraints excluded: chain 3 residue 30 THR Chi-restraints excluded: chain 3 residue 191 LEU Chi-restraints excluded: chain 4 residue 78 ASN Chi-restraints excluded: chain 4 residue 141 ILE Chi-restraints excluded: chain 4 residue 148 ASN Chi-restraints excluded: chain 5 residue 10 VAL Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 45 ARG Chi-restraints excluded: chain 6 residue 3 ARG Chi-restraints excluded: chain 6 residue 94 VAL Chi-restraints excluded: chain 6 residue 142 HIS Chi-restraints excluded: chain 7 residue 10 MET Chi-restraints excluded: chain 9 residue 5 ARG Chi-restraints excluded: chain 9 residue 15 HIS Chi-restraints excluded: chain 9 residue 65 TYR Chi-restraints excluded: chain D residue 31 ILE Chi-restraints excluded: chain D residue 52 PHE Chi-restraints excluded: chain D residue 93 ARG Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain E residue 46 ASN Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 58 ASP Chi-restraints excluded: chain G residue 6 MET Chi-restraints excluded: chain G residue 50 THR Chi-restraints excluded: chain G residue 65 ARG Chi-restraints excluded: chain G residue 79 LEU Chi-restraints excluded: chain G residue 96 LEU Chi-restraints excluded: chain H residue 4 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain t residue 16 LEU Chi-restraints excluded: chain t residue 81 ARG Chi-restraints excluded: chain u residue 4 ILE Chi-restraints excluded: chain u residue 66 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1037 random chunks: chunk 653 optimal weight: 5.9990 chunk 876 optimal weight: 2.9990 chunk 252 optimal weight: 40.0000 chunk 758 optimal weight: 40.0000 chunk 121 optimal weight: 5.9990 chunk 228 optimal weight: 20.0000 chunk 823 optimal weight: 2.9990 chunk 344 optimal weight: 20.0000 chunk 846 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 151 optimal weight: 30.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 239 ASN ** R 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 29 HIS R 92 HIS ** R 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 45 HIS ** T 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 133 GLN ** V 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 16 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 37 GLN ** C 172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 177 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 37 GLN 9 56 HIS E 46 ASN ** G 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** K 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.037380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.028760 restraints weight = 2222041.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.029189 restraints weight = 1325144.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.029567 restraints weight = 918111.156| |-----------------------------------------------------------------------------| r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 1.6039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.100 159807 Z= 0.195 Angle : 0.709 22.693 239012 Z= 0.357 Chirality : 0.037 0.337 30564 Planarity : 0.006 0.171 12801 Dihedral : 25.200 179.113 79844 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 35.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 10.25 % Favored : 89.62 % Rotamer: Outliers : 2.76 % Allowed : 27.93 % Favored : 69.30 % 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: -2.28 (0.10), residues: 5826 helix: -0.52 (0.12), residues: 1856 sheet: -1.48 (0.16), residues: 961 loop : -2.20 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP P 213 HIS 0.015 0.001 HIS 1 18 PHE 0.034 0.003 PHE S 100 TYR 0.035 0.002 TYR 5 59 ARG 0.020 0.001 ARG P 238 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29468.09 seconds wall clock time: 524 minutes 11.25 seconds (31451.25 seconds total)