Starting phenix.real_space_refine on Sun Mar 24 11:03:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/03_2024/7qgh_13955.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/03_2024/7qgh_13955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/03_2024/7qgh_13955.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/03_2024/7qgh_13955.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/03_2024/7qgh_13955.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qgh_13955/03_2024/7qgh_13955.pdb" } resolution = 4.48 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= 0.144 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 4717 5.49 5 Mg 2 5.21 5 S 152 5.16 5 C 74424 2.51 5 N 27554 2.21 5 O 41123 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 "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 "U GLU 45": "OE1" <-> "OE2" Residue "U GLU 53": "OE1" <-> "OE2" Residue "U GLU 127": "OE1" <-> "OE2" 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 "B ARG 56": "NH1" <-> "NH2" Residue "G PHE 16": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 28": "NH1" <-> "NH2" Residue "G PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 147973 Number of models: 1 Model: "" Number of chains: 58 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: "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: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 404 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} 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: "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: "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: "x" Number of atoms: 294 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 294 Classifications: {'RNA': 14} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 5, 'rna3p_pur': 3, 'rna3p_pyr': 3} Link IDs: {'rna2p': 8, 'rna3p': 5} Chain: "0" Number of atoms: 33015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1539, 33015 Classifications: {'RNA': 1539} Modifications used: {'rna2p_pur': 87, 'rna2p_pyr': 60, 'rna3p_pur': 787, 'rna3p_pyr': 605} Link IDs: {'rna2p': 147, 'rna3p': 1391} Chain: "1" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1704 Classifications: {'peptide': 218} Link IDs: {'CIS': 2, 'PTRANS': 7, 'TRANS': 208} Chain: "2" Number of atoms: 1624 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1624 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 7, 'TRANS': 198} Chain: "3" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1642 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "4" Number of atoms: 1105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1105 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain: "5" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 817 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "6" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "7" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 978 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "8" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1021 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "9" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 786 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 5, 'TRANS': 92} Chain: "A" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 876 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "B" Number of atoms: 954 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 954 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 7, 'TRANS': 115} Chain: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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: "J" 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: "K" 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: "s" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 425 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 2, 'TRANS': 48} Chain: "t" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 704 Classifications: {'peptide': 143} Incomplete info: {'truncation_to_alanine': 120} Link IDs: {'PTRANS': 3, 'TRANS': 139} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 412 Unresolved non-hydrogen angles: 526 Unresolved non-hydrogen dihedrals: 323 Unresolved non-hydrogen chiralities: 48 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 6, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 4, 'GLU:plan': 16, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 215 Chain: "u" Number of atoms: 1573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1573 Unusual residues: {' K': 1, ' MG': 2} Classifications: {'RNA': 73, 'undetermined': 3, 'water': 9} Modifications used: {'p5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 29, 'rna3p_pyr': 30} Link IDs: {'rna2p': 13, 'rna3p': 59, None: 12} Not linked: pdbres=" A u 73 " pdbres=" MG u 101 " Not linked: pdbres=" MG u 101 " pdbres=" MG u 102 " Not linked: pdbres=" MG u 102 " pdbres=" K u 103 " Not linked: pdbres=" K u 103 " pdbres="HOH u 201 " Not linked: pdbres="HOH u 201 " pdbres="HOH u 202 " ... (remaining 7 not shown) Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" P A U N2506 " occ=0.50 ... (38 atoms not shown) pdb=" C6 B U N2506 " occ=0.50 residue: pdb=" N GLN t 52 " occ=0.58 ... (3 atoms not shown) pdb=" CB GLN t 52 " occ=0.58 residue: pdb=" O HOH u 203 " occ=0.00 Time building chain proxies: 77.86, per 1000 atoms: 0.53 Number of scatterers: 147973 At special positions: 0 Unit cell: (236.53, 250.7, 298.66, 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 152 16.00 P 4717 15.00 Mg 2 11.99 O 41123 8.00 N 27554 7.00 C 74424 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 93926 O4' G x 451 .*. O " rejected from bonding due to valence issues. Atom "ATOM 67697 O4' A N1876 .*. O " rejected from bonding due to valence issues. Atom "ATOM 93425 O4' C M 55 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.14 Conformation dependent library (CDL) restraints added in 6.7 seconds 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11110 Finding SS restraints... Secondary structure from input PDB file: 182 helices and 79 sheets defined 33.2% alpha, 18.2% beta 1619 base pairs and 2611 stacking pairs defined. Time for finding SS restraints: 61.23 Creating SS restraints... Processing helix chain 'P' and resid 30 through 32 No H-bonds generated for 'chain 'P' and resid 30 through 32' Processing helix chain 'P' and resid 197 through 203 removed outlier: 3.616A pdb=" N ARG P 203 " --> pdb=" O HIS P 200 " (cutoff:3.500A) Processing helix chain 'P' and resid 207 through 213 removed outlier: 3.998A pdb=" N ALA P 211 " --> pdb=" O LYS P 207 " (cutoff:3.500A) Processing helix chain 'P' and resid 221 through 225 Processing helix chain 'Q' and resid 61 through 72 Processing helix chain 'Q' and resid 97 through 102 Processing helix chain 'Q' and resid 120 through 125 Processing helix chain 'R' and resid 15 through 20 Processing helix chain 'R' and resid 24 through 39 Processing helix chain 'R' and resid 97 through 115 Processing helix chain 'R' and resid 130 through 141 Processing helix chain 'R' and resid 154 through 161 Processing helix chain 'R' and resid 176 through 183 removed outlier: 3.560A pdb=" N LEU R 180 " --> pdb=" O ASP R 176 " (cutoff:3.500A) Processing helix chain 'R' and resid 190 through 200 Processing helix chain 'S' and resid 3 through 20 removed outlier: 5.074A pdb=" N VAL S 13 " --> pdb=" O LYS S 9 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 45 removed outlier: 3.763A 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 'V' and resid 24 through 29 Processing helix chain 'V' and resid 35 through 39 removed outlier: 3.677A pdb=" N PHE V 38 " --> pdb=" O ILE V 35 " (cutoff:3.500A) Processing helix chain 'V' and resid 40 through 45 Processing helix chain 'V' and resid 103 through 113 Processing helix chain 'V' and resid 125 through 136 removed outlier: 3.952A 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: 3.505A pdb=" N ARG X 108 " --> pdb=" O ARG X 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 112 through 118 removed outlier: 3.560A pdb=" N LEU X 118 " --> pdb=" O LYS X 114 " (cutoff:3.500A) Processing helix chain 'Y' and resid 56 through 61 removed outlier: 3.702A pdb=" N LEU Y 61 " --> pdb=" O LEU Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 128 through 138 Processing helix chain 'Z' and resid 43 through 57 Processing helix chain 'Z' and resid 109 through 121 Processing helix chain 'a' and resid 13 through 32 Processing helix chain 'a' and resid 38 through 56 removed outlier: 4.299A pdb=" N ARG a 46 " --> pdb=" O LYS a 42 " (cutoff:3.500A) Proline residue: a 50 - end of helix Processing helix chain 'a' and resid 59 through 69 removed outlier: 3.595A pdb=" N ARG a 69 " --> pdb=" O LEU a 65 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 82 removed outlier: 4.883A 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: 5.233A pdb=" N ALA b 14 " --> pdb=" O ARG b 10 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 60 Processing helix chain 'b' and resid 67 through 85 Processing helix chain 'b' and resid 101 through 113 Processing helix chain 'c' and resid 3 through 10 Processing helix chain 'c' and resid 53 through 56 removed outlier: 3.514A pdb=" N HIS c 56 " --> pdb=" O ARG c 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 53 through 56' Processing helix chain 'c' and resid 97 through 103 removed outlier: 3.525A pdb=" N ARG c 103 " --> pdb=" O LEU c 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 6 through 20 removed outlier: 3.563A pdb=" N ALA d 10 " --> pdb=" O ARG d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 25 through 30 Processing helix chain 'd' and resid 31 through 72 removed outlier: 4.482A pdb=" N GLN d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS d 54 " --> pdb=" O ARG d 50 " (cutoff:3.500A) Processing helix chain 'd' and resid 75 through 86 Processing helix chain 'd' and resid 91 through 102 Processing helix chain 'd' and resid 102 through 118 Processing helix chain 'f' and resid 13 through 25 removed outlier: 4.465A pdb=" N VAL f 20 " --> pdb=" O LYS f 16 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 38 removed outlier: 3.985A 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: 3.933A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL g 10 " --> pdb=" O ARG g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 17 through 28 removed outlier: 3.643A pdb=" N ASN g 28 " --> pdb=" O MET g 24 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 51 Processing helix chain 'i' and resid 13 through 23 removed outlier: 3.619A pdb=" N ALA i 23 " --> pdb=" O ARG i 19 " (cutoff:3.500A) Processing helix chain 'i' and resid 44 through 52 Processing helix chain 'k' and resid 54 through 63 Processing helix chain 'k' and resid 63 through 74 Processing helix chain 'l' and resid 9 through 23 Processing helix chain 'l' and resid 24 through 33 Processing helix chain 'l' and resid 40 through 61 removed outlier: 4.158A 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: 4.061A 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 'U' and resid 22 through 28 Processing helix chain 'U' and resid 40 through 49 Processing helix chain 'U' and resid 54 through 71 removed outlier: 3.625A pdb=" N LEU U 58 " --> pdb=" O LEU U 54 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ALA U 59 " --> pdb=" O GLU U 55 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLU U 60 " --> pdb=" O ALA U 56 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL U 61 " --> pdb=" O LYS U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 103 removed outlier: 3.759A pdb=" N ILE U 99 " --> pdb=" O GLY U 95 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ASP U 101 " --> pdb=" O ARG U 97 " (cutoff:3.500A) Processing helix chain 'U' and resid 111 through 113 No H-bonds generated for 'chain 'U' and resid 111 through 113' Processing helix chain '1' and resid 24 through 31 Proline residue: 1 29 - end of helix Processing helix chain '1' and resid 34 through 38 removed outlier: 4.415A pdb=" N LYS 1 37 " --> pdb=" O ALA 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 62 Proline residue: 1 48 - end of helix Processing helix chain '1' and resid 78 through 87 Processing helix chain '1' and resid 103 through 123 removed outlier: 3.829A pdb=" N VAL 1 107 " --> pdb=" O ASN 1 103 " (cutoff:3.500A) removed outlier: 3.630A 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: 3.740A 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: 3.624A pdb=" N ARG 1 222 " --> pdb=" O ALA 1 218 " (cutoff:3.500A) Processing helix chain '2' and resid 8 through 12 removed outlier: 3.711A pdb=" N LEU 2 12 " --> pdb=" O GLY 2 9 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 46 Processing helix chain '2' and resid 72 through 78 removed outlier: 3.592A 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: 4.029A pdb=" N LEU 2 144 " --> pdb=" O ASN 2 140 " (cutoff:3.500A) Processing helix chain '3' and resid 7 through 15 removed outlier: 3.987A pdb=" N LEU 3 11 " --> pdb=" O PRO 3 7 " (cutoff:3.500A) removed outlier: 3.506A 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: 3.712A 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: 3.897A pdb=" N ILE 3 200 " --> pdb=" O ASN 3 196 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 69 removed outlier: 4.040A pdb=" N ARG 4 69 " --> pdb=" O GLU 4 65 " (cutoff:3.500A) Processing helix chain '4' and resid 111 through 118 Processing helix chain '4' and resid 132 through 137 removed outlier: 3.817A pdb=" N VAL 4 137 " --> pdb=" O PRO 4 133 " (cutoff:3.500A) Processing helix chain '4' and resid 140 through 145 Processing helix chain '4' and resid 149 through 157 removed outlier: 3.536A pdb=" N ALA 4 155 " --> pdb=" O GLU 4 151 " (cutoff:3.500A) Processing helix chain '5' and resid 12 through 16 removed outlier: 5.361A pdb=" N GLU 5 16 " --> pdb=" O ASP 5 13 " (cutoff:3.500A) Processing helix chain '5' and resid 17 through 31 Processing helix chain '5' and resid 67 through 81 removed outlier: 3.645A pdb=" N ILE 5 71 " --> pdb=" O PRO 5 67 " (cutoff:3.500A) Processing helix chain '6' and resid 20 through 31 Processing helix chain '6' and resid 35 through 55 removed outlier: 3.666A pdb=" N ALA 6 39 " --> pdb=" O LYS 6 35 " (cutoff:3.500A) Processing helix chain '6' and resid 58 through 68 Processing helix chain '6' and resid 92 through 111 Processing helix chain '6' and resid 115 through 129 removed outlier: 3.802A 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: 3.617A 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: 3.757A 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: 4.093A pdb=" N GLU 8 97 " --> pdb=" O SER 8 93 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG 8 99 " --> pdb=" O ARG 8 95 " (cutoff:3.500A) Processing helix chain '9' and resid 14 through 33 Processing helix chain '9' and resid 80 through 86 Processing helix chain 'A' and resid 59 through 72 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.641A pdb=" N GLY A 78 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 101 Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 23 through 27 removed outlier: 3.849A pdb=" N CYS B 27 " --> pdb=" O LEU B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 118 removed outlier: 3.526A pdb=" N LYS B 116 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY B 118 " --> pdb=" O SER B 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 19 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 27 through 37 Processing helix chain 'D' and resid 49 through 61 Processing helix chain 'D' and resid 65 through 84 Processing helix chain 'D' and resid 85 through 94 removed outlier: 3.586A pdb=" N GLY D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 20 removed outlier: 3.713A pdb=" N LYS E 7 " --> pdb=" O LYS E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 31 removed outlier: 4.342A pdb=" N LYS E 28 " --> pdb=" O ARG E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 48 Processing helix chain 'E' and resid 56 through 60 removed outlier: 3.947A pdb=" N GLN E 60 " --> pdb=" O PRO E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 91 Processing helix chain 'F' and resid 4 through 16 Processing helix chain 'F' and resid 24 through 45 removed outlier: 4.091A pdb=" N GLU F 45 " --> pdb=" O GLY F 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 72 Processing helix chain 'F' and resid 74 through 86 Processing helix chain 'G' and resid 53 through 64 Processing helix chain 'G' and resid 68 through 76 Processing helix chain 'H' and resid 49 through 52 removed outlier: 4.553A pdb=" N GLU H 52 " --> pdb=" O GLU H 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 49 through 52' Processing helix chain 'I' and resid 25 through 32 Processing helix chain 'I' and resid 41 through 46 Processing helix chain 'I' and resid 48 through 65 Processing helix chain 'J' and resid 12 through 25 Processing helix chain 'J' and resid 41 through 45 removed outlier: 3.575A pdb=" N ILE J 45 " --> pdb=" O PRO J 42 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 removed outlier: 3.956A pdb=" N VAL J 67 " --> pdb=" O ASP J 64 " (cutoff:3.500A) Processing helix chain 'J' and resid 71 through 75 Processing helix chain 'K' and resid 6 through 39 removed outlier: 3.656A pdb=" N ARG K 10 " --> pdb=" O SER K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 43 through 65 removed outlier: 3.708A pdb=" N ALA K 47 " --> pdb=" O ASP K 43 " (cutoff:3.500A) Proline residue: K 56 - end of helix removed outlier: 3.517A pdb=" N GLY K 65 " --> pdb=" O GLN K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 69 through 87 Processing helix chain 's' and resid 27 through 32 removed outlier: 3.769A pdb=" N VAL s 32 " --> pdb=" O VAL s 28 " (cutoff:3.500A) Processing helix chain 's' and resid 39 through 52 Processing helix chain 't' and resid 49 through 53 Processing helix chain 't' and resid 94 through 97 Processing helix chain 't' and resid 98 through 103 Processing helix chain 't' and resid 172 through 177 Processing sheet with id=AA1, first strand: chain 'P' and resid 3 through 5 Processing sheet with id=AA2, first strand: chain 'P' and resid 34 through 36 Processing sheet with id=AA3, first strand: chain 'P' and resid 101 through 105 removed outlier: 6.203A pdb=" N LEU P 95 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N VAL P 78 " --> pdb=" O LEU P 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'P' and resid 129 through 131 removed outlier: 6.195A pdb=" N THR P 173 " --> pdb=" O VAL P 165 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N MET P 181 " --> pdb=" O VAL P 268 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'P' and resid 144 through 145 removed outlier: 5.979A pdb=" N VAL P 144 " --> pdb=" O GLN P 153 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Q' and resid 4 through 5 removed outlier: 6.566A pdb=" N VAL Q 109 " --> pdb=" O GLN Q 173 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLN Q 173 " --> pdb=" O VAL Q 109 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N GLY Q 111 " --> pdb=" O THR Q 171 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N THR Q 171 " --> pdb=" O GLY Q 111 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'Q' and resid 8 through 15 removed outlier: 5.804A pdb=" N LYS Q 8 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N GLU Q 28 " --> pdb=" O LYS Q 8 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY Q 10 " --> pdb=" O VAL Q 26 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU Q 186 " --> pdb=" O VAL Q 180 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL Q 180 " --> pdb=" O LEU Q 186 " (cutoff:3.500A) removed outlier: 6.428A 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: 6.593A 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: 6.493A pdb=" N GLN Q 49 " --> pdb=" O THR Q 35 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'Q' and resid 117 through 119 Processing sheet with id=AB1, first strand: chain 'R' and resid 2 through 4 Processing sheet with id=AB2, first strand: chain 'R' and resid 118 through 121 Processing sheet with id=AB3, first strand: chain 'S' and resid 66 through 69 Processing sheet with id=AB4, first strand: chain 'T' and resid 16 through 20 Processing sheet with id=AB5, first strand: chain 'T' and resid 41 through 44 Processing sheet with id=AB6, first strand: chain 'T' and resid 122 through 124 Processing sheet with id=AB7, first strand: chain 'T' and resid 95 through 99 Processing sheet with id=AB8, first strand: chain 'V' and resid 99 through 102 removed outlier: 6.726A pdb=" N GLY V 99 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N GLU V 141 " --> pdb=" O GLY V 99 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE V 101 " --> pdb=" O GLU V 141 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'W' and resid 122 through 124 removed outlier: 6.425A pdb=" N ILE W 54 " --> pdb=" O LYS W 123 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N TYR W 16 " --> pdb=" O ILE W 55 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N LEU W 57 " --> pdb=" O TYR W 16 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL W 18 " --> pdb=" O LEU W 57 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'W' and resid 73 through 77 Processing sheet with id=AC2, first strand: chain 'X' and resid 7 through 10 removed outlier: 3.994A pdb=" N VAL X 10 " --> pdb=" O ARG X 17 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ARG X 17 " --> pdb=" O VAL X 10 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ALA X 16 " --> pdb=" O ALA X 46 " (cutoff:3.500A) removed outlier: 6.239A 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: 6.650A 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: 8.082A 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: 6.309A pdb=" N VAL X 85 " --> pdb=" O VAL X 62 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N CYS X 84 " --> pdb=" O MET X 7 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ASN X 9 " --> pdb=" O CYS X 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 69 through 70 removed outlier: 3.571A 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: 4.963A 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: 5.625A pdb=" N ILE c 64 " --> pdb=" O GLU c 44 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N GLU c 44 " --> pdb=" O ILE c 64 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU c 27 " --> pdb=" O VAL c 86 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N VAL c 86 " --> pdb=" O GLU c 27 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N LYS c 29 " --> pdb=" O ILE c 84 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N ILE c 84 " --> pdb=" O LYS c 29 " (cutoff:3.500A) removed outlier: 7.935A 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=AC4, first strand: chain 'Y' and resid 89 through 90 removed outlier: 5.825A pdb=" N VAL Y 90 " --> pdb=" O ARG Y 123 " (cutoff:3.500A) Processing sheet with id=AC5, 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: 6.673A pdb=" N PHE Z 31 " --> pdb=" O GLU Z 104 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Z' and resid 40 through 42 removed outlier: 5.498A pdb=" N VAL Z 89 " --> pdb=" O GLU Z 75 " (cutoff:3.500A) removed outlier: 6.330A 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=AC7, first strand: chain 'a' and resid 33 through 37 removed outlier: 5.888A pdb=" N MET a 110 " --> pdb=" O CYS a 100 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 47 through 52 removed outlier: 6.595A pdb=" N VAL b 39 " --> pdb=" O LEU b 48 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA b 50 " --> pdb=" O ALA b 37 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA b 37 " --> pdb=" O ALA b 50 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N SER b 52 " --> pdb=" O ILE b 35 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ILE b 35 " --> pdb=" O SER b 52 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'c' and resid 90 through 91 removed outlier: 4.218A pdb=" N LYS c 111 " --> pdb=" O ALA c 91 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'e' and resid 11 through 14 removed outlier: 6.711A pdb=" N TYR e 2 " --> pdb=" O ILE e 41 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N ILE e 41 " --> pdb=" O TYR e 2 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N VAL e 4 " --> pdb=" O LEU e 39 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'e' and resid 19 through 23 removed outlier: 6.670A pdb=" N PHE e 93 " --> pdb=" O HIS e 66 " (cutoff:3.500A) removed outlier: 4.779A 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: 4.789A 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=AD3, 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=AD4, first strand: chain 'f' and resid 3 through 10 removed outlier: 5.732A 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: 4.302A pdb=" N VAL f 76 " --> pdb=" O HIS f 102 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N THR f 104 " --> pdb=" O ILE f 74 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ILE f 74 " --> pdb=" O THR f 104 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL f 106 " --> pdb=" O THR f 72 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'f' and resid 82 through 87 Processing sheet with id=AD6, 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: 4.276A pdb=" N LYS g 81 " --> pdb=" O VAL g 34 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'g' and resid 67 through 70 Processing sheet with id=AD8, first strand: chain 'h' and resid 65 through 66 Processing sheet with id=AD9, first strand: chain 'h' and resid 41 through 45 Processing sheet with id=AE1, first strand: chain 'h' and resid 83 through 88 Processing sheet with id=AE2, 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: 4.581A pdb=" N ASP i 43 " --> pdb=" O ASN i 5 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N LYS i 25 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 9.664A pdb=" N ILE i 89 " --> pdb=" O LYS i 25 " (cutoff:3.500A) removed outlier: 8.549A 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: 6.625A pdb=" N GLN i 78 " --> pdb=" O GLN i 87 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ILE i 89 " --> pdb=" O ASP i 76 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP i 76 " --> pdb=" O ILE i 89 " (cutoff:3.500A) removed outlier: 6.451A 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: 6.413A pdb=" N ARG i 93 " --> pdb=" O VAL i 72 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N VAL i 72 " --> pdb=" O ARG i 93 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'j' and resid 22 through 23 removed outlier: 6.799A pdb=" N LEU j 59 " --> pdb=" O ILE j 37 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'j' and resid 30 through 31 Processing sheet with id=AE5, first strand: chain 'k' and resid 13 through 17 Processing sheet with id=AE6, first strand: chain 'k' and resid 34 through 40 Processing sheet with id=AE7, first strand: chain 'm' and resid 36 through 38 Processing sheet with id=AE8, first strand: chain 'n' and resid 29 through 30 Processing sheet with id=AE9, first strand: chain 'n' and resid 48 through 49 Processing sheet with id=AF1, first strand: chain 'o' and resid 20 through 25 Processing sheet with id=AF2, first strand: chain 'q' and resid 14 through 16 Processing sheet with id=AF3, 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=AF4, first strand: chain 'L' and resid 21 through 25 removed outlier: 9.297A 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=AF5, first strand: chain 'C' and resid 20 through 21 removed outlier: 7.917A pdb=" N TYR C 21 " --> pdb=" O GLY C 221 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA C 223 " --> pdb=" O TYR C 21 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N VAL C 212 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N LYS C 211 " --> pdb=" O ASN C 47 " (cutoff:3.500A) removed outlier: 7.214A 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: 3.625A pdb=" N VAL C 46 " --> pdb=" O ILE C 171 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AF7, first strand: chain 'U' and resid 4 through 5 Processing sheet with id=AF8, first strand: chain 'U' and resid 77 through 82 removed outlier: 7.207A pdb=" N VAL U 78 " --> pdb=" O ASN U 145 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N VAL U 147 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE U 80 " --> pdb=" O VAL U 147 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL U 142 " --> pdb=" O VAL U 130 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N VAL U 130 " --> pdb=" O VAL U 142 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N SER U 131 " --> pdb=" O ARG U 116 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '1' and resid 91 through 92 removed outlier: 6.641A pdb=" N PHE 1 69 " --> pdb=" O VAL 1 92 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU 1 161 " --> pdb=" O PHE 1 184 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE 1 186 " --> pdb=" O LEU 1 161 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL 1 163 " --> pdb=" O ILE 1 186 " (cutoff:3.500A) removed outlier: 6.792A 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: 6.480A pdb=" N ALA 1 185 " --> pdb=" O ILE 1 200 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain '2' and resid 52 through 56 removed outlier: 6.731A pdb=" N HIS 2 69 " --> pdb=" O SER 2 53 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N ILE 2 55 " --> pdb=" O THR 2 67 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N THR 2 67 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) Processing sheet with id=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: 5.326A 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: 4.138A 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: 5.326A 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: 4.138A pdb=" N GLY 5 43 " --> pdb=" O TYR 5 59 " (cutoff:3.500A) removed outlier: 5.037A 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 77 Processing sheet with id=AH1, first strand: chain '7' and resid 24 through 28 removed outlier: 6.221A pdb=" N GLU 7 58 " --> pdb=" O VAL 7 51 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL 7 51 " --> pdb=" O GLU 7 58 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N GLU 7 60 " --> pdb=" O PHE 7 49 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N PHE 7 49 " --> pdb=" O GLU 7 60 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N THR 7 62 " --> pdb=" O GLU 7 47 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain '7' and resid 75 through 77 Processing sheet with id=AH3, first strand: chain '7' and resid 75 through 77 removed outlier: 6.559A pdb=" N VAL 7 103 " --> pdb=" O ILE 7 126 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain '8' and resid 6 through 8 removed outlier: 5.990A 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 'A' and resid 41 through 46 removed outlier: 6.716A pdb=" N ALA A 41 " --> pdb=" O ASP A 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ASP A 36 " --> pdb=" O ALA A 41 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LEU A 82 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN A 109 " --> pdb=" O LEU A 82 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 30 through 32 Processing sheet with id=AH9, first strand: chain 'B' and resid 36 through 40 removed outlier: 4.279A pdb=" N TYR B 95 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'E' and resid 73 through 74 removed outlier: 3.566A pdb=" N LEU E 79 " --> pdb=" O LEU E 74 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AI3, first strand: chain 'G' and resid 37 through 39 removed outlier: 3.731A pdb=" N ARG G 51 " --> pdb=" O PHE G 38 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 8 through 14 removed outlier: 7.813A pdb=" N GLN H 9 " --> pdb=" O GLU H 26 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLU H 26 " --> pdb=" O GLN H 9 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N VAL H 22 " --> pdb=" O VAL H 13 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N TRP H 73 " --> pdb=" O HIS H 45 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N GLU H 60 " --> pdb=" O VAL H 76 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N VAL H 78 " --> pdb=" O VAL H 58 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL H 58 " --> pdb=" O VAL H 78 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'J' and resid 31 through 33 Processing sheet with id=AI6, first strand: chain 't' and resid 46 through 48 removed outlier: 3.887A pdb=" N ALA t 30 " --> pdb=" O LEU t 37 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ASP t 39 " --> pdb=" O VAL t 28 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N VAL t 28 " --> pdb=" O ASP t 39 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 't' and resid 112 through 115 removed outlier: 6.963A pdb=" N THR t 121 " --> pdb=" O ASN t 113 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS t 115 " --> pdb=" O GLY t 119 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY t 119 " --> pdb=" O LYS t 115 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N VAL t 122 " --> pdb=" O ALA t 129 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ARG t 128 " --> pdb=" O VAL t 166 " (cutoff:3.500A) 1856 hydrogen bonds defined for protein. 5142 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 4070 hydrogen bonds 6370 hydrogen bond angles 0 basepair planarities 1619 basepair parallelities 2611 stacking parallelities Total time for adding SS restraints: 251.69 Time building geometry restraints manager: 63.99 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: 10392 1.25 - 1.41: 57921 1.41 - 1.57: 84211 1.57 - 1.74: 7913 1.74 - 1.90: 272 Bond restraints: 160709 Sorted by residual: bond pdb=" P G N2502 " pdb=" OP2 G N2502 " ideal model delta sigma weight residual 1.485 1.768 -0.283 2.00e-02 2.50e+03 2.00e+02 bond pdb=" P A N1156 " pdb=" OP2 A N1156 " ideal model delta sigma weight residual 1.485 1.743 -0.258 2.00e-02 2.50e+03 1.66e+02 bond pdb=" P G N1333 " pdb=" OP2 G N1333 " ideal model delta sigma weight residual 1.485 1.703 -0.218 2.00e-02 2.50e+03 1.19e+02 bond pdb=" P A N 783 " pdb=" OP2 A N 783 " ideal model delta sigma weight residual 1.485 1.701 -0.216 2.00e-02 2.50e+03 1.17e+02 bond pdb=" C ALA 4 127 " pdb=" O ALA 4 127 " ideal model delta sigma weight residual 1.234 1.105 0.129 1.22e-02 6.72e+03 1.11e+02 ... (remaining 160704 not shown) Histogram of bond angle deviations from ideal: 80.76 - 93.23: 9 93.23 - 105.70: 27854 105.70 - 118.18: 126168 118.18 - 130.65: 84642 130.65 - 143.12: 1675 Bond angle restraints: 240348 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 104.00 131.33 -27.33 1.50e+00 4.44e-01 3.32e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" O5' C N2507 " ideal model delta sigma weight residual 104.00 80.76 23.24 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 119.47 134.22 -14.75 1.16e+00 7.43e-01 1.62e+02 angle pdb=" O3'A U N2506 " pdb=" P C N2507 " pdb=" OP1 C N2507 " ideal model delta sigma weight residual 108.00 142.87 -34.87 3.00e+00 1.11e-01 1.35e+02 angle pdb=" C4' A N1936 " pdb=" C3' A N1936 " pdb=" O3' A N1936 " ideal model delta sigma weight residual 113.00 96.43 16.57 1.50e+00 4.44e-01 1.22e+02 ... (remaining 240343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.88: 91139 35.88 - 71.75: 10817 71.75 - 107.63: 946 107.63 - 143.50: 27 143.50 - 179.38: 35 Dihedral angle restraints: 102964 sinusoidal: 85749 harmonic: 17215 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 -48.31 -131.69 0 5.00e+00 4.00e-02 6.94e+02 dihedral pdb=" CA ASN 5 52 " pdb=" C ASN 5 52 " pdb=" N LYS 5 53 " pdb=" CA LYS 5 53 " ideal model delta harmonic sigma weight residual -180.00 -115.17 -64.83 0 5.00e+00 4.00e-02 1.68e+02 dihedral pdb=" CA LYS A 125 " pdb=" C LYS A 125 " pdb=" N LYS A 126 " pdb=" CA LYS A 126 " ideal model delta harmonic sigma weight residual -180.00 -115.38 -64.62 0 5.00e+00 4.00e-02 1.67e+02 ... (remaining 102961 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.215: 29213 0.215 - 0.430: 1440 0.430 - 0.645: 93 0.645 - 0.860: 11 0.860 - 1.075: 5 Chirality restraints: 30762 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 1.08 2.00e-01 2.50e+01 2.89e+01 chirality pdb=" C3' G 01347 " pdb=" C4' G 01347 " pdb=" O3' G 01347 " pdb=" C2' G 01347 " both_signs ideal model delta sigma weight residual False -2.74 -1.85 -0.89 2.00e-01 2.50e+01 2.00e+01 chirality pdb=" CA VAL P 204 " pdb=" N VAL P 204 " pdb=" C VAL P 204 " pdb=" CB VAL P 204 " both_signs ideal model delta sigma weight residual False 2.44 1.56 0.88 2.00e-01 2.50e+01 1.94e+01 ... (remaining 30759 not shown) Planarity restraints: 12915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A N2765 " 0.012 2.00e-02 2.50e+03 8.69e-02 2.08e+02 pdb=" N9 A N2765 " -0.010 2.00e-02 2.50e+03 pdb=" C8 A N2765 " 0.062 2.00e-02 2.50e+03 pdb=" N7 A N2765 " 0.045 2.00e-02 2.50e+03 pdb=" C5 A N2765 " -0.058 2.00e-02 2.50e+03 pdb=" C6 A N2765 " -0.083 2.00e-02 2.50e+03 pdb=" N6 A N2765 " -0.070 2.00e-02 2.50e+03 pdb=" N1 A N2765 " 0.235 2.00e-02 2.50e+03 pdb=" C2 A N2765 " -0.026 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 " -0.111 2.00e-02 2.50e+03 7.16e-02 1.41e+02 pdb=" N9 A N1802 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A N1802 " -0.039 2.00e-02 2.50e+03 pdb=" N7 A N1802 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A N1802 " 0.068 2.00e-02 2.50e+03 pdb=" C6 A N1802 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A N1802 " -0.024 2.00e-02 2.50e+03 pdb=" N1 A N1802 " -0.079 2.00e-02 2.50e+03 pdb=" C2 A N1802 " -0.062 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 " -0.021 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 " 0.023 2.00e-02 2.50e+03 pdb=" O4 U N2522 " 0.092 2.00e-02 2.50e+03 pdb=" C5 U N2522 " -0.048 2.00e-02 2.50e+03 pdb=" C6 U N2522 " 0.002 2.00e-02 2.50e+03 ... (remaining 12912 not shown) Histogram of nonbonded interaction distances: 0.20 - 1.19: 17 1.19 - 2.17: 108 2.17 - 3.16: 110627 3.16 - 4.15: 571223 4.15 - 5.14: 939569 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1621544 Sorted by model distance: nonbonded pdb=" O2' U N1923 " pdb=" O2' C M 12 " model vdw 0.197 2.440 nonbonded pdb=" CD2 HIS 1 18 " pdb=" CB LYS t 43 " model vdw 0.223 3.660 nonbonded pdb=" CG ASP S 113 " pdb=" NH1 ARG D 71 " model vdw 0.295 3.350 nonbonded pdb=" OD1 ASP S 113 " pdb=" CZ ARG D 71 " model vdw 0.638 3.270 nonbonded pdb=" NE2 HIS 1 18 " pdb=" CA LYS t 43 " model vdw 0.697 3.550 ... (remaining 1621539 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: 11.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.110 Extract box with map and model: 43.880 Check model and map are aligned: 1.510 Set scattering table: 0.940 Process input model: 559.100 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 623.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3860 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.283 160709 Z= 0.978 Angle : 1.619 34.873 240348 Z= 0.965 Chirality : 0.112 1.075 30762 Planarity : 0.015 0.113 12915 Dihedral : 22.930 179.379 91851 Min Nonbonded Distance : 0.197 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 1.01 % Allowed : 8.79 % Favored : 90.20 % Rotamer: Outliers : 1.41 % Allowed : 4.96 % Favored : 93.63 % Cbeta Deviations : 1.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.05 (0.09), residues: 5936 helix: -2.92 (0.08), residues: 1857 sheet: -2.32 (0.13), residues: 1110 loop : -2.63 (0.09), residues: 2969 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 0.068 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) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 824 time to evaluate : 6.183 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: Q 11 MET cc_start: -0.0653 (mtp) cc_final: -0.1836 (mmt) REVERT: R 69 ARG cc_start: -0.0364 (OUTLIER) cc_final: -0.0631 (mtt90) REVERT: V 82 LYS cc_start: 0.0646 (pttm) cc_final: -0.1124 (pttt) REVERT: V 136 MET cc_start: 0.2813 (mtm) cc_final: 0.1236 (mmp) REVERT: a 1 MET cc_start: 0.4815 (ptp) cc_final: 0.4291 (mmt) REVERT: b 87 ILE cc_start: 0.5889 (mm) cc_final: 0.5656 (mm) REVERT: d 83 LEU cc_start: 0.3927 (mt) cc_final: 0.3717 (tp) REVERT: U 55 GLU cc_start: 0.2148 (mp0) cc_final: 0.1797 (mt-10) REVERT: 1 116 ASP cc_start: 0.9152 (m-30) cc_final: 0.8916 (t0) REVERT: 1 145 GLU cc_start: 0.8518 (tp30) cc_final: 0.7891 (tm-30) REVERT: 5 26 THR cc_start: 0.7981 (m) cc_final: 0.7623 (p) REVERT: 5 69 GLU cc_start: 0.8834 (tm-30) cc_final: 0.8535 (pm20) REVERT: 6 104 ILE cc_start: 0.7135 (mt) cc_final: 0.6843 (tp) outliers start: 68 outliers final: 6 residues processed: 883 average time/residue: 1.4436 time to fit residues: 2126.9367 Evaluate side-chains 410 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 403 time to evaluate : 6.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 887 optimal weight: 10.0000 chunk 796 optimal weight: 20.0000 chunk 442 optimal weight: 5.9990 chunk 272 optimal weight: 7.9990 chunk 537 optimal weight: 50.0000 chunk 425 optimal weight: 50.0000 chunk 823 optimal weight: 7.9990 chunk 318 optimal weight: 8.9990 chunk 500 optimal weight: 6.9990 chunk 613 optimal weight: 5.9990 chunk 954 optimal weight: 8.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 86 ASN P 134 ASN P 153 GLN ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 243 HIS Q 32 ASN ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 165 HIS T 22 GLN T 88 GLN T 143 GLN V 12 GLN V 43 ASN W 40 HIS X 3 GLN ** a 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 HIS b 38 GLN b 98 GLN c 12 GLN d 37 GLN d 44 GLN f 15 GLN i 49 ASN ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN l 58 ASN m 20 HIS n 19 HIS o 19 HIS q 26 HIS q 28 ASN L 20 ASN L 41 HIS C 172 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 2 GLN U 28 ASN U 43 ASN ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN 1 94 HIS 1 170 HIS ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN 6 122 ASN ** 6 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 32 GLN 8 81 HIS ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 ASN E 49 GLN ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 63 GLN H 31 HIS I 52 GLN J 57 HIS ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 70 ASN K 75 HIS Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4169 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 160709 Z= 0.226 Angle : 0.723 13.313 240348 Z= 0.369 Chirality : 0.039 0.414 30762 Planarity : 0.006 0.131 12915 Dihedral : 23.769 179.012 80269 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.08 % Favored : 92.71 % Rotamer: Outliers : 0.29 % Allowed : 3.40 % Favored : 96.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.38 % 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: -2.66 (0.10), residues: 5936 helix: -1.03 (0.11), residues: 1870 sheet: -1.97 (0.14), residues: 1119 loop : -2.14 (0.10), residues: 2947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP P 213 HIS 0.018 0.002 HIS 1 18 PHE 0.032 0.003 PHE 5 80 TYR 0.038 0.002 TYR 5 59 ARG 0.026 0.001 ARG 2 132 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 546 time to evaluate : 6.240 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: Q 11 MET cc_start: 0.0083 (mtp) cc_final: -0.0626 (mpp) REVERT: T 101 ASN cc_start: 0.5861 (t0) cc_final: 0.5645 (t0) REVERT: V 100 LYS cc_start: 0.6016 (mmpt) cc_final: 0.3836 (tptt) REVERT: V 130 GLU cc_start: 0.8260 (mp0) cc_final: 0.6966 (tp30) REVERT: V 136 MET cc_start: 0.1597 (mtm) cc_final: 0.0771 (mmp) REVERT: X 8 LEU cc_start: 0.6309 (mp) cc_final: 0.6016 (mt) REVERT: a 1 MET cc_start: 0.5947 (ptp) cc_final: 0.5526 (tpt) REVERT: 1 161 LEU cc_start: 0.8194 (tp) cc_final: 0.7793 (tp) REVERT: 2 42 TYR cc_start: 0.6495 (t80) cc_final: 0.6147 (t80) REVERT: 2 165 THR cc_start: 0.6096 (p) cc_final: 0.5820 (p) REVERT: 4 54 ARG cc_start: 0.6402 (mmt180) cc_final: 0.5609 (mmt180) REVERT: 4 136 VAL cc_start: 0.8653 (OUTLIER) cc_final: 0.8213 (p) REVERT: 5 21 MET cc_start: 0.6403 (mtm) cc_final: 0.6124 (ptt) REVERT: 5 26 THR cc_start: 0.8101 (m) cc_final: 0.7802 (p) REVERT: 5 69 GLU cc_start: 0.8882 (tm-30) cc_final: 0.8679 (pm20) REVERT: 9 97 ASP cc_start: 0.7863 (m-30) cc_final: 0.7408 (m-30) REVERT: A 77 TYR cc_start: 0.6239 (m-80) cc_final: 0.5971 (m-80) outliers start: 14 outliers final: 3 residues processed: 556 average time/residue: 1.3968 time to fit residues: 1309.5854 Evaluate side-chains 376 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 372 time to evaluate : 6.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 530 optimal weight: 50.0000 chunk 296 optimal weight: 9.9990 chunk 794 optimal weight: 40.0000 chunk 649 optimal weight: 50.0000 chunk 263 optimal weight: 8.9990 chunk 956 optimal weight: 30.0000 chunk 1032 optimal weight: 20.0000 chunk 851 optimal weight: 9.9990 chunk 948 optimal weight: 10.0000 chunk 325 optimal weight: 40.0000 chunk 767 optimal weight: 20.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 142 HIS ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 200 HIS ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 260 ASN ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 88 GLN T 128 GLN W 58 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 62 ASN a 81 ASN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 86 GLN g 15 HIS ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 45 HIS ** h 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 25 GLN l 58 ASN n 42 HIS ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 57 GLN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 HIS 1 51 ASN 1 94 HIS ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 69 HIS 2 139 GLN ** 2 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 74 ASN ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 28 ASN ** 7 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 16 ASN ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN D 8 ASN D 105 ASN ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 HIS ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4730 moved from start: 0.6720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.174 160709 Z= 0.352 Angle : 0.916 12.592 240348 Z= 0.462 Chirality : 0.045 0.415 30762 Planarity : 0.008 0.146 12915 Dihedral : 24.795 177.513 80269 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 42.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.42 % Favored : 91.43 % Rotamer: Outliers : 0.64 % Allowed : 5.15 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.52 % Twisted General : 0.31 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.10), residues: 5936 helix: -0.90 (0.11), residues: 1865 sheet: -1.91 (0.14), residues: 1089 loop : -2.12 (0.10), residues: 2982 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.004 TRP 5 42 HIS 0.049 0.003 HIS 4 83 PHE 0.057 0.004 PHE P 240 TYR 0.042 0.003 TYR 8 6 ARG 0.054 0.002 ARG 7 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 512 time to evaluate : 5.666 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: P 160 THR cc_start: -0.1900 (OUTLIER) cc_final: -0.2102 (m) REVERT: Q 11 MET cc_start: 0.1568 (mtp) cc_final: 0.0519 (mpp) REVERT: V 100 LYS cc_start: 0.6585 (mmpt) cc_final: 0.6205 (tppt) REVERT: W 1 MET cc_start: 0.1058 (tpt) cc_final: 0.0829 (tpt) REVERT: X 1 MET cc_start: 0.1309 (ttt) cc_final: 0.0117 (ttp) REVERT: X 8 LEU cc_start: 0.6661 (mp) cc_final: 0.6401 (tp) REVERT: a 1 MET cc_start: 0.7613 (ptp) cc_final: 0.5619 (tpt) REVERT: b 87 ILE cc_start: 0.6303 (mm) cc_final: 0.6061 (mm) REVERT: U 70 GLU cc_start: 0.4059 (OUTLIER) cc_final: 0.3490 (tm-30) REVERT: U 87 GLU cc_start: -0.0358 (mm-30) cc_final: -0.0749 (mm-30) REVERT: 1 161 LEU cc_start: 0.8405 (tp) cc_final: 0.7934 (tp) REVERT: 2 37 PHE cc_start: 0.8807 (t80) cc_final: 0.8604 (m-80) REVERT: 2 134 MET cc_start: 0.3865 (ttt) cc_final: 0.3159 (ttt) REVERT: 3 65 TYR cc_start: 0.7357 (m-10) cc_final: 0.7046 (m-10) REVERT: 3 85 ASN cc_start: 0.8279 (t0) cc_final: 0.7410 (t0) REVERT: 3 95 GLU cc_start: 0.7574 (mm-30) cc_final: 0.7304 (mm-30) REVERT: 4 54 ARG cc_start: 0.6858 (mmt180) cc_final: 0.6511 (mmt180) REVERT: 5 26 THR cc_start: 0.8427 (m) cc_final: 0.8075 (p) REVERT: 5 70 VAL cc_start: 0.8018 (p) cc_final: 0.7730 (p) REVERT: 9 97 ASP cc_start: 0.7376 (m-30) cc_final: 0.6850 (m-30) REVERT: E 96 LEU cc_start: 0.6886 (tp) cc_final: 0.6533 (tp) outliers start: 31 outliers final: 5 residues processed: 533 average time/residue: 1.3780 time to fit residues: 1260.7791 Evaluate side-chains 373 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 366 time to evaluate : 6.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 944 optimal weight: 20.0000 chunk 718 optimal weight: 30.0000 chunk 496 optimal weight: 40.0000 chunk 105 optimal weight: 30.0000 chunk 456 optimal weight: 20.0000 chunk 642 optimal weight: 50.0000 chunk 959 optimal weight: 20.0000 chunk 1015 optimal weight: 10.0000 chunk 501 optimal weight: 40.0000 chunk 909 optimal weight: 40.0000 chunk 273 optimal weight: 50.0000 overall best weight: 20.0000 ------------------------------------------------------------------------------- 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 70 ASN ** P 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 230 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN ** T 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 HIS ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 107 ASN b 38 GLN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 71 GLN d 72 ASN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 ASN L 41 HIS ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 43 ASN U 119 ASN U 133 GLN ** 1 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 190 HIS ** 3 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 120 HIS ** 3 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 82 GLN ** 4 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 112 GLN E 60 GLN ** E 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 42 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 HIS ** I 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 75 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5125 moved from start: 1.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.177 160709 Z= 0.487 Angle : 1.174 22.548 240348 Z= 0.587 Chirality : 0.055 0.665 30762 Planarity : 0.010 0.163 12915 Dihedral : 26.074 179.662 80269 Min Nonbonded Distance : 1.757 Molprobity Statistics. All-atom Clashscore : 70.99 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.76 % Favored : 88.95 % Rotamer: Outliers : 0.60 % Allowed : 7.02 % Favored : 92.38 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 1.01 % Twisted General : 0.36 % 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: -3.28 (0.10), residues: 5936 helix: -1.75 (0.10), residues: 1859 sheet: -2.16 (0.15), residues: 972 loop : -2.46 (0.10), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.005 TRP 2 201 HIS 0.024 0.004 HIS F 42 PHE 0.061 0.004 PHE 5 8 TYR 0.044 0.004 TYR I 64 ARG 0.040 0.002 ARG E 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 488 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 459 time to evaluate : 6.338 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: Q 11 MET cc_start: 0.1930 (mtp) cc_final: 0.1291 (mpp) REVERT: X 1 MET cc_start: 0.1344 (ttt) cc_final: 0.0135 (ttp) REVERT: X 8 LEU cc_start: 0.6495 (mp) cc_final: 0.6182 (mp) REVERT: g 24 MET cc_start: 0.7908 (mpp) cc_final: 0.7191 (mpp) REVERT: i 77 VAL cc_start: 0.2497 (OUTLIER) cc_final: 0.2245 (p) REVERT: 1 69 PHE cc_start: 0.7833 (OUTLIER) cc_final: 0.7328 (m-10) REVERT: 1 161 LEU cc_start: 0.8821 (tp) cc_final: 0.8566 (tp) REVERT: 2 134 MET cc_start: 0.5973 (ttt) cc_final: 0.4754 (ptm) REVERT: 3 105 MET cc_start: 0.3622 (mmt) cc_final: 0.3413 (mmt) REVERT: 5 62 MET cc_start: 0.7089 (mpp) cc_final: 0.6733 (mpp) REVERT: 6 101 MET cc_start: 0.4359 (ptm) cc_final: 0.4136 (ptm) REVERT: 6 116 MET cc_start: 0.6175 (mmm) cc_final: 0.5861 (mmm) REVERT: 8 27 LYS cc_start: 0.8306 (ptmm) cc_final: 0.8094 (ptmm) REVERT: 8 88 MET cc_start: 0.5722 (ppp) cc_final: 0.5133 (ppp) REVERT: A 105 PHE cc_start: 0.7784 (m-10) cc_final: 0.7447 (m-10) REVERT: E 96 LEU cc_start: 0.7144 (tp) cc_final: 0.6736 (tp) REVERT: H 17 MET cc_start: -0.1682 (tpt) cc_final: -0.2086 (tpt) outliers start: 29 outliers final: 12 residues processed: 484 average time/residue: 1.3420 time to fit residues: 1124.1392 Evaluate side-chains 350 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 336 time to evaluate : 6.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 846 optimal weight: 9.9990 chunk 576 optimal weight: 40.0000 chunk 14 optimal weight: 0.6980 chunk 756 optimal weight: 30.0000 chunk 419 optimal weight: 30.0000 chunk 866 optimal weight: 7.9990 chunk 702 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 chunk 518 optimal weight: 30.0000 chunk 911 optimal weight: 6.9990 chunk 256 optimal weight: 50.0000 overall best weight: 11.1390 ------------------------------------------------------------------------------- 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 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 88 GLN T 104 ASN T 128 GLN ** V 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 38 GLN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 44 GLN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 15 ASN ** l 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 58 ASN p 6 GLN ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 39 HIS ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 89 ASN ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 152 GLN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 58 HIS ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN I 31 ASN ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4993 moved from start: 1.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 160709 Z= 0.273 Angle : 0.810 13.157 240348 Z= 0.413 Chirality : 0.043 0.353 30762 Planarity : 0.006 0.131 12915 Dihedral : 25.700 179.228 80269 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 44.06 Ramachandran Plot: Outliers : 0.10 % Allowed : 9.52 % Favored : 90.38 % Rotamer: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.10), residues: 5936 helix: -1.08 (0.11), residues: 1877 sheet: -1.95 (0.16), residues: 993 loop : -2.30 (0.10), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP 1 104 HIS 0.010 0.002 HIS h 45 PHE 0.034 0.003 PHE 5 80 TYR 0.030 0.002 TYR o 21 ARG 0.024 0.001 ARG 3 81 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 458 time to evaluate : 6.239 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: V 100 LYS cc_start: 0.7070 (mmpt) cc_final: 0.5726 (tppt) REVERT: V 126 THR cc_start: 0.8795 (m) cc_final: 0.8399 (m) REVERT: X 1 MET cc_start: 0.0836 (ttt) cc_final: 0.0490 (ttt) REVERT: a 20 MET cc_start: 0.3598 (mmt) cc_final: 0.3156 (mmt) REVERT: c 5 ILE cc_start: -0.1088 (mm) cc_final: -0.1344 (mm) REVERT: c 13 MET cc_start: 0.3118 (mmt) cc_final: 0.2143 (ptt) REVERT: 1 161 LEU cc_start: 0.8920 (tp) cc_final: 0.8651 (tp) REVERT: 3 136 GLN cc_start: 0.8150 (mm110) cc_final: 0.7771 (mm110) REVERT: 4 41 ASP cc_start: 0.7521 (p0) cc_final: 0.7234 (p0) REVERT: 9 19 ASP cc_start: 0.8102 (m-30) cc_final: 0.7797 (m-30) REVERT: E 96 LEU cc_start: 0.7062 (tp) cc_final: 0.5750 (tp) REVERT: F 68 ASP cc_start: 0.9043 (m-30) cc_final: 0.8617 (p0) REVERT: J 61 PHE cc_start: 0.7563 (t80) cc_final: 0.7298 (t80) outliers start: 0 outliers final: 0 residues processed: 458 average time/residue: 1.3389 time to fit residues: 1068.1542 Evaluate side-chains 341 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 341 time to evaluate : 6.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 341 optimal weight: 30.0000 chunk 914 optimal weight: 0.7980 chunk 200 optimal weight: 40.0000 chunk 596 optimal weight: 30.0000 chunk 250 optimal weight: 5.9990 chunk 1016 optimal weight: 9.9990 chunk 844 optimal weight: 4.9990 chunk 470 optimal weight: 40.0000 chunk 84 optimal weight: 40.0000 chunk 336 optimal weight: 50.0000 chunk 533 optimal weight: 50.0000 overall best weight: 10.3590 ------------------------------------------------------------------------------- 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 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN ** T 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 73 ASN T 88 GLN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 29 HIS b 98 GLN ** d 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 37 GLN ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 27 ASN ** o 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 13 ASN ** C 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 19 GLN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 70 ASN ** 4 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 20 GLN ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN G 79 ASN J 69 HIS ** K 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5035 moved from start: 1.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.123 160709 Z= 0.274 Angle : 0.793 14.440 240348 Z= 0.403 Chirality : 0.042 0.361 30762 Planarity : 0.007 0.137 12915 Dihedral : 25.600 178.376 80269 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 46.67 Ramachandran Plot: Outliers : 0.10 % Allowed : 10.46 % Favored : 89.44 % Rotamer: Outliers : 0.02 % Allowed : 3.47 % Favored : 96.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.10), residues: 5936 helix: -0.80 (0.11), residues: 1877 sheet: -1.93 (0.16), residues: 1002 loop : -2.23 (0.10), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP P 213 HIS 0.025 0.002 HIS c 56 PHE 0.037 0.003 PHE 5 80 TYR 0.058 0.003 TYR 1 213 ARG 0.028 0.001 ARG 3 146 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 453 time to evaluate : 6.279 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: Q 11 MET cc_start: 0.1669 (mtt) cc_final: 0.0544 (mpp) REVERT: Q 77 ARG cc_start: 0.3076 (tpt170) cc_final: 0.2770 (tpt170) REVERT: R 141 MET cc_start: 0.5627 (ptp) cc_final: 0.5353 (ptp) REVERT: T 30 ASN cc_start: 0.3132 (OUTLIER) cc_final: 0.2536 (m110) REVERT: V 100 LYS cc_start: 0.6880 (mmpt) cc_final: 0.5530 (tppt) REVERT: V 125 MET cc_start: -0.1537 (tpp) cc_final: -0.1872 (mmt) REVERT: W 1 MET cc_start: 0.2861 (mmt) cc_final: 0.2540 (mmt) REVERT: X 1 MET cc_start: 0.0640 (ttt) cc_final: 0.0341 (ttt) REVERT: Z 53 MET cc_start: 0.6051 (tpt) cc_final: 0.5312 (tmm) REVERT: a 20 MET cc_start: 0.3482 (mmt) cc_final: 0.2920 (mmt) REVERT: c 13 MET cc_start: 0.3359 (mmt) cc_final: 0.2945 (ptt) REVERT: l 1 MET cc_start: 0.5702 (mtm) cc_final: 0.5294 (ppp) REVERT: L 18 CYS cc_start: 0.7229 (m) cc_final: 0.6825 (t) REVERT: U 5 LEU cc_start: 0.6956 (mm) cc_final: 0.6370 (pp) REVERT: U 60 GLU cc_start: 0.7970 (mp0) cc_final: 0.7614 (pm20) REVERT: U 87 GLU cc_start: 0.2974 (mm-30) cc_final: 0.1700 (mt-10) REVERT: 1 151 ILE cc_start: 0.8906 (pt) cc_final: 0.8552 (tp) REVERT: 1 161 LEU cc_start: 0.9032 (tp) cc_final: 0.8721 (tp) REVERT: 4 34 THR cc_start: 0.7324 (p) cc_final: 0.7115 (p) REVERT: 8 88 MET cc_start: 0.6608 (ppp) cc_final: 0.4897 (mmt) REVERT: 9 19 ASP cc_start: 0.8198 (m-30) cc_final: 0.7935 (m-30) REVERT: D 52 GLN cc_start: 0.8132 (mt0) cc_final: 0.7841 (mt0) REVERT: E 89 MET cc_start: 0.1360 (mmp) cc_final: 0.0748 (mmt) REVERT: F 68 ASP cc_start: 0.9028 (m-30) cc_final: 0.8544 (p0) outliers start: 1 outliers final: 0 residues processed: 454 average time/residue: 1.2981 time to fit residues: 1024.6100 Evaluate side-chains 349 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 348 time to evaluate : 8.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 980 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 579 optimal weight: 30.0000 chunk 742 optimal weight: 30.0000 chunk 575 optimal weight: 50.0000 chunk 856 optimal weight: 8.9990 chunk 567 optimal weight: 40.0000 chunk 1012 optimal weight: 50.0000 chunk 633 optimal weight: 8.9990 chunk 617 optimal weight: 5.9990 chunk 467 optimal weight: 50.0000 overall best weight: 5.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 46 ASN ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN T 88 GLN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 54 GLN ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 3 ASN ** c 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN h 74 ASN i 49 ASN ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 16 HIS ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 188 ASN U 66 ASN ** 1 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 109 GLN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 176 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 89 ASN ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 11 HIS ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 9 58 ASN ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 35 GLN G 29 ASN J 69 HIS K 52 ASN ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4900 moved from start: 1.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 160709 Z= 0.179 Angle : 0.675 15.566 240348 Z= 0.344 Chirality : 0.037 0.348 30762 Planarity : 0.005 0.105 12915 Dihedral : 25.283 179.266 80269 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 32.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 8.76 % Favored : 91.14 % Rotamer: Outliers : 0.02 % Allowed : 1.64 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.10), residues: 5936 helix: -0.35 (0.12), residues: 1876 sheet: -1.77 (0.16), residues: 977 loop : -2.10 (0.10), residues: 3083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP P 213 HIS 0.012 0.001 HIS r 33 PHE 0.032 0.002 PHE 5 80 TYR 0.031 0.002 TYR 8 6 ARG 0.021 0.001 ARG f 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 451 time to evaluate : 6.243 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: X 1 MET cc_start: 0.0416 (ttt) cc_final: -0.0026 (ttt) REVERT: Z 53 MET cc_start: 0.5774 (tpt) cc_final: 0.5070 (tmm) REVERT: c 13 MET cc_start: 0.3953 (mmt) cc_final: 0.3160 (ptt) REVERT: n 15 MET cc_start: 0.7986 (ptp) cc_final: 0.7786 (ptp) REVERT: L 18 CYS cc_start: 0.7174 (m) cc_final: 0.6732 (t) REVERT: U 60 GLU cc_start: 0.8196 (mp0) cc_final: 0.7979 (mp0) REVERT: U 87 GLU cc_start: 0.3123 (mm-30) cc_final: 0.2026 (mt-10) REVERT: 1 64 LYS cc_start: 0.6990 (mmpt) cc_final: 0.6715 (mmmt) REVERT: 1 154 MET cc_start: 0.8094 (tpt) cc_final: 0.7647 (tmm) REVERT: 3 136 GLN cc_start: 0.8139 (mm110) cc_final: 0.7445 (mm110) REVERT: 8 88 MET cc_start: 0.7157 (ppp) cc_final: 0.5982 (mmt) REVERT: D 52 GLN cc_start: 0.8065 (mt0) cc_final: 0.7806 (mt0) REVERT: E 6 MET cc_start: -0.3786 (mmt) cc_final: -0.4287 (mtt) REVERT: F 68 ASP cc_start: 0.8821 (m-30) cc_final: 0.8428 (p0) outliers start: 1 outliers final: 0 residues processed: 451 average time/residue: 1.5056 time to fit residues: 1202.4248 Evaluate side-chains 346 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 6.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 626 optimal weight: 7.9990 chunk 404 optimal weight: 40.0000 chunk 605 optimal weight: 50.0000 chunk 305 optimal weight: 6.9990 chunk 199 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 644 optimal weight: 50.0000 chunk 690 optimal weight: 30.0000 chunk 500 optimal weight: 40.0000 chunk 94 optimal weight: 8.9990 chunk 796 optimal weight: 30.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN T 88 GLN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 52 ASN c 75 GLN c 77 HIS ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 109 GLN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 176 HIS ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 89 ASN ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 38 ASN ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 81 HIS ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 29 ASN J 69 HIS ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4963 moved from start: 1.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 160709 Z= 0.206 Angle : 0.687 13.049 240348 Z= 0.349 Chirality : 0.037 0.375 30762 Planarity : 0.005 0.120 12915 Dihedral : 25.266 178.590 80269 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 38.35 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.43 % Rotamer: Outliers : 0.02 % Allowed : 1.06 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.10), residues: 5936 helix: -0.27 (0.12), residues: 1859 sheet: -1.82 (0.16), residues: 965 loop : -2.07 (0.10), residues: 3112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP P 213 HIS 0.011 0.001 HIS Z 13 PHE 0.044 0.002 PHE 7 45 TYR 0.046 0.002 TYR 1 213 ARG 0.030 0.001 ARG 2 126 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 428 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 427 time to evaluate : 6.283 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: V 100 LYS cc_start: 0.6635 (mmpt) cc_final: 0.5814 (tppt) REVERT: X 1 MET cc_start: 0.0695 (ttt) cc_final: 0.0349 (ttt) REVERT: X 84 CYS cc_start: 0.5883 (p) cc_final: 0.4503 (p) REVERT: Z 33 LEU cc_start: 0.5935 (mt) cc_final: 0.5682 (mt) REVERT: Z 53 MET cc_start: 0.5890 (tpt) cc_final: 0.5229 (tmm) REVERT: c 13 MET cc_start: 0.3819 (mmt) cc_final: 0.3558 (ptt) REVERT: l 1 MET cc_start: 0.4739 (ttt) cc_final: 0.3435 (tmm) REVERT: L 18 CYS cc_start: 0.7468 (m) cc_final: 0.6787 (t) REVERT: U 60 GLU cc_start: 0.8411 (mp0) cc_final: 0.8184 (mp0) REVERT: U 87 GLU cc_start: 0.3283 (mm-30) cc_final: 0.2204 (mt-10) REVERT: 1 154 MET cc_start: 0.8252 (tpt) cc_final: 0.7942 (tmm) REVERT: 4 41 ASP cc_start: 0.8189 (p0) cc_final: 0.7799 (p0) REVERT: 4 116 GLU cc_start: 0.8201 (mp0) cc_final: 0.7870 (pp20) REVERT: D 52 GLN cc_start: 0.8046 (mt0) cc_final: 0.7825 (mt0) REVERT: E 6 MET cc_start: -0.3843 (mmt) cc_final: -0.4525 (mtt) outliers start: 1 outliers final: 1 residues processed: 427 average time/residue: 1.3173 time to fit residues: 989.3141 Evaluate side-chains 334 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 333 time to evaluate : 5.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 921 optimal weight: 20.0000 chunk 970 optimal weight: 0.7980 chunk 885 optimal weight: 8.9990 chunk 943 optimal weight: 40.0000 chunk 568 optimal weight: 40.0000 chunk 411 optimal weight: 50.0000 chunk 741 optimal weight: 40.0000 chunk 289 optimal weight: 10.0000 chunk 853 optimal weight: 6.9990 chunk 892 optimal weight: 20.0000 chunk 940 optimal weight: 50.0000 overall best weight: 9.3592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 167 ASN R 165 HIS ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN T 88 GLN T 115 HIS V 19 ASN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 67 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 46 GLN h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 109 GLN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 49 GLN J 69 HIS ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 1.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 160709 Z= 0.245 Angle : 0.753 24.837 240348 Z= 0.382 Chirality : 0.040 0.514 30762 Planarity : 0.006 0.170 12915 Dihedral : 25.506 179.675 80269 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 44.70 Ramachandran Plot: Outliers : 0.12 % Allowed : 10.09 % Favored : 89.79 % Rotamer: Outliers : 0.04 % Allowed : 0.89 % Favored : 99.07 % Cbeta Deviations : 0.00 % 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: -2.37 (0.10), residues: 5936 helix: -0.55 (0.11), residues: 1869 sheet: -1.84 (0.16), residues: 969 loop : -2.15 (0.10), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP 6 103 HIS 0.024 0.002 HIS Q 140 PHE 0.056 0.003 PHE 6 62 TYR 0.049 0.002 TYR 1 213 ARG 0.041 0.001 ARG A 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 429 time to evaluate : 6.287 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: P 146 MET cc_start: 0.0516 (mpp) cc_final: 0.0198 (tpt) REVERT: Q 11 MET cc_start: 0.2413 (mtt) cc_final: 0.1097 (mpp) REVERT: X 1 MET cc_start: 0.0692 (ttt) cc_final: 0.0447 (ttm) REVERT: X 7 MET cc_start: 0.2640 (pmm) cc_final: 0.2397 (pmm) REVERT: Z 33 LEU cc_start: 0.5774 (mt) cc_final: 0.5425 (mt) REVERT: Z 53 MET cc_start: 0.5727 (tpt) cc_final: 0.5189 (tmm) REVERT: c 13 MET cc_start: 0.3753 (mmt) cc_final: 0.3311 (ptt) REVERT: l 1 MET cc_start: 0.4388 (ttt) cc_final: 0.2730 (tmm) REVERT: l 30 MET cc_start: 0.5982 (ptp) cc_final: 0.5640 (ptp) REVERT: L 18 CYS cc_start: 0.7789 (m) cc_final: 0.7079 (t) REVERT: U 60 GLU cc_start: 0.8685 (mp0) cc_final: 0.8400 (mp0) REVERT: U 87 GLU cc_start: 0.3870 (mm-30) cc_final: 0.3503 (mt-10) REVERT: U 122 LEU cc_start: 0.3118 (tt) cc_final: 0.2712 (mp) REVERT: U 129 GLU cc_start: 0.2715 (tp30) cc_final: -0.1290 (mp0) REVERT: 1 213 TYR cc_start: 0.8012 (m-80) cc_final: 0.7795 (m-80) REVERT: 2 41 GLN cc_start: 0.8664 (pt0) cc_final: 0.8372 (tp-100) REVERT: 4 147 MET cc_start: 0.7942 (mmp) cc_final: 0.7605 (mmm) REVERT: 9 19 ASP cc_start: 0.8412 (m-30) cc_final: 0.8158 (m-30) REVERT: A 108 THR cc_start: 0.8299 (p) cc_final: 0.8097 (p) REVERT: E 6 MET cc_start: -0.3929 (mmt) cc_final: -0.4808 (mtt) REVERT: E 96 LEU cc_start: 0.6904 (tp) cc_final: 0.6369 (tp) outliers start: 2 outliers final: 0 residues processed: 430 average time/residue: 1.4206 time to fit residues: 1090.4933 Evaluate side-chains 339 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 339 time to evaluate : 6.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 619 optimal weight: 6.9990 chunk 998 optimal weight: 0.3980 chunk 609 optimal weight: 50.0000 chunk 473 optimal weight: 50.0000 chunk 693 optimal weight: 30.0000 chunk 1047 optimal weight: 50.0000 chunk 963 optimal weight: 9.9990 chunk 833 optimal weight: 0.2980 chunk 86 optimal weight: 20.0000 chunk 644 optimal weight: 50.0000 chunk 511 optimal weight: 50.0000 overall best weight: 7.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN T 88 GLN V 19 ASN ** X 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 73 ASN ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** d 71 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 66 ASN 1 109 GLN ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 100 ASN ** 3 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 140 ASN ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 82 GLN 4 97 GLN 4 121 HIS ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 31 ASN ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 6 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 35 ASN ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 HIS ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5008 moved from start: 1.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 160709 Z= 0.204 Angle : 0.697 16.075 240348 Z= 0.355 Chirality : 0.038 0.512 30762 Planarity : 0.005 0.102 12915 Dihedral : 25.392 179.199 80269 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 38.98 Ramachandran Plot: Outliers : 0.07 % Allowed : 9.47 % Favored : 90.46 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.05 % Twisted Proline : 0.51 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.10), residues: 5936 helix: -0.37 (0.12), residues: 1864 sheet: -1.81 (0.16), residues: 994 loop : -2.08 (0.11), residues: 3078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP P 213 HIS 0.013 0.001 HIS Z 13 PHE 0.032 0.002 PHE 1 126 TYR 0.050 0.002 TYR 1 213 ARG 0.012 0.001 ARG 6 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11872 Ramachandran restraints generated. 5936 Oldfield, 0 Emsley, 5936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 439 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 438 time to evaluate : 8.818 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: P 146 MET cc_start: 0.0862 (mpp) cc_final: 0.0338 (tpt) REVERT: S 38 MET cc_start: 0.6828 (tmm) cc_final: 0.6522 (tmm) REVERT: X 1 MET cc_start: 0.0738 (ttt) cc_final: 0.0493 (ttt) REVERT: Z 33 LEU cc_start: 0.5890 (mt) cc_final: 0.5496 (mt) REVERT: Z 53 MET cc_start: 0.6046 (tpt) cc_final: 0.5360 (tmm) REVERT: c 13 MET cc_start: 0.3671 (mmt) cc_final: 0.3291 (ptt) REVERT: l 1 MET cc_start: 0.4216 (ttt) cc_final: 0.3105 (tmm) REVERT: m 47 MET cc_start: 0.5512 (mmm) cc_final: 0.5260 (mmm) REVERT: n 15 MET cc_start: 0.8294 (ptp) cc_final: 0.8066 (ptp) REVERT: L 18 CYS cc_start: 0.7815 (m) cc_final: 0.7084 (t) REVERT: U 60 GLU cc_start: 0.8734 (mp0) cc_final: 0.8438 (mp0) REVERT: U 87 GLU cc_start: 0.3756 (mm-30) cc_final: 0.3394 (mt-10) REVERT: U 129 GLU cc_start: 0.2365 (tp30) cc_final: -0.1315 (mp0) REVERT: 1 50 PHE cc_start: 0.7555 (m-80) cc_final: 0.6869 (m-80) REVERT: 1 213 TYR cc_start: 0.8039 (m-80) cc_final: 0.7834 (m-80) REVERT: 4 147 MET cc_start: 0.7730 (mmp) cc_final: 0.7272 (mmm) REVERT: 7 27 MET cc_start: 0.2519 (ttt) cc_final: 0.2119 (ttt) REVERT: 8 41 ARG cc_start: 0.4446 (ttt-90) cc_final: 0.3204 (tmt170) REVERT: 8 62 ASP cc_start: 0.8494 (m-30) cc_final: 0.8260 (m-30) REVERT: 9 19 ASP cc_start: 0.8476 (m-30) cc_final: 0.8238 (m-30) REVERT: 9 85 ASP cc_start: 0.9273 (m-30) cc_final: 0.8977 (m-30) REVERT: B 57 LEU cc_start: 0.7131 (tp) cc_final: 0.6930 (tp) REVERT: E 6 MET cc_start: -0.4099 (mmt) cc_final: -0.4861 (mtt) REVERT: E 96 LEU cc_start: 0.7113 (tp) cc_final: 0.6630 (tp) outliers start: 1 outliers final: 0 residues processed: 438 average time/residue: 1.3116 time to fit residues: 1013.7994 Evaluate side-chains 349 residues out of total 4941 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 349 time to evaluate : 6.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1051 random chunks: chunk 662 optimal weight: 40.0000 chunk 888 optimal weight: 9.9990 chunk 255 optimal weight: 0.0020 chunk 768 optimal weight: 30.0000 chunk 123 optimal weight: 50.0000 chunk 231 optimal weight: 8.9990 chunk 835 optimal weight: 30.0000 chunk 349 optimal weight: 50.0000 chunk 857 optimal weight: 8.9990 chunk 105 optimal weight: 0.0870 chunk 153 optimal weight: 30.0000 overall best weight: 5.6172 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 163 GLN ** P 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 226 ASN ** Q 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 30 ASN T 88 GLN V 19 ASN ** V 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 77 HIS ** e 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 74 ASN ** i 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 1 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 109 GLN ** 1 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 97 GLN ** 5 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 38 GLN B 6 GLN ** D 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 69 HIS ** K 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.054570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.040200 restraints weight = 2613489.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.040487 restraints weight = 2187311.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.040611 restraints weight = 1810356.241| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.033 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 1.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 160709 Z= 0.175 Angle : 0.650 13.480 240348 Z= 0.330 Chirality : 0.036 0.385 30762 Planarity : 0.005 0.101 12915 Dihedral : 25.180 179.469 80269 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 34.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 8.81 % Favored : 91.12 % Rotamer: Outliers : 0.02 % Allowed : 0.37 % Favored : 99.61 % 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: -2.08 (0.10), residues: 5936 helix: -0.18 (0.12), residues: 1867 sheet: -1.75 (0.16), residues: 979 loop : -2.03 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP P 213 HIS 0.014 0.001 HIS Z 13 PHE 0.036 0.002 PHE S 177 TYR 0.048 0.002 TYR 1 213 ARG 0.016 0.001 ARG 5 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25392.66 seconds wall clock time: 455 minutes 50.00 seconds (27350.00 seconds total)