Starting phenix.real_space_refine on Fri Mar 22 06:23:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oif_12928/03_2024/7oif_12928_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 Zn 2 6.06 5 P 4651 5.49 5 Mg 416 5.21 5 S 150 5.16 5 C 72657 2.51 5 N 26976 2.21 5 O 40300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 53": "OE1" <-> "OE2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 34": "NH1" <-> "NH2" Residue "I ARG 37": "NH1" <-> "NH2" Residue "I ARG 95": "NH1" <-> "NH2" Residue "I ARG 96": "NH1" <-> "NH2" Residue "I ARG 120": "NH1" <-> "NH2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K ARG 60": "NH1" <-> "NH2" Residue "K ARG 78": "NH1" <-> "NH2" Residue "K ARG 123": "NH1" <-> "NH2" Residue "K ARG 126": "NH1" <-> "NH2" Residue "L ARG 10": "NH1" <-> "NH2" Residue "L ARG 18": "NH1" <-> "NH2" Residue "L ARG 40": "NH1" <-> "NH2" Residue "L ARG 50": "NH1" <-> "NH2" Residue "L ARG 55": "NH1" <-> "NH2" Residue "L GLU 111": "OE1" <-> "OE2" Residue "L ARG 114": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O ARG 89": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 82": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 94": "NH1" <-> "NH2" Residue "U ARG 19": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 45": "NH1" <-> "NH2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 30": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f ARG 74": "NH1" <-> "NH2" Residue "f ARG 208": "NH1" <-> "NH2" Residue "f ARG 225": "NH1" <-> "NH2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 131": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g ARG 164": "NH1" <-> "NH2" Residue "h ARG 73": "NH1" <-> "NH2" Residue "h ARG 81": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 69": "NH1" <-> "NH2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i GLU 116": "OE1" <-> "OE2" Residue "i ARG 157": "NH1" <-> "NH2" Residue "j PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j GLU 75": "OE1" <-> "OE2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 4": "NH1" <-> "NH2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ARG 92": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m ARG 130": "NH1" <-> "NH2" Residue "n ARG 5": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 89": "NH1" <-> "NH2" Residue "o ARG 37": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "o ARG 93": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 50": "NH1" <-> "NH2" Residue "p GLU 62": "OE1" <-> "OE2" Residue "p ARG 83": "NH1" <-> "NH2" Residue "q ARG 29": "NH1" <-> "NH2" Residue "q ARG 70": "NH1" <-> "NH2" Residue "q ARG 87": "NH1" <-> "NH2" Residue "q ARG 109": "NH1" <-> "NH2" Residue "r ARG 59": "NH1" <-> "NH2" Residue "r ARG 63": "NH1" <-> "NH2" Residue "r ARG 65": "NH1" <-> "NH2" Residue "r ARG 69": "NH1" <-> "NH2" Residue "r ARG 85": "NH1" <-> "NH2" Residue "s ARG 72": "NH1" <-> "NH2" Residue "s ARG 89": "NH1" <-> "NH2" Residue "t ARG 28": "NH1" <-> "NH2" Residue "t GLU 48": "OE1" <-> "OE2" Residue "t ARG 51": "NH1" <-> "NH2" Residue "u ARG 11": "NH1" <-> "NH2" Residue "u ARG 27": "NH1" <-> "NH2" Residue "u ARG 65": "NH1" <-> "NH2" Residue "u ARG 77": "NH1" <-> "NH2" Residue "v ARG 61": "NH1" <-> "NH2" Residue "w ARG 32": "NH1" <-> "NH2" Residue "x ARG 60": "NH1" <-> "NH2" Residue "x ARG 74": "NH1" <-> "NH2" Residue "y GLU 24": "OE1" <-> "OE2" Residue "y ARG 33": "NH1" <-> "NH2" Residue "y GLU 44": "OE1" <-> "OE2" Residue "y ARG 45": "NH1" <-> "NH2" Residue "y ARG 55": "NH1" <-> "NH2" Residue "y ARG 62": "NH1" <-> "NH2" Residue "y ARG 67": "NH1" <-> "NH2" Residue "y ARG 69": "NH1" <-> "NH2" 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: 145152 Number of models: 1 Model: "" Number of chains: 70 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 290, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1377, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 460, 'rna3p': 2442} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 206, 'rna3p': 1327} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 2, 'rna3p_pyr': 4} Link IDs: {'rna3p': 5} Chain: "C" 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: "D" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "E" 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: "F" 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: "G" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "H" 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: "I" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "J" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "K" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "L" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "M" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "N" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "O" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "P" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Q" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "R" 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: "S" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "T" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "U" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "V" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 601 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "W" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "X" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Y" 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: "Z" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "a" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "b" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "d" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "e" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "f" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "g" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "h" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "i" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "j" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "k" 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: "l" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "m" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "n" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "o" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "p" Number of atoms: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 115} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "q" Number of atoms: 900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 900 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "r" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "s" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "t" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "u" 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: "v" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "w" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "x" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "y" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "z" Number of atoms: 1891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1891 Inner-chain residues flagged as termini: ['pdbres=" U z 8 "', 'pdbres=" G z 9 "', 'pdbres=" U z 20 "', 'pdbres=" U z 67 "'] Classifications: {'RNA': 88} Modifications used: {'p5*END': 4, 'rna2p': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p': 1, 'rna3p_pur': 40, 'rna3p_pyr': 34} Link IDs: {'rna2p': 12, 'rna3p': 75} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 205 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 276 Unusual residues: {' MG': 276} Classifications: {'undetermined': 276} Link IDs: {None: 275} Chain: "2" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 119 Unusual residues: {' MG': 119} Classifications: {'undetermined': 119} Link IDs: {None: 118} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0GBZ SG CYS Z 16 64.834 59.002 105.671 1.00 93.08 S ATOM A0GCB SG CYS Z 18 63.017 57.586 102.446 1.00 94.77 S ATOM A0GG9 SG CYS Z 37 65.707 57.944 101.600 1.00 92.43 S ATOM A0GGU SG CYS Z 40 64.408 60.988 102.158 1.00 93.45 S ATOM A0I1V SG CYS e 11 143.286 115.698 47.887 1.00 68.94 S ATOM A0I2K SG CYS e 14 145.807 114.135 49.286 1.00 66.37 S ATOM A0I5F SG CYS e 27 145.597 117.933 47.679 1.00 67.22 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13142 " occ=0.50 Time building chain proxies: 57.62, per 1000 atoms: 0.40 Number of scatterers: 145152 At special positions: 0 Unit cell: (276.06, 266.43, 230.05, 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) Zn 2 29.99 S 150 16.00 P 4651 15.00 Mg 416 11.99 O 40300 8.00 N 26976 7.00 C 72657 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 62.46 Conformation dependent library (CDL) restraints added in 6.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN Z 101 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 37 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 16 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 40 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 18 " pdb=" ZN e 101 " pdb="ZN ZN e 101 " - pdb=" ND1 HIS e 33 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 27 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 14 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 11 " Number of angles added : 9 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10532 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 175 helices and 72 sheets defined 39.1% alpha, 20.0% beta 1576 base pairs and 2654 stacking pairs defined. Time for finding SS restraints: 77.46 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.511A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.981A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N GLU C 35 " --> pdb=" O ALA C 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 30 through 35' Processing helix chain 'C' and resid 131 through 136 Proline residue: C 136 - end of helix Processing helix chain 'C' and resid 207 through 215 removed outlier: 3.978A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.478A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N ASN C 226 " --> pdb=" O GLY C 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 221 through 226' Processing helix chain 'C' and resid 260 through 268 removed outlier: 3.975A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.806A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N VAL C 268 " --> pdb=" O ASP C 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 260 through 268' Processing helix chain 'D' and resid 56 through 61 removed outlier: 5.782A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.728A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.092A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ASP D 103 " --> pdb=" O GLU D 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 98 through 103' Processing helix chain 'D' and resid 120 through 125 Processing helix chain 'E' and resid 15 through 20 Processing helix chain 'E' and resid 24 through 41 removed outlier: 3.718A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.470A pdb=" N THR E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 116 Processing helix chain 'E' and resid 130 through 142 Processing helix chain 'E' and resid 154 through 163 removed outlier: 4.556A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 6.176A pdb=" N ASP E 184 " --> pdb=" O LEU E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 189 through 201 Processing helix chain 'F' and resid 2 through 21 removed outlier: 5.212A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.209A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 47' Processing helix chain 'F' and resid 48 through 62 removed outlier: 3.892A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.426A pdb=" N VAL F 108 " --> pdb=" O ILE F 104 " (cutoff:3.500A) Proline residue: F 109 - end of helix Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.409A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.812A pdb=" N ILE F 137 " --> pdb=" O GLU F 134 " (cutoff:3.500A) Proline residue: F 139 - end of helix Processing helix chain 'G' and resid 2 through 8 removed outlier: 3.810A pdb=" N ALA G 7 " --> pdb=" O ARG G 3 " (cutoff:3.500A) Proline residue: G 8 - end of helix Processing helix chain 'G' and resid 60 through 81 Processing helix chain 'G' and resid 137 through 153 removed outlier: 3.700A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ARG G 152 " --> pdb=" O LEU G 148 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 28 Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 40 through 49 removed outlier: 3.746A pdb=" N GLU H 45 " --> pdb=" O LYS H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 50 through 74 removed outlier: 3.616A pdb=" N LEU H 54 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU H 62 " --> pdb=" O LEU H 58 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N ALA H 74 " --> pdb=" O GLU H 70 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'I' and resid 24 through 38 removed outlier: 4.098A pdb=" N GLU I 31 " --> pdb=" O ARG I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 96 Processing helix chain 'I' and resid 97 through 110 removed outlier: 4.418A pdb=" N ILE I 101 " --> pdb=" O PRO I 97 " (cutoff:3.500A) Proline residue: I 110 - end of helix Processing helix chain 'I' and resid 112 through 123 removed outlier: 3.937A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N LYS I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'K' and resid 37 through 42 removed outlier: 4.121A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N SER K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 37 through 42' Processing helix chain 'K' and resid 56 through 62 Proline residue: K 62 - end of helix Processing helix chain 'K' and resid 68 through 75 removed outlier: 4.039A pdb=" N ALA K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N ALA K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 85 removed outlier: 4.132A pdb=" N LEU K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N LYS K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 78 through 85' Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 128 through 139 Processing helix chain 'L' and resid 42 through 58 Processing helix chain 'L' and resid 109 through 125 removed outlier: 4.265A pdb=" N LYS L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Proline residue: L 125 - end of helix Processing helix chain 'M' and resid 13 through 32 Processing helix chain 'M' and resid 38 through 57 removed outlier: 4.370A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.584A pdb=" N THR M 57 " --> pdb=" O THR M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 71 Processing helix chain 'M' and resid 72 through 88 removed outlier: 3.693A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N GLY M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) Proline residue: M 85 - end of helix Processing helix chain 'N' and resid 2 through 22 removed outlier: 4.620A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ARG N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 5.074A pdb=" N GLN N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N LYS N 63 " --> pdb=" O ALA N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 86 Processing helix chain 'N' and resid 101 through 114 Processing helix chain 'O' and resid 2 through 13 removed outlier: 3.547A pdb=" N GLU O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN O 12 " --> pdb=" O LEU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 104 removed outlier: 4.867A pdb=" N ARG O 101 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N GLU O 102 " --> pdb=" O TYR O 98 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ARG O 103 " --> pdb=" O TYR O 99 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N THR O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 97 through 104' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.834A pdb=" N ILE P 17 " --> pdb=" O ARG P 13 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.819A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.986A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 removed outlier: 3.644A pdb=" N ASN P 81 " --> pdb=" O SER P 77 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 102 Processing helix chain 'P' and resid 103 through 118 Processing helix chain 'R' and resid 13 through 25 removed outlier: 3.781A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG R 25 " --> pdb=" O ALA R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 39 Processing helix chain 'R' and resid 41 through 61 removed outlier: 3.775A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 70 removed outlier: 3.697A pdb=" N LEU R 69 " --> pdb=" O ASP R 65 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LYS R 70 " --> pdb=" O ILE R 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 65 through 70' Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.347A pdb=" N LEU S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 26 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'T' and resid 66 through 71 removed outlier: 3.762A pdb=" N VAL T 70 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ALA T 71 " --> pdb=" O VAL T 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 66 through 71' Processing helix chain 'U' and resid 13 through 24 Processing helix chain 'U' and resid 43 through 53 removed outlier: 3.611A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA U 52 " --> pdb=" O MET U 48 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) Processing helix chain 'U' and resid 54 through 59 Processing helix chain 'W' and resid 52 through 63 Processing helix chain 'W' and resid 64 through 75 Processing helix chain 'X' and resid 2 through 10 removed outlier: 3.964A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N LYS X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 4.117A pdb=" N GLY X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 40 through 62 removed outlier: 4.308A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N GLY X 62 " --> pdb=" O ASN X 58 " (cutoff:3.500A) Processing helix chain 'Y' and resid 17 through 28 Processing helix chain 'Y' and resid 41 through 52 Processing helix chain 'Z' and resid 44 through 51 removed outlier: 5.385A pdb=" N GLN Z 48 " --> pdb=" O PHE Z 44 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N VAL Z 51 " --> pdb=" O LYS Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 65 removed outlier: 4.079A pdb=" N PHE Z 64 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ASN Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 21 removed outlier: 4.752A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ASP a 20 " --> pdb=" O ARG a 16 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N ALA a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 Proline residue: b 31 - end of helix Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 25 removed outlier: 4.286A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LYS c 25 " --> pdb=" O ARG c 21 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 38 Processing helix chain 'd' and resid 7 through 14 Processing helix chain 'd' and resid 32 through 37 removed outlier: 4.562A pdb=" N LYS d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ALA d 37 " --> pdb=" O LEU d 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 32 through 37' Processing helix chain 'd' and resid 38 through 46 Proline residue: d 46 - end of helix Processing helix chain 'd' and resid 51 through 63 removed outlier: 4.716A pdb=" N GLY d 56 " --> pdb=" O LYS d 52 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU d 57 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N VAL d 58 " --> pdb=" O ASP d 54 " (cutoff:3.500A) Proline residue: d 63 - end of helix Processing helix chain 'f' and resid 5 through 13 Processing helix chain 'f' and resid 42 through 64 Proline residue: f 48 - end of helix removed outlier: 3.591A pdb=" N ARG f 63 " --> pdb=" O LYS f 59 " (cutoff:3.500A) Processing helix chain 'f' and resid 73 through 88 removed outlier: 6.285A pdb=" N SER f 77 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N GLU f 78 " --> pdb=" O ARG f 74 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA f 79 " --> pdb=" O ALA f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.259A pdb=" N GLN f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER f 110 " --> pdb=" O THR f 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 130 through 148 Processing helix chain 'f' and resid 165 through 170 Processing helix chain 'f' and resid 171 through 180 Processing helix chain 'f' and resid 206 through 227 Processing helix chain 'g' and resid 6 through 12 Processing helix chain 'g' and resid 28 through 48 Processing helix chain 'g' and resid 72 through 78 removed outlier: 4.403A pdb=" N VAL g 76 " --> pdb=" O ARG g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 96 removed outlier: 3.710A pdb=" N VAL g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 113 removed outlier: 4.302A pdb=" N ASP g 112 " --> pdb=" O LYS g 108 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ALA g 113 " --> pdb=" O PRO g 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 108 through 113' Processing helix chain 'g' and resid 114 through 127 Processing helix chain 'g' and resid 129 through 145 Processing helix chain 'h' and resid 7 through 16 removed outlier: 4.197A pdb=" N LEU h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 27 through 32 Processing helix chain 'h' and resid 49 through 66 Processing helix chain 'h' and resid 68 through 83 removed outlier: 5.267A pdb=" N LYS h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 97 removed outlier: 3.624A pdb=" N ARG h 97 " --> pdb=" O LEU h 93 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 106 Processing helix chain 'h' and resid 110 through 121 Processing helix chain 'h' and resid 152 through 166 removed outlier: 3.999A pdb=" N LYS h 156 " --> pdb=" O GLN h 152 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N GLU h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 192 removed outlier: 3.709A pdb=" N LEU h 191 " --> pdb=" O GLU h 187 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N SER h 192 " --> pdb=" O ARG h 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 187 through 192' Processing helix chain 'h' and resid 196 through 206 removed outlier: 4.005A pdb=" N ILE h 200 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N LYS h 206 " --> pdb=" O GLU h 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 71 removed outlier: 3.675A pdb=" N ARG i 69 " --> pdb=" O GLU i 65 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ASN i 70 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N MET i 71 " --> pdb=" O ALA i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 109 through 119 removed outlier: 3.824A pdb=" N ALA i 113 " --> pdb=" O GLY i 109 " (cutoff:3.500A) Processing helix chain 'i' and resid 132 through 147 Processing helix chain 'i' and resid 149 through 158 Processing helix chain 'i' and resid 160 through 165 Processing helix chain 'j' and resid 11 through 16 removed outlier: 3.849A pdb=" N SER j 15 " --> pdb=" O HIS j 11 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N GLU j 16 " --> pdb=" O PRO j 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 11 through 16' Processing helix chain 'j' and resid 17 through 33 Processing helix chain 'j' and resid 67 through 81 removed outlier: 3.622A pdb=" N ILE j 71 " --> pdb=" O PRO j 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 31 removed outlier: 3.682A pdb=" N ALA k 24 " --> pdb=" O SER k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 35 through 55 removed outlier: 3.648A pdb=" N ALA k 39 " --> pdb=" O LYS k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 70 removed outlier: 3.759A pdb=" N VAL k 69 " --> pdb=" O ALA k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 112 removed outlier: 6.110A pdb=" N GLY k 112 " --> pdb=" O ALA k 108 " (cutoff:3.500A) Processing helix chain 'k' and resid 115 through 130 Processing helix chain 'k' and resid 132 through 149 Processing helix chain 'l' and resid 5 through 21 Processing helix chain 'l' and resid 30 through 44 Processing helix chain 'l' and resid 112 through 120 Processing helix chain 'm' and resid 34 through 40 removed outlier: 4.847A pdb=" N GLY m 40 " --> pdb=" O GLU m 36 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 56 removed outlier: 3.687A pdb=" N ARG m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 51 - end of helix removed outlier: 4.245A pdb=" N ASP m 56 " --> pdb=" O LEU m 52 " (cutoff:3.500A) Processing helix chain 'm' and resid 71 through 92 Processing helix chain 'm' and resid 94 through 102 removed outlier: 4.072A pdb=" N LYS m 100 " --> pdb=" O SER m 96 " (cutoff:3.500A) Processing helix chain 'n' and resid 14 through 33 Processing helix chain 'n' and resid 80 through 91 removed outlier: 3.747A pdb=" N VAL n 84 " --> pdb=" O THR n 80 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP n 85 " --> pdb=" O GLU n 81 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 removed outlier: 4.070A pdb=" N GLY o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 59 removed outlier: 3.868A pdb=" N SER o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR o 59 " --> pdb=" O SER o 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 54 through 59' Processing helix chain 'o' and resid 60 through 75 Processing helix chain 'o' and resid 92 through 104 removed outlier: 4.034A pdb=" N THR o 96 " --> pdb=" O GLY o 92 " (cutoff:3.500A) removed outlier: 5.135A pdb=" N ILE o 97 " --> pdb=" O ARG o 93 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N GLY o 104 " --> pdb=" O LEU o 100 " (cutoff:3.500A) Processing helix chain 'p' and resid 3 through 10 Processing helix chain 'p' and resid 113 through 118 removed outlier: 3.853A pdb=" N TYR p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 23 removed outlier: 4.222A pdb=" N ILE q 22 " --> pdb=" O ALA q 18 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N TYR q 23 " --> pdb=" O LEU q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 38 Processing helix chain 'q' and resid 49 through 64 removed outlier: 4.046A pdb=" N PHE q 63 " --> pdb=" O GLU q 59 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N VAL q 64 " --> pdb=" O VAL q 60 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 84 Processing helix chain 'q' and resid 85 through 94 Processing helix chain 'q' and resid 106 through 111 Processing helix chain 'r' and resid 3 through 21 removed outlier: 3.849A pdb=" N PHE r 21 " --> pdb=" O ALA r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 22 through 33 Processing helix chain 'r' and resid 37 through 52 Proline residue: r 52 - end of helix Processing helix chain 'r' and resid 56 through 61 removed outlier: 3.976A pdb=" N GLN r 60 " --> pdb=" O SER r 56 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N ARG r 61 " --> pdb=" O PRO r 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'r' and resid 56 through 61' Processing helix chain 'r' and resid 80 through 91 removed outlier: 3.588A pdb=" N ARG r 85 " --> pdb=" O ARG r 81 " (cutoff:3.500A) Processing helix chain 's' and resid 4 through 16 Processing helix chain 's' and resid 24 through 43 removed outlier: 4.626A pdb=" N GLY s 41 " --> pdb=" O ASN s 37 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N HIS s 42 " --> pdb=" O HIS s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 49 through 74 removed outlier: 3.890A pdb=" N GLY s 55 " --> pdb=" O HIS s 51 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 86 Processing helix chain 't' and resid 53 through 64 Processing helix chain 't' and resid 68 through 82 Processing helix chain 'v' and resid 11 through 17 Processing helix chain 'v' and resid 25 through 34 removed outlier: 5.636A pdb=" N THR v 34 " --> pdb=" O LYS v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 46 removed outlier: 3.601A pdb=" N THR v 45 " --> pdb=" O PRO v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 66 removed outlier: 3.752A pdb=" N ARG v 61 " --> pdb=" O ARG v 57 " (cutoff:3.500A) Processing helix chain 'w' and resid 12 through 26 Processing helix chain 'w' and resid 70 through 76 removed outlier: 4.530A pdb=" N PHE w 74 " --> pdb=" O LYS w 70 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA w 75 " --> pdb=" O LEU w 71 " (cutoff:3.500A) Proline residue: w 76 - end of helix No H-bonds generated for 'chain 'w' and resid 70 through 76' Processing helix chain 'w' and resid 64 through 69 removed outlier: 3.537A pdb=" N VAL w 67 " --> pdb=" O ASP w 64 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N GLY w 68 " --> pdb=" O GLU w 65 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N HIS w 69 " --> pdb=" O MET w 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 64 through 69' Processing helix chain 'x' and resid 4 through 41 Processing helix chain 'x' and resid 44 through 65 Proline residue: x 56 - end of helix Processing helix chain 'x' and resid 68 through 87 removed outlier: 4.656A pdb=" N ALA x 87 " --> pdb=" O ILE x 83 " (cutoff:3.500A) Processing helix chain 'y' and resid 11 through 27 Processing helix chain 'y' and resid 28 through 37 removed outlier: 5.080A pdb=" N PHE y 37 " --> pdb=" O ARG y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 69 removed outlier: 3.845A pdb=" N ARG y 67 " --> pdb=" O GLU y 63 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N THR y 68 " --> pdb=" O ASN y 64 " (cutoff:3.500A) removed outlier: 5.836A pdb=" N ARG y 69 " --> pdb=" O ALA y 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 1 through 15 removed outlier: 3.890A pdb=" N ALA B 14 " --> pdb=" O LYS B 10 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.652A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ASP C 114 " --> pdb=" O VAL C 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'C' and resid 138 through 142 removed outlier: 4.223A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU C 180 " --> pdb=" O LEU C 176 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'C' and resid 90 through 96 removed outlier: 5.401A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU C 100 " --> pdb=" O TYR C 96 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'D' and resid 3 through 9 removed outlier: 4.195A pdb=" N SER D 199 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 13.388A pdb=" N GLY D 198 " --> pdb=" O LYS D 114 " (cutoff:3.500A) removed outlier: 11.918A pdb=" N LYS D 114 " --> pdb=" O GLY D 198 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU D 168 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'D' and resid 10 through 16 removed outlier: 3.816A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VAL D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'D' and resid 36 through 40 removed outlier: 3.842A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N GLN D 94 " --> pdb=" O VAL D 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 46 through 51 removed outlier: 5.960A pdb=" N ARG D 46 " --> pdb=" O LEU D 84 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'D' and resid 105 through 108 removed outlier: 6.095A pdb=" N LYS D 105 " --> pdb=" O VAL D 177 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 1 through 6 removed outlier: 4.271A pdb=" N SER E 10 " --> pdb=" O LEU E 5 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'E' and resid 117 through 120 Processing sheet with id= 12, first strand: chain 'F' and resid 65 through 69 removed outlier: 5.073A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 14, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 15, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.846A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 17, first strand: chain 'H' and resid 17 through 20 removed outlier: 4.535A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LYS H 35 " --> pdb=" O LEU H 6 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 76 through 82 removed outlier: 5.545A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.780A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'I' and resid 74 through 78 removed outlier: 7.161A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.153A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 38 through 41 Processing sheet with id= 23, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.759A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.664A pdb=" N TYR L 103 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU L 33 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LYS L 100 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 73 through 76 removed outlier: 6.852A pdb=" N ILE L 73 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 30 through 36 removed outlier: 7.834A pdb=" N SER L 30 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N LYS L 127 " --> pdb=" O VAL L 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.162A pdb=" N ARG M 103 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE M 113 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE M 97 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU M 115 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N THR M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'N' and resid 49 through 52 removed outlier: 3.853A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 38 through 45 removed outlier: 6.773A pdb=" N THR O 25 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.743A pdb=" N ALA O 49 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N ARG O 53 " --> pdb=" O HIS O 56 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N SER O 57 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.618A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.580A pdb=" N GLN Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ASP Q 95 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N LYS Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'Q' and resid 65 through 77 removed outlier: 4.973A pdb=" N GLN Q 91 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N LYS Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLN Q 87 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 4.580A pdb=" N VAL Q 75 " --> pdb=" O LYS Q 85 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LYS Q 85 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE Q 77 " --> pdb=" O TYR Q 83 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N TYR Q 83 " --> pdb=" O PHE Q 77 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 36, first strand: chain 'S' and resid 12 through 15 removed outlier: 5.161A pdb=" N VAL S 31 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ASN S 28 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS S 66 " --> pdb=" O ARG S 77 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N ASP S 79 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LYS S 64 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LYS S 81 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL S 62 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N ALA S 83 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N THR S 60 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL S 85 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N VAL S 58 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 40 through 45 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= 39, first strand: chain 'U' and resid 69 through 72 removed outlier: 6.766A pdb=" N ALA U 39 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.423A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 42, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.554A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 35 through 41 Processing sheet with id= 44, first strand: chain 'Y' and resid 33 through 39 removed outlier: 4.039A pdb=" N HIS Y 34 " --> pdb=" O GLN Y 9 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N MET Y 54 " --> pdb=" O THR Y 10 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 20 through 25 removed outlier: 4.210A pdb=" N ASN Z 20 " --> pdb=" O CYS Z 16 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 29 through 32 removed outlier: 4.305A pdb=" N GLU a 36 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'b' and resid 19 through 25 removed outlier: 6.080A pdb=" N HIS b 19 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE b 48 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU b 34 " --> pdb=" O GLU b 51 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'd' and resid 22 through 25 removed outlier: 5.520A pdb=" N PHE d 22 " --> pdb=" O VAL d 50 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'e' and resid 14 through 19 Processing sheet with id= 50, first strand: chain 'f' and resid 15 through 18 removed outlier: 5.116A pdb=" N HIS f 15 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N GLY f 17 " --> pdb=" O HIS f 39 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N HIS f 39 " --> pdb=" O GLY f 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'f' and resid 89 through 93 Processing sheet with id= 52, first strand: chain 'g' and resid 53 through 59 removed outlier: 3.531A pdb=" N ARG g 54 " --> pdb=" O HIS g 69 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.019A pdb=" N ARG g 164 " --> pdb=" O GLY g 155 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ASP g 181 " --> pdb=" O LYS g 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'h' and resid 141 through 145 removed outlier: 6.681A pdb=" N MET h 178 " --> pdb=" O ILE h 145 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'i' and resid 11 through 16 removed outlier: 6.986A pdb=" N LEU i 36 " --> pdb=" O ILE i 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 84 through 88 removed outlier: 3.546A pdb=" N ALA i 99 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASN i 122 " --> pdb=" O ALA i 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 33 through 41 removed outlier: 6.663A pdb=" N ARG i 45 " --> pdb=" O ASP i 41 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 38 through 43 removed outlier: 5.603A pdb=" N TYR j 59 " --> pdb=" O TRP j 42 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N HIS j 3 " --> pdb=" O THR j 92 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 44 through 47 removed outlier: 7.252A pdb=" N HIS j 55 " --> pdb=" O LEU j 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'k' and resid 72 through 79 removed outlier: 6.163A pdb=" N THR k 72 " --> pdb=" O VAL k 91 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N TYR k 85 " --> pdb=" O ARG k 78 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'l' and resid 23 through 29 removed outlier: 6.780A pdb=" N ALA l 23 " --> pdb=" O LEU l 63 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASP l 48 " --> pdb=" O THR l 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 74 through 77 removed outlier: 3.691A pdb=" N CYS l 127 " --> pdb=" O VAL l 103 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL l 103 " --> pdb=" O ILE l 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'm' and resid 5 through 11 removed outlier: 3.997A pdb=" N LYS m 27 " --> pdb=" O LEU m 61 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'n' and resid 35 through 38 removed outlier: 7.619A pdb=" N GLN n 35 " --> pdb=" O VAL n 77 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP n 75 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ARG n 5 " --> pdb=" O GLY n 103 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 42 through 52 removed outlier: 4.797A pdb=" N LEU n 71 " --> pdb=" O PRO n 43 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 30 through 35 Processing sheet with id= 67, first strand: chain 'p' and resid 29 through 33 removed outlier: 5.287A pdb=" N LEU p 81 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 5.987A pdb=" N HIS p 96 " --> pdb=" O ARG p 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 36 through 41 removed outlier: 5.079A pdb=" N LYS p 51 " --> pdb=" O ILE p 67 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N PHE p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 't' and resid 4 through 10 removed outlier: 4.149A pdb=" N PHE t 16 " --> pdb=" O HIS t 9 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N GLY t 49 " --> pdb=" O ASN t 40 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'u' and resid 7 through 11 removed outlier: 7.237A pdb=" N GLU u 60 " --> pdb=" O VAL u 76 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 19 through 30 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.503A pdb=" N LEU w 47 " --> pdb=" O VAL w 62 " (cutoff:3.500A) 1968 hydrogen bonds defined for protein. 5811 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3971 hydrogen bonds 6248 hydrogen bond angles 0 basepair planarities 1576 basepair parallelities 2654 stacking parallelities Total time for adding SS restraints: 269.80 Time building geometry restraints manager: 67.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.04 - 1.20: 29 1.20 - 1.35: 42764 1.35 - 1.51: 81590 1.51 - 1.66: 32667 1.66 - 1.82: 269 Bond restraints: 157319 Sorted by residual: bond pdb=" C5 5MU z 66 " pdb=" C6 5MU z 66 " ideal model delta sigma weight residual 1.155 1.424 -0.269 2.00e-02 2.50e+03 1.81e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.420 -0.265 2.00e-02 2.50e+03 1.76e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.412 -0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.582 0.220 2.00e-02 2.50e+03 1.21e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.584 0.218 2.00e-02 2.50e+03 1.19e+02 ... (remaining 157314 not shown) Histogram of bond angle deviations from ideal: 42.05 - 62.78: 2 62.78 - 83.52: 5 83.52 - 104.26: 19461 104.26 - 124.99: 197679 124.99 - 145.73: 18291 Bond angle restraints: 235438 Sorted by residual: angle pdb=" OP1 U z 8 " pdb=" P U z 8 " pdb=" OP3 U z 8 " ideal model delta sigma weight residual 109.47 42.05 67.42 3.00e+00 1.11e-01 5.05e+02 angle pdb=" OP1 U z 67 " pdb=" P U z 67 " pdb=" OP3 U z 67 " ideal model delta sigma weight residual 109.47 46.47 63.00 3.00e+00 1.11e-01 4.41e+02 angle pdb=" O6 OMG z 17 " pdb=" C6 OMG z 17 " pdb=" N1 OMG z 17 " ideal model delta sigma weight residual 119.94 63.06 56.88 3.00e+00 1.11e-01 3.59e+02 angle pdb=" C5 OMG z 17 " pdb=" C6 OMG z 17 " pdb=" O6 OMG z 17 " ideal model delta sigma weight residual 120.11 63.37 56.74 3.00e+00 1.11e-01 3.58e+02 angle pdb=" OP1 G z 9 " pdb=" P G z 9 " pdb=" OP3 G z 9 " ideal model delta sigma weight residual 109.47 78.26 31.21 3.00e+00 1.11e-01 1.08e+02 ... (remaining 235433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 88623 35.66 - 71.33: 10976 71.33 - 106.99: 1013 106.99 - 142.65: 13 142.65 - 178.32: 45 Dihedral angle restraints: 100670 sinusoidal: 84340 harmonic: 16330 Sorted by residual: dihedral pdb=" C4' G 12116 " pdb=" C3' G 12116 " pdb=" C2' G 12116 " pdb=" C1' G 12116 " ideal model delta sinusoidal sigma weight residual -35.00 31.56 -66.56 1 8.00e+00 1.56e-02 9.03e+01 dihedral pdb=" O4' U z 67 " pdb=" C1' U z 67 " pdb=" N1 U z 67 " pdb=" C2 U z 67 " ideal model delta sinusoidal sigma weight residual 200.00 33.87 166.13 1 1.50e+01 4.44e-03 8.41e+01 dihedral pdb=" O4' U z 34 " pdb=" C1' U z 34 " pdb=" N1 U z 34 " pdb=" C2 U z 34 " ideal model delta sinusoidal sigma weight residual 200.00 40.64 159.36 1 1.50e+01 4.44e-03 8.26e+01 ... (remaining 100667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.439: 29986 0.439 - 0.879: 5 0.879 - 1.318: 2 1.318 - 1.757: 0 1.757 - 2.196: 1 Chirality restraints: 29994 Sorted by residual: chirality pdb=" P U z 20 " pdb=" OP1 U z 20 " pdb=" OP2 U z 20 " pdb=" O5' U z 20 " both_signs ideal model delta sigma weight residual True 2.41 -0.21 2.20 2.00e-01 2.50e+01 1.21e+02 chirality pdb=" P G z 9 " pdb=" OP1 G z 9 " pdb=" OP2 G z 9 " pdb=" O5' G z 9 " both_signs ideal model delta sigma weight residual True 2.41 -1.31 1.10 2.00e-01 2.50e+01 3.01e+01 chirality pdb=" C1* PSU 12580 " pdb=" O4* PSU 12580 " pdb=" C2* PSU 12580 " pdb=" C5 PSU 12580 " both_signs ideal model delta sigma weight residual False 2.55 1.67 0.88 2.00e-01 2.50e+01 1.93e+01 ... (remaining 29991 not shown) Planarity restraints: 12546 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.092 2.00e-02 2.50e+03 6.45e-01 9.36e+03 pdb=" C4' 2MG 21516 " -0.485 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.757 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.582 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.690 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.180 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.990 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.164 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 1.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " -0.041 2.00e-02 2.50e+03 6.17e-01 8.55e+03 pdb=" C4' 2MG 12445 " -0.478 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.819 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.582 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.583 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.247 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.900 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.150 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.974 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.071 2.00e-02 2.50e+03 6.16e-01 8.53e+03 pdb=" C4' OMC 12498 " -0.423 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.594 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.619 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.682 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.134 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -1.045 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.231 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.929 2.00e-02 2.50e+03 ... (remaining 12543 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.14: 320 2.14 - 2.83: 43906 2.83 - 3.52: 203616 3.52 - 4.21: 481542 4.21 - 4.90: 635376 Nonbonded interactions: 1364760 Sorted by model distance: nonbonded pdb=" O3' A z 88 " pdb=" C SER B 27 " model vdw 1.454 3.270 nonbonded pdb=" O6 OMG z 17 " pdb=" C2 OMG z 17 " model vdw 1.651 2.608 nonbonded pdb=" C4 A 2 397 " pdb="MG MG 21680 " model vdw 1.701 2.390 nonbonded pdb=" O6 G 1 776 " pdb="MG MG 13116 " model vdw 1.701 2.170 nonbonded pdb=" OP1 G 2 450 " pdb="MG MG 21682 " model vdw 1.711 2.170 ... (remaining 1364755 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 17.640 Check model and map are aligned: 1.640 Set scattering table: 1.040 Process input model: 598.360 Find NCS groups from input model: 2.850 Set up NCS constraints: 0.330 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 636.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 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 : 0.018 0.269 157319 Z= 1.082 Angle : 1.177 67.423 235438 Z= 0.601 Chirality : 0.076 2.196 29994 Planarity : 0.021 0.645 12546 Dihedral : 22.840 178.316 90138 Min Nonbonded Distance : 1.454 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.69 % Favored : 96.15 % Rotamer: Outliers : 0.21 % Allowed : 2.58 % Favored : 97.21 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.85 (0.09), residues: 5634 helix: -3.59 (0.06), residues: 1923 sheet: -1.88 (0.14), residues: 1156 loop : -1.84 (0.10), residues: 2555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.004 TRP E 78 HIS 0.027 0.004 HIS C 53 PHE 0.084 0.005 PHE M 80 TYR 0.043 0.004 TYR b 49 ARG 0.053 0.003 ARG c 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1789 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1779 time to evaluate : 6.384 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: C 171 TYR cc_start: 0.7571 (m-80) cc_final: 0.7090 (m-10) REVERT: D 2 ILE cc_start: 0.8332 (pt) cc_final: 0.7194 (pp) REVERT: G 58 TYR cc_start: 0.7286 (m-80) cc_final: 0.6110 (m-80) REVERT: H 33 GLN cc_start: 0.7899 (mt0) cc_final: 0.7497 (mt0) REVERT: H 112 LYS cc_start: 0.2602 (pttm) cc_final: 0.1377 (pttt) REVERT: J 89 ASN cc_start: 0.7834 (m-40) cc_final: 0.7574 (m-40) REVERT: Q 55 ASP cc_start: 0.7152 (p0) cc_final: 0.6895 (p0) REVERT: Q 95 ASP cc_start: 0.7317 (m-30) cc_final: 0.6842 (m-30) REVERT: W 25 THR cc_start: 0.7639 (p) cc_final: 0.6234 (p) REVERT: Z 65 ASN cc_start: 0.7654 (m-40) cc_final: 0.7445 (m-40) REVERT: a 48 TYR cc_start: 0.7369 (m-80) cc_final: 0.6893 (m-80) REVERT: e 1 MET cc_start: 0.7894 (tpp) cc_final: 0.7375 (tpp) REVERT: f 6 MET cc_start: 0.7558 (ttp) cc_final: 0.7353 (ttm) REVERT: f 192 ASP cc_start: 0.7970 (t0) cc_final: 0.7541 (t0) REVERT: g 37 PHE cc_start: 0.8516 (t80) cc_final: 0.8213 (t80) REVERT: g 102 ASN cc_start: 0.8307 (m-40) cc_final: 0.7966 (m-40) REVERT: g 154 SER cc_start: 0.7994 (m) cc_final: 0.7784 (t) REVERT: g 190 HIS cc_start: 0.7409 (m-70) cc_final: 0.7150 (m-70) REVERT: i 12 GLN cc_start: 0.7600 (pt0) cc_final: 0.6201 (pt0) REVERT: j 59 TYR cc_start: 0.7419 (m-10) cc_final: 0.6982 (m-80) REVERT: n 24 GLU cc_start: 0.7677 (tm-30) cc_final: 0.7333 (tm-30) REVERT: p 73 ASN cc_start: 0.8556 (p0) cc_final: 0.8298 (p0) REVERT: p 74 LEU cc_start: 0.8483 (mm) cc_final: 0.8166 (mm) REVERT: y 31 GLU cc_start: 0.6905 (tp30) cc_final: 0.6028 (tp30) outliers start: 10 outliers final: 14 residues processed: 1785 average time/residue: 2.2468 time to fit residues: 5706.1803 Evaluate side-chains 1128 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1114 time to evaluate : 6.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 92 ASN Chi-restraints excluded: chain T residue 89 ASP Chi-restraints excluded: chain W residue 59 ILE Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain j residue 72 ASP Chi-restraints excluded: chain u residue 60 GLU Chi-restraints excluded: chain B residue 9 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 855 optimal weight: 5.9990 chunk 767 optimal weight: 20.0000 chunk 426 optimal weight: 5.9990 chunk 262 optimal weight: 1.9990 chunk 517 optimal weight: 5.9990 chunk 410 optimal weight: 5.9990 chunk 793 optimal weight: 6.9990 chunk 307 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 590 optimal weight: 5.9990 chunk 919 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 117 GLN D 173 GLN E 115 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN ** I 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 5 GLN ** K 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 116 GLN ** O 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 23 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 58 ASN ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 36 GLN h 71 GLN h 126 ASN h 164 GLN j 58 HIS k 68 ASN k 122 ASN r 62 ASN r 66 GLN s 62 GLN v 31 ASN ** w 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 57 HIS y 9 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.177 157319 Z= 0.251 Angle : 0.733 61.196 235438 Z= 0.375 Chirality : 0.037 1.204 29994 Planarity : 0.007 0.137 12546 Dihedral : 23.826 179.660 78877 Min Nonbonded Distance : 1.721 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.16 % Favored : 96.81 % Rotamer: Outliers : 4.01 % Allowed : 20.71 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.10), residues: 5634 helix: -0.59 (0.11), residues: 1930 sheet: -1.21 (0.15), residues: 1109 loop : -1.34 (0.11), residues: 2595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 11 HIS 0.010 0.001 HIS g 190 PHE 0.035 0.002 PHE B 12 TYR 0.021 0.002 TYR C 96 ARG 0.014 0.001 ARG u 11 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1676 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 188 poor density : 1488 time to evaluate : 5.818 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 171 TYR cc_start: 0.7164 (m-80) cc_final: 0.6820 (m-10) REVERT: H 112 LYS cc_start: 0.2183 (pttm) cc_final: 0.1950 (pttt) REVERT: L 112 LEU cc_start: 0.8487 (tp) cc_final: 0.8052 (tm) REVERT: M 5 LYS cc_start: 0.7751 (mtpt) cc_final: 0.7130 (mttt) REVERT: Q 1 MET cc_start: 0.7130 (tpp) cc_final: 0.6488 (tpt) REVERT: Q 55 ASP cc_start: 0.6973 (p0) cc_final: 0.6764 (p0) REVERT: S 77 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7888 (mtt-85) REVERT: U 90 ASP cc_start: 0.6935 (m-30) cc_final: 0.6180 (m-30) REVERT: W 76 GLU cc_start: 0.6389 (tt0) cc_final: 0.6164 (tt0) REVERT: Z 65 ASN cc_start: 0.7520 (m-40) cc_final: 0.7274 (m-40) REVERT: b 7 GLU cc_start: 0.6971 (pm20) cc_final: 0.6291 (pm20) REVERT: b 26 ASN cc_start: 0.8089 (t0) cc_final: 0.7479 (t0) REVERT: e 1 MET cc_start: 0.7899 (tpp) cc_final: 0.7324 (tpp) REVERT: f 192 ASP cc_start: 0.7743 (t0) cc_final: 0.7517 (t0) REVERT: h 196 ASN cc_start: 0.7626 (m-40) cc_final: 0.7349 (m110) REVERT: i 61 GLN cc_start: 0.7586 (tp-100) cc_final: 0.7381 (tp-100) REVERT: i 112 ARG cc_start: 0.7890 (mtp85) cc_final: 0.6789 (mtp85) REVERT: i 142 ASP cc_start: 0.6788 (p0) cc_final: 0.5986 (p0) REVERT: j 13 ASP cc_start: 0.8197 (p0) cc_final: 0.7940 (p0) REVERT: j 68 GLN cc_start: 0.7901 (pm20) cc_final: 0.7501 (pm20) REVERT: j 88 MET cc_start: 0.7920 (tmm) cc_final: 0.7580 (tmt) REVERT: l 90 ASP cc_start: 0.7578 (OUTLIER) cc_final: 0.7361 (p0) REVERT: o 65 VAL cc_start: 0.9185 (m) cc_final: 0.8727 (t) REVERT: p 56 ARG cc_start: 0.7417 (tpp80) cc_final: 0.7002 (tpp80) REVERT: p 73 ASN cc_start: 0.8262 (p0) cc_final: 0.7969 (p0) REVERT: v 21 ILE cc_start: 0.9036 (mt) cc_final: 0.8672 (mt) REVERT: y 31 GLU cc_start: 0.7236 (tp30) cc_final: 0.6912 (mm-30) REVERT: y 40 LYS cc_start: 0.7794 (mtmt) cc_final: 0.6969 (mtmt) outliers start: 188 outliers final: 67 residues processed: 1551 average time/residue: 1.9880 time to fit residues: 4489.9829 Evaluate side-chains 1282 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1213 time to evaluate : 6.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 26 ILE Chi-restraints excluded: chain G residue 114 ASP Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 128 ASN Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 77 ARG Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain g residue 83 ASP Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 74 LEU Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 71 LEU Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 58 SER Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain q residue 46 SER Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain u residue 57 ASP Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 36 SER Chi-restraints excluded: chain w residue 15 LEU Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 64 ASP Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain B residue 2 SER Chi-restraints excluded: chain B residue 12 PHE Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 27 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 511 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 765 optimal weight: 9.9990 chunk 626 optimal weight: 1.9990 chunk 253 optimal weight: 20.0000 chunk 921 optimal weight: 30.0000 chunk 995 optimal weight: 10.0000 chunk 820 optimal weight: 9.9990 chunk 913 optimal weight: 20.0000 chunk 314 optimal weight: 20.0000 chunk 739 optimal weight: 6.9990 overall best weight: 7.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 239 ASN D 173 GLN E 90 GLN G 22 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 11 ASN I 136 GLN J 3 GLN L 13 HIS M 62 ASN N 38 GLN S 48 GLN W 23 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 8 ASN h 40 GLN h 54 GLN ** i 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** o 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN s 62 GLN ** u 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 21 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.181 157319 Z= 0.332 Angle : 0.730 60.239 235438 Z= 0.376 Chirality : 0.038 1.171 29994 Planarity : 0.006 0.131 12546 Dihedral : 23.661 179.666 78854 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 5.16 % Allowed : 21.05 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.11), residues: 5634 helix: 0.42 (0.11), residues: 1935 sheet: -0.84 (0.15), residues: 1072 loop : -1.09 (0.12), residues: 2627 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP j 42 HIS 0.009 0.001 HIS j 94 PHE 0.036 0.002 PHE H 46 TYR 0.027 0.002 TYR h 65 ARG 0.011 0.001 ARG y 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1595 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1353 time to evaluate : 6.362 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: D 108 ASP cc_start: 0.7265 (m-30) cc_final: 0.7025 (m-30) REVERT: G 35 ARG cc_start: 0.7875 (tpp80) cc_final: 0.7662 (tpp80) REVERT: G 39 ASP cc_start: 0.7513 (p0) cc_final: 0.7303 (p0) REVERT: G 58 TYR cc_start: 0.6641 (m-80) cc_final: 0.6331 (m-10) REVERT: H 44 ILE cc_start: 0.9347 (mt) cc_final: 0.9058 (tt) REVERT: H 75 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.4595 (tt) REVERT: H 83 LYS cc_start: 0.5506 (tptp) cc_final: 0.5274 (tptp) REVERT: I 128 ASN cc_start: 0.8269 (t0) cc_final: 0.7928 (t0) REVERT: L 112 LEU cc_start: 0.8625 (tp) cc_final: 0.8418 (tm) REVERT: M 1 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7898 (mpp) REVERT: M 5 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7479 (mttm) REVERT: N 17 LYS cc_start: 0.8746 (tppp) cc_final: 0.8409 (tppp) REVERT: P 97 ASP cc_start: 0.6763 (t0) cc_final: 0.6091 (t0) REVERT: Q 13 ARG cc_start: 0.7846 (tmm-80) cc_final: 0.7609 (tmm-80) REVERT: Q 55 ASP cc_start: 0.7182 (p0) cc_final: 0.6935 (p0) REVERT: Q 84 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.7151 (ptt-90) REVERT: V 72 LYS cc_start: 0.7800 (mtmm) cc_final: 0.6942 (mtmm) REVERT: Y 41 THR cc_start: 0.8352 (p) cc_final: 0.8055 (p) REVERT: Z 65 ASN cc_start: 0.7564 (m-40) cc_final: 0.7285 (m-40) REVERT: a 4 GLN cc_start: 0.7329 (OUTLIER) cc_final: 0.6895 (pt0) REVERT: e 1 MET cc_start: 0.8018 (tpp) cc_final: 0.7414 (tpp) REVERT: f 110 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8522 (p) REVERT: h 196 ASN cc_start: 0.7610 (m-40) cc_final: 0.7344 (m110) REVERT: i 111 MET cc_start: 0.7770 (mtm) cc_final: 0.7568 (mtm) REVERT: i 142 ASP cc_start: 0.7000 (p0) cc_final: 0.6332 (p0) REVERT: l 52 GLU cc_start: 0.6358 (mp0) cc_final: 0.6104 (mp0) REVERT: l 90 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7624 (p0) REVERT: n 87 LEU cc_start: 0.8034 (mm) cc_final: 0.7720 (mm) REVERT: o 65 VAL cc_start: 0.9196 (m) cc_final: 0.8952 (t) REVERT: o 126 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8350 (mmpt) REVERT: p 90 LEU cc_start: 0.8747 (OUTLIER) cc_final: 0.8529 (mp) REVERT: s 72 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7420 (ptt90) REVERT: t 76 LYS cc_start: 0.8346 (ptmm) cc_final: 0.8096 (ptmm) REVERT: u 44 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8584 (mp) REVERT: v 21 ILE cc_start: 0.9169 (mt) cc_final: 0.8953 (mt) REVERT: w 13 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8481 (tp) outliers start: 242 outliers final: 90 residues processed: 1449 average time/residue: 2.0166 time to fit residues: 4262.7751 Evaluate side-chains 1272 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1171 time to evaluate : 5.699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain F residue 52 ASN Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain Q residue 84 ARG Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain R residue 77 ASP Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 110 SER Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 181 ASP Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 106 ILE Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 90 MET Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 51 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 126 LYS Chi-restraints excluded: chain p residue 3 THR Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 34 CYS Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 69 ASP Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain u residue 44 LEU Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 28 THR Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 13 LEU Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 64 ASP Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 36 GLU Chi-restraints excluded: chain B residue 2 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 910 optimal weight: 20.0000 chunk 692 optimal weight: 3.9990 chunk 478 optimal weight: 9.9990 chunk 102 optimal weight: 20.0000 chunk 439 optimal weight: 20.0000 chunk 618 optimal weight: 20.0000 chunk 924 optimal weight: 7.9990 chunk 979 optimal weight: 6.9990 chunk 483 optimal weight: 5.9990 chunk 876 optimal weight: 7.9990 chunk 263 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN E 90 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN H 33 GLN J 3 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN S 48 GLN W 23 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 9 GLN ** Z 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 123 GLN h 40 GLN h 131 ASN ** k 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 24 HIS q 8 ASN s 62 GLN x 52 ASN x 84 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 157319 Z= 0.277 Angle : 0.704 60.298 235438 Z= 0.362 Chirality : 0.036 1.170 29994 Planarity : 0.006 0.128 12546 Dihedral : 23.655 179.351 78848 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 15.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 4.71 % Allowed : 24.12 % Favored : 71.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.11), residues: 5634 helix: 0.62 (0.12), residues: 1948 sheet: -0.68 (0.15), residues: 1074 loop : -0.99 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 11 HIS 0.008 0.001 HIS N 100 PHE 0.029 0.002 PHE B 12 TYR 0.024 0.002 TYR h 65 ARG 0.012 0.001 ARG c 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1517 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1296 time to evaluate : 6.457 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: G 58 TYR cc_start: 0.6599 (m-80) cc_final: 0.6059 (m-10) REVERT: H 44 ILE cc_start: 0.9359 (mt) cc_final: 0.9077 (tt) REVERT: H 83 LYS cc_start: 0.5752 (tptp) cc_final: 0.5539 (tptp) REVERT: M 5 LYS cc_start: 0.7804 (mtpt) cc_final: 0.7245 (mttt) REVERT: O 55 LEU cc_start: 0.8857 (tm) cc_final: 0.8281 (tm) REVERT: Q 1 MET cc_start: 0.7014 (tpt) cc_final: 0.6151 (tpt) REVERT: Q 55 ASP cc_start: 0.7270 (p0) cc_final: 0.7003 (p0) REVERT: Z 31 ASP cc_start: 0.7649 (t0) cc_final: 0.7315 (t0) REVERT: e 1 MET cc_start: 0.8115 (tpp) cc_final: 0.7606 (tpp) REVERT: e 4 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7406 (mtp85) REVERT: h 196 ASN cc_start: 0.7599 (m-40) cc_final: 0.7380 (m110) REVERT: i 142 ASP cc_start: 0.7067 (p0) cc_final: 0.6623 (p0) REVERT: l 54 ASP cc_start: 0.7310 (p0) cc_final: 0.7077 (p0) REVERT: l 55 THR cc_start: 0.8509 (OUTLIER) cc_final: 0.8287 (t) REVERT: l 90 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7561 (p0) REVERT: n 24 GLU cc_start: 0.8189 (tm-30) cc_final: 0.7954 (pp20) REVERT: n 32 THR cc_start: 0.9053 (p) cc_final: 0.8815 (t) REVERT: q 54 ASP cc_start: 0.7531 (p0) cc_final: 0.7302 (p0) REVERT: s 72 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7333 (ptt90) REVERT: u 44 LEU cc_start: 0.8888 (OUTLIER) cc_final: 0.8554 (mp) outliers start: 221 outliers final: 96 residues processed: 1394 average time/residue: 2.0024 time to fit residues: 4087.9556 Evaluate side-chains 1260 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1159 time to evaluate : 6.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 91 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain S residue 27 SER Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 207 ILE Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 64 ILE Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 91 ASP Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 51 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain o residue 58 SER Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain q residue 31 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain u residue 44 LEU Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 13 LEU Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 64 ASP Chi-restraints excluded: chain w residue 79 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 815 optimal weight: 7.9990 chunk 555 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 729 optimal weight: 4.9990 chunk 404 optimal weight: 20.0000 chunk 835 optimal weight: 8.9990 chunk 676 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 499 optimal weight: 2.9990 chunk 878 optimal weight: 9.9990 chunk 247 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 90 GLN ** H 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN ** I 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN J 3 GLN ** J 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN W 23 ASN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 62 ASN s 62 GLN x 48 GLN x 52 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 157319 Z= 0.270 Angle : 0.704 60.256 235438 Z= 0.361 Chirality : 0.036 1.170 29994 Planarity : 0.006 0.128 12546 Dihedral : 23.628 179.668 78848 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.14 % Allowed : 26.96 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.11), residues: 5634 helix: 0.70 (0.12), residues: 1940 sheet: -0.56 (0.15), residues: 1069 loop : -0.93 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP B 11 HIS 0.011 0.001 HIS j 3 PHE 0.053 0.002 PHE B 12 TYR 0.026 0.002 TYR Q 2 ARG 0.015 0.001 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1266 time to evaluate : 6.413 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: H 44 ILE cc_start: 0.9396 (mt) cc_final: 0.9195 (tt) REVERT: H 83 LYS cc_start: 0.5722 (tptp) cc_final: 0.5453 (tptp) REVERT: I 90 GLU cc_start: 0.7219 (pm20) cc_final: 0.6761 (pm20) REVERT: M 5 LYS cc_start: 0.7799 (mtpt) cc_final: 0.7279 (mttt) REVERT: O 99 TYR cc_start: 0.8044 (p90) cc_final: 0.7831 (p90) REVERT: Q 55 ASP cc_start: 0.7337 (p0) cc_final: 0.7071 (p0) REVERT: R 68 ASP cc_start: 0.7323 (p0) cc_final: 0.7107 (p0) REVERT: V 68 LYS cc_start: 0.7750 (ttpp) cc_final: 0.7381 (ttmm) REVERT: Z 31 ASP cc_start: 0.7663 (t0) cc_final: 0.7308 (t0) REVERT: e 1 MET cc_start: 0.8106 (tpp) cc_final: 0.7582 (tpp) REVERT: e 4 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7404 (mtp85) REVERT: i 142 ASP cc_start: 0.7043 (p0) cc_final: 0.6640 (p0) REVERT: l 38 ASN cc_start: 0.7948 (p0) cc_final: 0.7437 (p0) REVERT: l 54 ASP cc_start: 0.7390 (p0) cc_final: 0.7142 (p0) REVERT: l 55 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8148 (t) REVERT: m 59 GLU cc_start: 0.7767 (pm20) cc_final: 0.7565 (pm20) REVERT: q 31 LYS cc_start: 0.8568 (mttp) cc_final: 0.8368 (mttp) REVERT: q 54 ASP cc_start: 0.7542 (p0) cc_final: 0.7226 (p0) REVERT: s 72 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7382 (ptt90) REVERT: t 80 LYS cc_start: 0.7941 (mttp) cc_final: 0.7701 (mttp) outliers start: 194 outliers final: 108 residues processed: 1349 average time/residue: 1.9940 time to fit residues: 3944.1971 Evaluate side-chains 1272 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1161 time to evaluate : 6.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 33 LEU Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 27 SER Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 29 THR Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 33 LEU Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 129 VAL Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 190 ASP Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 106 ILE Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 47 GLU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 55 THR Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 50 GLN Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 51 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 58 SER Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 25 THR Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain B residue 11 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 329 optimal weight: 20.0000 chunk 881 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 574 optimal weight: 6.9990 chunk 241 optimal weight: 10.0000 chunk 980 optimal weight: 20.0000 chunk 813 optimal weight: 20.0000 chunk 453 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 324 optimal weight: 10.0000 chunk 514 optimal weight: 0.0050 overall best weight: 6.6006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 90 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN J 3 GLN M 9 GLN N 38 GLN Q 82 HIS Q 86 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 61 GLN ** l 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 24 HIS ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 157319 Z= 0.282 Angle : 0.714 60.301 235438 Z= 0.366 Chirality : 0.036 1.170 29994 Planarity : 0.006 0.128 12546 Dihedral : 23.608 179.877 78848 Min Nonbonded Distance : 1.726 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 4.29 % Allowed : 27.83 % Favored : 67.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.11), residues: 5634 helix: 0.68 (0.12), residues: 1934 sheet: -0.50 (0.15), residues: 1074 loop : -0.87 (0.12), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 11 HIS 0.007 0.001 HIS O 77 PHE 0.050 0.002 PHE B 12 TYR 0.026 0.002 TYR q 86 ARG 0.012 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1446 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1245 time to evaluate : 6.514 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: D 176 ASP cc_start: 0.7427 (OUTLIER) cc_final: 0.7138 (p0) REVERT: E 1 MET cc_start: 0.6443 (pmm) cc_final: 0.6141 (pmm) REVERT: G 39 ASP cc_start: 0.7467 (p0) cc_final: 0.7208 (p0) REVERT: H 83 LYS cc_start: 0.5973 (tptp) cc_final: 0.5728 (tptp) REVERT: M 5 LYS cc_start: 0.7827 (mtpt) cc_final: 0.7301 (mttt) REVERT: P 97 ASP cc_start: 0.6841 (t0) cc_final: 0.6206 (t0) REVERT: Q 55 ASP cc_start: 0.7404 (p0) cc_final: 0.7146 (p0) REVERT: V 37 ILE cc_start: 0.8308 (mp) cc_final: 0.8060 (mm) REVERT: Z 31 ASP cc_start: 0.7788 (t0) cc_final: 0.7396 (t0) REVERT: e 1 MET cc_start: 0.8131 (tpp) cc_final: 0.7583 (tpp) REVERT: e 4 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7425 (mtp85) REVERT: j 23 GLU cc_start: 0.8101 (pp20) cc_final: 0.6952 (pp20) REVERT: j 93 LYS cc_start: 0.8178 (pmtt) cc_final: 0.7262 (pmtt) REVERT: q 54 ASP cc_start: 0.7408 (p0) cc_final: 0.7111 (p0) REVERT: s 72 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7478 (ptt90) REVERT: s 78 TYR cc_start: 0.7173 (t80) cc_final: 0.6929 (t80) outliers start: 201 outliers final: 114 residues processed: 1331 average time/residue: 1.9960 time to fit residues: 3895.7515 Evaluate side-chains 1265 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1148 time to evaluate : 6.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 187 ASP Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 15 LEU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 27 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 26 ASP Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 47 VAL Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain V residue 68 LYS Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain c residue 12 ARG Chi-restraints excluded: chain c residue 30 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 190 ASP Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 130 SER Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 ILE Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 50 GLN Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 LEU Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 25 THR Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain s residue 89 ARG Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain t residue 80 LYS Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain B residue 11 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 944 optimal weight: 3.9990 chunk 110 optimal weight: 40.0000 chunk 558 optimal weight: 1.9990 chunk 715 optimal weight: 10.0000 chunk 554 optimal weight: 0.2980 chunk 825 optimal weight: 8.9990 chunk 547 optimal weight: 20.0000 chunk 976 optimal weight: 0.8980 chunk 611 optimal weight: 10.0000 chunk 595 optimal weight: 8.9990 chunk 450 optimal weight: 20.0000 overall best weight: 3.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 90 GLN ** F 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 128 ASN J 3 GLN M 9 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** R 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN l 18 GLN m 50 GLN ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 GLN x 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 157319 Z= 0.187 Angle : 0.704 60.089 235438 Z= 0.359 Chirality : 0.035 1.166 29994 Planarity : 0.006 0.125 12546 Dihedral : 23.600 179.890 78848 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.67 % Allowed : 29.35 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.11), residues: 5634 helix: 0.62 (0.12), residues: 1936 sheet: -0.48 (0.15), residues: 1093 loop : -0.83 (0.12), residues: 2605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 11 HIS 0.009 0.001 HIS o 118 PHE 0.041 0.001 PHE H 46 TYR 0.033 0.002 TYR Q 2 ARG 0.021 0.001 ARG G 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 172 poor density : 1272 time to evaluate : 6.575 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: D 176 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7143 (p0) REVERT: H 141 LYS cc_start: 0.7896 (pmtt) cc_final: 0.7660 (mppt) REVERT: M 5 LYS cc_start: 0.7796 (mtpt) cc_final: 0.7340 (mttt) REVERT: Q 55 ASP cc_start: 0.7460 (p0) cc_final: 0.7153 (p0) REVERT: R 94 ASP cc_start: 0.6705 (t0) cc_final: 0.6502 (t0) REVERT: Z 31 ASP cc_start: 0.7740 (t0) cc_final: 0.7333 (t0) REVERT: d 55 LEU cc_start: 0.8642 (tp) cc_final: 0.8246 (tp) REVERT: e 1 MET cc_start: 0.8111 (tpp) cc_final: 0.7645 (tpp) REVERT: e 4 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7424 (mtp85) REVERT: i 142 ASP cc_start: 0.7199 (OUTLIER) cc_final: 0.6892 (p0) REVERT: j 88 MET cc_start: 0.7869 (tmt) cc_final: 0.7573 (tmt) REVERT: j 94 HIS cc_start: 0.7277 (p-80) cc_final: 0.7064 (p90) REVERT: j 102 MET cc_start: 0.7790 (ppp) cc_final: 0.7161 (ppp) REVERT: l 91 GLU cc_start: 0.7769 (pm20) cc_final: 0.7444 (pm20) REVERT: n 32 THR cc_start: 0.9082 (p) cc_final: 0.8832 (t) REVERT: q 50 GLU cc_start: 0.6931 (tp30) cc_final: 0.6493 (tp30) REVERT: q 54 ASP cc_start: 0.7392 (p0) cc_final: 0.7016 (p0) REVERT: s 72 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7477 (ptt90) REVERT: u 50 ASN cc_start: 0.8679 (p0) cc_final: 0.8418 (p0) outliers start: 172 outliers final: 99 residues processed: 1350 average time/residue: 2.0492 time to fit residues: 4055.8547 Evaluate side-chains 1248 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1145 time to evaluate : 6.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 145 ASN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain N residue 38 GLN Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 40 ILE Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 45 ASP Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 17 THR Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 190 ASP Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 142 ASP Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 50 GLN Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 17 SER Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 16 LEU Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain s residue 61 SER Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain s residue 89 ARG Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 68 SER Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain t residue 80 LYS Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain B residue 11 TRP Chi-restraints excluded: chain B residue 21 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 604 optimal weight: 20.0000 chunk 389 optimal weight: 30.0000 chunk 583 optimal weight: 8.9990 chunk 294 optimal weight: 20.0000 chunk 191 optimal weight: 20.0000 chunk 189 optimal weight: 20.0000 chunk 620 optimal weight: 7.9990 chunk 665 optimal weight: 10.0000 chunk 482 optimal weight: 8.9990 chunk 90 optimal weight: 20.0000 chunk 767 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN I 128 ASN J 3 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN ** Q 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN T 66 GLN ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 ASN ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 131 ASN i 77 ASN ** k 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 62 ASN s 62 GLN x 52 ASN x 84 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.180 157319 Z= 0.350 Angle : 0.756 60.389 235438 Z= 0.385 Chirality : 0.038 1.172 29994 Planarity : 0.006 0.132 12546 Dihedral : 23.554 179.529 78848 Min Nonbonded Distance : 1.725 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.97 % Allowed : 30.56 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5634 helix: 0.58 (0.12), residues: 1938 sheet: -0.47 (0.15), residues: 1078 loop : -0.83 (0.12), residues: 2618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP B 11 HIS 0.008 0.001 HIS O 77 PHE 0.026 0.002 PHE K 107 TYR 0.030 0.002 TYR q 86 ARG 0.017 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1394 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 1208 time to evaluate : 6.472 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: D 176 ASP cc_start: 0.7511 (OUTLIER) cc_final: 0.7220 (p0) REVERT: M 5 LYS cc_start: 0.7978 (mtpt) cc_final: 0.7481 (mttt) REVERT: Q 55 ASP cc_start: 0.7408 (OUTLIER) cc_final: 0.7128 (p0) REVERT: R 94 ASP cc_start: 0.6763 (t0) cc_final: 0.6521 (t0) REVERT: V 37 ILE cc_start: 0.8334 (mp) cc_final: 0.8087 (mm) REVERT: b 51 GLU cc_start: 0.7249 (tm-30) cc_final: 0.6991 (tm-30) REVERT: c 1 MET cc_start: 0.5934 (mtt) cc_final: 0.5579 (mtm) REVERT: d 49 MET cc_start: 0.7487 (mmm) cc_final: 0.7223 (tpt) REVERT: e 1 MET cc_start: 0.8167 (tpp) cc_final: 0.7641 (tpp) REVERT: e 4 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7499 (mtp85) REVERT: i 142 ASP cc_start: 0.7210 (OUTLIER) cc_final: 0.6926 (p0) REVERT: j 88 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7697 (tmt) REVERT: j 102 MET cc_start: 0.8095 (ppp) cc_final: 0.7413 (ppp) REVERT: l 90 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7647 (p0) REVERT: o 72 ASP cc_start: 0.8384 (p0) cc_final: 0.8102 (p0) REVERT: q 50 GLU cc_start: 0.7124 (tp30) cc_final: 0.6737 (tp30) REVERT: q 54 ASP cc_start: 0.7505 (p0) cc_final: 0.7153 (p0) REVERT: q 72 GLU cc_start: 0.7866 (pp20) cc_final: 0.7655 (pp20) REVERT: r 35 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8422 (m-40) REVERT: s 72 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7517 (ptt90) REVERT: y 40 LYS cc_start: 0.7827 (tttt) cc_final: 0.7519 (tttt) outliers start: 186 outliers final: 116 residues processed: 1290 average time/residue: 1.9719 time to fit residues: 3764.1761 Evaluate side-chains 1262 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1138 time to evaluate : 6.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 121 ASP Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 86 GLU Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 2 ARG Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain O residue 48 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 31 VAL Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain T residue 8 ASP Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 47 LYS Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain b residue 11 LEU Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 90 LEU Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 190 ASP Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 142 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 51 ILE Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 74 SER Chi-restraints excluded: chain l residue 85 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 25 ILE Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain n residue 97 ASP Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 112 ASP Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 82 ILE Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain q residue 13 LYS Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 35 ASN Chi-restraints excluded: chain s residue 25 THR Chi-restraints excluded: chain s residue 61 SER Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain s residue 89 ARG Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 25 ARG Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain t residue 80 LYS Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain B residue 11 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 888 optimal weight: 10.0000 chunk 935 optimal weight: 9.9990 chunk 853 optimal weight: 7.9990 chunk 909 optimal weight: 3.9990 chunk 547 optimal weight: 20.0000 chunk 396 optimal weight: 10.0000 chunk 714 optimal weight: 3.9990 chunk 279 optimal weight: 20.0000 chunk 822 optimal weight: 5.9990 chunk 860 optimal weight: 6.9990 chunk 906 optimal weight: 20.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN H 2 GLN I 128 ASN J 3 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Q 87 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 ASN k 148 ASN m 50 GLN ** m 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 GLN x 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.3741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.179 157319 Z= 0.266 Angle : 0.742 60.274 235438 Z= 0.378 Chirality : 0.036 1.168 29994 Planarity : 0.006 0.127 12546 Dihedral : 23.590 179.486 78848 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.01 % Allowed : 31.93 % Favored : 65.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5634 helix: 0.53 (0.12), residues: 1932 sheet: -0.42 (0.15), residues: 1079 loop : -0.81 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 11 HIS 0.008 0.001 HIS o 118 PHE 0.046 0.002 PHE H 46 TYR 0.031 0.002 TYR Q 2 ARG 0.018 0.001 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1346 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 1205 time to evaluate : 6.441 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: D 176 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7210 (p0) REVERT: H 54 LEU cc_start: 0.7859 (pp) cc_final: 0.7535 (pp) REVERT: L 1 MET cc_start: 0.7045 (tpp) cc_final: 0.6712 (tpp) REVERT: M 5 LYS cc_start: 0.7973 (mtpt) cc_final: 0.7496 (mttt) REVERT: Q 55 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.7135 (p0) REVERT: R 94 ASP cc_start: 0.6715 (t0) cc_final: 0.6500 (t0) REVERT: V 37 ILE cc_start: 0.8368 (mp) cc_final: 0.8121 (mm) REVERT: W 77 LYS cc_start: 0.8149 (mmpt) cc_final: 0.7899 (mmtt) REVERT: Z 31 ASP cc_start: 0.7783 (t0) cc_final: 0.7432 (t0) REVERT: d 49 MET cc_start: 0.7564 (mmm) cc_final: 0.7330 (tpt) REVERT: e 1 MET cc_start: 0.8183 (tpp) cc_final: 0.7739 (tpp) REVERT: e 4 ARG cc_start: 0.7865 (OUTLIER) cc_final: 0.7471 (mtp85) REVERT: i 142 ASP cc_start: 0.7164 (OUTLIER) cc_final: 0.6802 (p0) REVERT: j 88 MET cc_start: 0.8031 (OUTLIER) cc_final: 0.7299 (tmt) REVERT: j 102 MET cc_start: 0.8007 (ppp) cc_final: 0.7326 (ppp) REVERT: l 90 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7558 (p0) REVERT: n 32 THR cc_start: 0.9059 (p) cc_final: 0.8807 (t) REVERT: q 50 GLU cc_start: 0.7175 (tp30) cc_final: 0.6772 (tp30) REVERT: q 54 ASP cc_start: 0.7495 (p0) cc_final: 0.7074 (p0) REVERT: s 72 ARG cc_start: 0.7961 (OUTLIER) cc_final: 0.7514 (ptt90) REVERT: y 20 LYS cc_start: 0.8496 (pttt) cc_final: 0.8014 (pptt) REVERT: y 46 LYS cc_start: 0.8274 (ttmm) cc_final: 0.7962 (mttm) outliers start: 141 outliers final: 102 residues processed: 1266 average time/residue: 1.9583 time to fit residues: 3654.8445 Evaluate side-chains 1260 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 1151 time to evaluate : 6.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 2 GLN Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 10 THR Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 141 ASP Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 96 ILE Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 18 GLN Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 112 GLU Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 34 VAL Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 55 ASP Chi-restraints excluded: chain Q residue 98 ILE Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain R residue 67 ASP Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain T residue 14 LEU Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 13 THR Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 190 ASP Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 142 ASP Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 21 MET Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 74 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 50 GLN Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 17 SER Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain o residue 112 ASP Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain p residue 94 ARG Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain s residue 61 SER Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain s residue 89 ARG Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain t residue 80 LYS Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 5 LYS Chi-restraints excluded: chain B residue 11 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 597 optimal weight: 20.0000 chunk 962 optimal weight: 0.7980 chunk 587 optimal weight: 7.9990 chunk 456 optimal weight: 4.9990 chunk 668 optimal weight: 8.9990 chunk 1009 optimal weight: 1.9990 chunk 928 optimal weight: 7.9990 chunk 803 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 620 optimal weight: 7.9990 chunk 492 optimal weight: 0.0970 overall best weight: 3.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 90 GLN ** E 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 33 GLN I 128 ASN J 3 GLN J 5 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Q 86 GLN Q 87 GLN ** U 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 GLN x 84 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.179 157319 Z= 0.201 Angle : 0.740 60.103 235438 Z= 0.377 Chirality : 0.035 1.165 29994 Planarity : 0.006 0.124 12546 Dihedral : 23.577 179.396 78848 Min Nonbonded Distance : 1.730 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.37 % Allowed : 32.89 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.11), residues: 5634 helix: 0.47 (0.12), residues: 1928 sheet: -0.37 (0.15), residues: 1081 loop : -0.77 (0.12), residues: 2625 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP B 11 HIS 0.010 0.001 HIS o 118 PHE 0.051 0.001 PHE B 12 TYR 0.031 0.002 TYR Q 2 ARG 0.016 0.001 ARG E 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11268 Ramachandran restraints generated. 5634 Oldfield, 0 Emsley, 5634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1335 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 1224 time to evaluate : 6.610 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: D 176 ASP cc_start: 0.7495 (OUTLIER) cc_final: 0.7226 (p0) REVERT: H 83 LYS cc_start: 0.5233 (tptp) cc_final: 0.4984 (tptp) REVERT: M 5 LYS cc_start: 0.7946 (mtpt) cc_final: 0.7490 (mttt) REVERT: O 13 MET cc_start: 0.7403 (mmm) cc_final: 0.7092 (mmm) REVERT: V 37 ILE cc_start: 0.8307 (mp) cc_final: 0.8042 (mm) REVERT: Z 31 ASP cc_start: 0.7792 (t0) cc_final: 0.7446 (t0) REVERT: c 1 MET cc_start: 0.5861 (mtt) cc_final: 0.5568 (mtm) REVERT: e 1 MET cc_start: 0.8151 (tpp) cc_final: 0.7692 (tpp) REVERT: e 4 ARG cc_start: 0.7818 (OUTLIER) cc_final: 0.7378 (mtp85) REVERT: j 59 TYR cc_start: 0.7171 (m-10) cc_final: 0.6827 (m-10) REVERT: j 88 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7603 (tmt) REVERT: j 102 MET cc_start: 0.7823 (ppp) cc_final: 0.7141 (ppp) REVERT: l 90 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7511 (p0) REVERT: n 32 THR cc_start: 0.9059 (p) cc_final: 0.8834 (t) REVERT: q 50 GLU cc_start: 0.7107 (tp30) cc_final: 0.6565 (tp30) REVERT: q 54 ASP cc_start: 0.7461 (p0) cc_final: 0.6894 (p0) REVERT: s 72 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7493 (ptt90) REVERT: t 12 LYS cc_start: 0.8885 (ttpt) cc_final: 0.8495 (ttpp) outliers start: 111 outliers final: 88 residues processed: 1276 average time/residue: 1.9601 time to fit residues: 3691.5485 Evaluate side-chains 1254 residues out of total 4689 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1161 time to evaluate : 6.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 103 ASP Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 44 LYS Chi-restraints excluded: chain G residue 104 ASN Chi-restraints excluded: chain H residue 43 ASN Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain I residue 60 ASP Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain J residue 58 LEU Chi-restraints excluded: chain K residue 67 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 122 VAL Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 112 LEU Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 14 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 102 SER Chi-restraints excluded: chain S residue 30 ILE Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 93 LEU Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain V residue 12 ASN Chi-restraints excluded: chain V residue 50 ASN Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 35 SER Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 24 LEU Chi-restraints excluded: chain Y residue 40 ASP Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 53 THR Chi-restraints excluded: chain a residue 23 THR Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain f residue 191 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 44 ARG Chi-restraints excluded: chain h residue 169 THR Chi-restraints excluded: chain h residue 190 ASP Chi-restraints excluded: chain h residue 195 ILE Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain j residue 1 MET Chi-restraints excluded: chain j residue 7 VAL Chi-restraints excluded: chain j residue 21 MET Chi-restraints excluded: chain j residue 88 MET Chi-restraints excluded: chain k residue 133 THR Chi-restraints excluded: chain l residue 46 ILE Chi-restraints excluded: chain l residue 47 GLU Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 74 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 29 VAL Chi-restraints excluded: chain m residue 57 MET Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 19 ASP Chi-restraints excluded: chain n residue 36 VAL Chi-restraints excluded: chain n residue 60 ASP Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain n residue 84 VAL Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 7 LEU Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 90 LEU Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain s residue 61 SER Chi-restraints excluded: chain s residue 72 ARG Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 44 SER Chi-restraints excluded: chain t residue 52 LEU Chi-restraints excluded: chain v residue 25 ASP Chi-restraints excluded: chain w residue 58 VAL Chi-restraints excluded: chain B residue 11 TRP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1013 random chunks: chunk 638 optimal weight: 7.9990 chunk 856 optimal weight: 8.9990 chunk 246 optimal weight: 20.0000 chunk 740 optimal weight: 5.9990 chunk 118 optimal weight: 20.0000 chunk 223 optimal weight: 10.0000 chunk 804 optimal weight: 10.0000 chunk 336 optimal weight: 20.0000 chunk 826 optimal weight: 0.0030 chunk 101 optimal weight: 20.0000 chunk 148 optimal weight: 20.0000 overall best weight: 6.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN H 73 ASN I 128 ASN J 3 GLN ** M 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Q 87 GLN ** U 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 14 HIS r 62 ASN s 62 GLN ** t 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 61 GLN x 84 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.036403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.028888 restraints weight = 1107748.331| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.23 r_work: 0.2621 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2618 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2618 r_free = 0.2618 target_work(ls_wunit_k1) = 0.026 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2618 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8940 moved from start: 0.3885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.179 157319 Z= 0.291 Angle : 0.759 60.354 235438 Z= 0.387 Chirality : 0.037 1.170 29994 Planarity : 0.006 0.128 12546 Dihedral : 23.531 179.594 78848 Min Nonbonded Distance : 1.727 Molprobity Statistics. All-atom Clashscore : 18.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.58 % Allowed : 33.08 % Favored : 64.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.11), residues: 5634 helix: 0.40 (0.12), residues: 1940 sheet: -0.41 (0.15), residues: 1080 loop : -0.77 (0.12), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP B 11 HIS 0.008 0.001 HIS t 59 PHE 0.043 0.002 PHE H 46 TYR 0.046 0.002 TYR s 78 ARG 0.018 0.001 ARG E 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 53652.53 seconds wall clock time: 929 minutes 44.69 seconds (55784.69 seconds total)