Starting phenix.real_space_refine on Sat Feb 24 06:36:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930_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/7oii_12930/02_2024/7oii_12930_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oii_12930/02_2024/7oii_12930_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= 0.009 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 4648 5.49 5 Mg 422 5.21 5 S 148 5.16 5 C 72685 2.51 5 N 26979 2.21 5 O 40287 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 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 "J GLU 45": "OE1" <-> "OE2" Residue "J GLU 106": "OE1" <-> "OE2" Residue "J GLU 110": "OE1" <-> "OE2" 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 75": "OE1" <-> "OE2" 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 GLU 68": "OE1" <-> "OE2" 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 GLU 5": "OE1" <-> "OE2" 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 "g GLU 166": "OE1" <-> "OE2" 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 GLU 60": "OE1" <-> "OE2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ARG 92": "NH1" <-> "NH2" Residue "k GLU 106": "OE1" <-> "OE2" 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 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 ARG 33": "NH1" <-> "NH2" Residue "y GLU 36": "OE1" <-> "OE2" 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 145171 Number of models: 1 Model: "" Number of chains: 69 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': 288, 'rna2p_pyr': 166, 'rna3p': 16, 'rna3p_pur': 1379, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 459, 'rna3p': 2443} 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: "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: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} 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: "4" Number of atoms: 122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 122 Classifications: {'RNA': 6} Modifications used: {'rna3p_pur': 1, 'rna3p_pyr': 5} Link IDs: {'rna3p': 5} Chain: "z" Number of atoms: 1830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 1830 Classifications: {'RNA': 85} Modifications used: {'rna2p': 2, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p': 10, 'rna3p_pur': 35, 'rna3p_pyr': 25} Link IDs: {'rna2p': 14, 'rna3p': 70} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 250 Classifications: {'peptide': 39} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 37} Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'TYR:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 36 Chain: "1" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 282 Unusual residues: {' MG': 282} Classifications: {'undetermined': 282} Link IDs: {None: 281} 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: "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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 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: "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: "4" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0G9E SG CYS Z 16 64.490 60.339 105.598 1.00 74.18 S ATOM A0GDO SG CYS Z 37 65.794 59.231 101.507 1.00 74.04 S ATOM A0GE9 SG CYS Z 40 64.168 62.198 102.149 1.00 74.66 S ATOM A0HZA SG CYS e 11 142.978 116.664 47.898 1.00 50.10 S ATOM A0HZZ SG CYS e 14 145.628 115.218 49.380 1.00 49.18 S ATOM A0I2U SG CYS e 27 145.384 118.927 47.911 1.00 49.39 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13144 " occ=0.50 Time building chain proxies: 58.37, per 1000 atoms: 0.40 Number of scatterers: 145171 At special positions: 0 Unit cell: (276.06, 267.5, 228.98, 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 148 16.00 P 4648 15.00 Mg 422 11.99 O 40287 8.00 N 26979 7.00 C 72685 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 60.11 Conformation dependent library (CDL) restraints added in 6.9 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 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 11 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 14 " Number of angles added : 3 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10562 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 68 sheets defined 39.0% alpha, 19.5% beta 1587 base pairs and 2710 stacking pairs defined. Time for finding SS restraints: 79.30 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: 5.099A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.987A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.711A 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: 4.007A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.512A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.312A 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: 3.949A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.540A 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: 5.833A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.657A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.203A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.096A 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: 3.679A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.489A 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: 4.483A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 6.317A 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: 5.206A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 4.117A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.867A 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: 3.579A pdb=" N ALA F 55 " --> pdb=" O ASP F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.476A 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 142 through 147 removed outlier: 5.482A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.428A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.798A 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: 3.730A 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: 3.613A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.562A 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 50 removed outlier: 4.494A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 74 removed outlier: 4.365A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.498A 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: 4.148A 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: 4.413A 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: 3.868A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 5.511A 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: 4.098A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 5.519A 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: 4.050A pdb=" N ALA K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ALA K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 85 removed outlier: 4.104A pdb=" N LEU K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 4.098A 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: 3.954A pdb=" N LYS L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 3.558A 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: 4.426A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.597A 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: 3.676A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.803A 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: 4.530A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 4.901A pdb=" N GLN N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N LEU N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.217A 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: 3.505A pdb=" N GLU O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN O 12 " --> pdb=" O LEU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 97 through 104 removed outlier: 4.818A pdb=" N ARG O 101 " --> pdb=" O LEU O 97 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLU O 102 " --> pdb=" O TYR O 98 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG O 103 " --> pdb=" O TYR O 99 " (cutoff:3.500A) removed outlier: 5.218A 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: 3.856A pdb=" N ILE P 17 " --> pdb=" O ARG P 13 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.816A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 4.025A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 75 through 87 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: 3.778A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.800A 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: 3.787A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.321A 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: 3.796A pdb=" N VAL T 70 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 5.065A 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: 3.607A pdb=" N VAL U 47 " --> pdb=" O ASP U 43 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA U 52 " --> pdb=" O MET U 48 " (cutoff:3.500A) removed outlier: 4.553A 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: 3.863A pdb=" N LYS X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 4.091A pdb=" N GLY X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 62 removed outlier: 4.756A pdb=" N LEU X 43 " --> pdb=" O GLN X 39 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.457A 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: 5.285A pdb=" N GLN Z 48 " --> pdb=" O PHE Z 44 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL Z 51 " --> pdb=" O LYS Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 65 removed outlier: 3.986A pdb=" N PHE Z 64 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ASN Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 21 removed outlier: 4.798A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N ASP a 20 " --> pdb=" O ARG a 16 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ALA a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 25 removed outlier: 4.229A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) removed outlier: 5.409A 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: 4.434A pdb=" N LYS d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) removed outlier: 5.785A 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: 4.648A pdb=" N GLY d 56 " --> pdb=" O LYS d 52 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N LEU d 57 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N VAL d 58 " --> pdb=" O ASP d 54 " (cutoff:3.500A) Proline residue: d 63 - end of helix Processing helix chain 'd' and resid 26 through 31 removed outlier: 4.885A pdb=" N LEU d 29 " --> pdb=" O HIS d 26 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ARG d 30 " --> pdb=" O ALA d 27 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N HIS d 31 " --> pdb=" O ASN d 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 26 through 31' 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 Processing helix chain 'f' and resid 73 through 88 removed outlier: 6.297A pdb=" N SER f 77 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N GLU f 78 " --> pdb=" O ARG f 74 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N ALA f 79 " --> pdb=" O ALA f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.237A pdb=" N GLN f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.815A 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: 4.406A pdb=" N VAL g 76 " --> pdb=" O ARG g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 96 removed outlier: 3.568A pdb=" N VAL g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 113 removed outlier: 4.269A pdb=" N ASP g 112 " --> pdb=" O LYS g 108 " (cutoff:3.500A) removed outlier: 5.903A 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: 4.228A 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: 5.199A pdb=" N LYS h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 97 removed outlier: 3.635A 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: 3.993A pdb=" N LYS h 156 " --> pdb=" O GLN h 152 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 192 removed outlier: 3.624A pdb=" N LEU h 191 " --> pdb=" O GLU h 187 " (cutoff:3.500A) removed outlier: 4.906A 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: 3.922A pdb=" N ILE h 200 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS h 206 " --> pdb=" O GLU h 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 71 removed outlier: 3.654A pdb=" N ARG i 69 " --> pdb=" O GLU i 65 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ASN i 70 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N MET i 71 " --> pdb=" O ALA i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 109 through 119 removed outlier: 3.745A 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: 3.927A pdb=" N SER j 15 " --> pdb=" O HIS j 11 " (cutoff:3.500A) removed outlier: 5.556A 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: 3.688A pdb=" N ILE j 71 " --> pdb=" O PRO j 67 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 31 removed outlier: 3.661A pdb=" N ALA k 24 " --> pdb=" O SER k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 35 through 55 removed outlier: 3.688A pdb=" N ALA k 39 " --> pdb=" O LYS k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 70 removed outlier: 3.724A pdb=" N VAL k 69 " --> pdb=" O ALA k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 112 removed outlier: 6.132A 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 39 Processing helix chain 'm' and resid 41 through 56 removed outlier: 3.615A pdb=" N ARG m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 51 - end of helix removed outlier: 4.114A 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: 4.081A 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: 4.858A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 removed outlier: 4.136A pdb=" N GLY o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 59 removed outlier: 3.720A pdb=" N SER o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 4.684A 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 93 through 104 removed outlier: 5.109A pdb=" N ILE o 97 " --> pdb=" O ARG o 93 " (cutoff:3.500A) removed outlier: 4.258A 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: 3.800A pdb=" N TYR p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 22 removed outlier: 4.290A pdb=" N ILE q 22 " --> pdb=" O ALA q 18 " (cutoff:3.500A) Processing helix chain 'q' and resid 26 through 38 Processing helix chain 'q' and resid 49 through 64 removed outlier: 4.015A pdb=" N PHE q 63 " --> pdb=" O GLU q 59 " (cutoff:3.500A) removed outlier: 4.885A 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: 3.846A 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: 4.028A pdb=" N GLN r 60 " --> pdb=" O SER r 56 " (cutoff:3.500A) removed outlier: 5.652A 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 Processing helix chain 's' and resid 4 through 16 Processing helix chain 's' and resid 24 through 43 removed outlier: 4.645A pdb=" N GLY s 41 " --> pdb=" O ASN s 37 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N HIS s 42 " --> pdb=" O HIS s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 49 through 74 removed outlier: 3.830A 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: 5.581A pdb=" N THR v 34 " --> pdb=" O LYS v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 46 removed outlier: 3.704A pdb=" N THR v 45 " --> pdb=" O PRO v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 66 removed outlier: 3.786A 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: 4.527A pdb=" N PHE w 74 " --> pdb=" O LYS w 70 " (cutoff:3.500A) removed outlier: 4.030A 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: 4.532A pdb=" N GLY w 68 " --> pdb=" O GLU w 65 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N HIS w 69 " --> pdb=" O MET w 66 " (cutoff:3.500A) 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: 4.817A 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: 4.906A pdb=" N PHE y 37 " --> pdb=" O ARG y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 69 removed outlier: 4.093A pdb=" N ARG y 67 " --> pdb=" O GLU y 63 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR y 68 " --> pdb=" O ASN y 64 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ARG y 69 " --> pdb=" O ALA y 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 44 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: 6.577A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.592A 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: 4.192A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.166A 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: 5.456A pdb=" N ASN C 90 " --> pdb=" O ALA C 106 " (cutoff:3.500A) removed outlier: 4.298A 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 7 removed outlier: 7.038A pdb=" N ASP D 200 " --> pdb=" O THR D 112 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N THR D 112 " --> pdb=" O ASP D 200 " (cutoff:3.500A) removed outlier: 4.124A 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: 3.783A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.452A 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: 3.929A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.749A 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: 5.653A 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: 6.056A 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 5 removed outlier: 4.387A 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: 5.025A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (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: 5.841A 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: 4.490A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.920A 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: 5.494A pdb=" N GLU H 76 " --> pdb=" O LYS H 141 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER H 131 " --> pdb=" O ARG H 116 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.899A 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: 7.120A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'J' and resid 56 through 61 removed outlier: 4.646A pdb=" N ASP J 56 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N LYS J 40 " --> pdb=" O ILE J 22 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.750A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.636A pdb=" N TYR L 103 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU L 33 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS L 100 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'L' and resid 73 through 76 removed outlier: 6.795A pdb=" N ILE L 73 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'L' and resid 30 through 36 removed outlier: 7.877A pdb=" N SER L 30 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LYS L 127 " --> pdb=" O VAL L 36 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.220A pdb=" N ARG M 103 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE M 113 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ILE M 97 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU M 115 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N THR M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 49 through 52 removed outlier: 3.928A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 38 through 45 removed outlier: 6.649A pdb=" N THR O 25 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.787A pdb=" N ALA O 49 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ARG O 53 " --> pdb=" O HIS O 56 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER O 57 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'Q' and resid 11 through 15 removed outlier: 3.598A pdb=" N MET Q 40 " --> pdb=" O VAL Q 4 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.652A pdb=" N GLN Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N TYR Q 83 " --> pdb=" O PHE Q 77 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N PHE Q 77 " --> pdb=" O TYR Q 83 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS Q 85 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N VAL Q 75 " --> pdb=" O LYS Q 85 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN Q 87 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N LYS Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N GLN Q 91 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 2 through 8 Processing sheet with id= 33, first strand: chain 'S' and resid 12 through 15 removed outlier: 5.198A pdb=" N VAL S 31 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N ASN S 28 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS S 66 " --> pdb=" O ARG S 77 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASP S 79 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LYS S 64 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS S 81 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL S 62 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ALA S 83 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N THR S 60 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL S 85 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL S 58 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'T' and resid 40 through 46 removed outlier: 4.922A pdb=" N ASN T 40 " --> pdb=" O ALA T 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= 36, first strand: chain 'U' and resid 69 through 72 removed outlier: 6.697A pdb=" N ALA U 39 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.414A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'V' and resid 65 through 71 Processing sheet with id= 39, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.502A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'W' and resid 35 through 41 Processing sheet with id= 41, first strand: chain 'Y' and resid 33 through 39 removed outlier: 4.057A pdb=" N HIS Y 34 " --> pdb=" O GLN Y 9 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET Y 54 " --> pdb=" O THR Y 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'Z' and resid 20 through 25 removed outlier: 4.106A pdb=" N ASN Z 20 " --> pdb=" O CYS Z 16 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'a' and resid 29 through 32 removed outlier: 4.365A pdb=" N GLU a 36 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'b' and resid 19 through 25 removed outlier: 6.155A pdb=" N HIS b 19 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ILE b 48 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N LEU b 34 " --> pdb=" O GLU b 51 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'd' and resid 22 through 25 removed outlier: 5.536A pdb=" N PHE d 22 " --> pdb=" O VAL d 50 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'e' and resid 13 through 19 removed outlier: 8.438A pdb=" N ASN e 13 " --> pdb=" O SER e 28 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SER e 28 " --> pdb=" O ASN e 13 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'f' and resid 15 through 18 removed outlier: 4.991A pdb=" N HIS f 15 " --> pdb=" O ILE f 41 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLY f 17 " --> pdb=" O HIS f 39 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N HIS f 39 " --> pdb=" O GLY f 17 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'f' and resid 89 through 93 Processing sheet with id= 49, first strand: chain 'g' and resid 53 through 59 removed outlier: 3.647A pdb=" N ARG g 54 " --> pdb=" O HIS g 69 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.033A pdb=" N ARG g 164 " --> pdb=" O GLY g 155 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ASP g 181 " --> pdb=" O LYS g 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'h' and resid 141 through 145 removed outlier: 6.511A pdb=" N MET h 178 " --> pdb=" O ILE h 145 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'i' and resid 11 through 16 removed outlier: 7.025A pdb=" N LEU i 36 " --> pdb=" O ILE i 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'i' and resid 84 through 88 removed outlier: 3.691A pdb=" N ALA i 99 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N ASN i 122 " --> pdb=" O ALA i 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 33 through 41 removed outlier: 6.685A pdb=" N ARG i 45 " --> pdb=" O ASP i 41 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 38 through 43 removed outlier: 5.513A pdb=" N TYR j 59 " --> pdb=" O TRP j 42 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS j 3 " --> pdb=" O THR j 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 44 through 47 removed outlier: 7.165A pdb=" N HIS j 55 " --> pdb=" O LEU j 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'k' and resid 72 through 79 removed outlier: 6.171A pdb=" N THR k 72 " --> pdb=" O VAL k 91 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N TYR k 85 " --> pdb=" O ARG k 78 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'l' and resid 23 through 29 removed outlier: 6.825A pdb=" N ALA l 23 " --> pdb=" O LEU l 63 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ASP l 48 " --> pdb=" O THR l 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'l' and resid 74 through 77 removed outlier: 3.531A pdb=" N CYS l 127 " --> pdb=" O VAL l 103 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL l 103 " --> pdb=" O ILE l 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'm' and resid 5 through 11 Processing sheet with id= 61, first strand: chain 'n' and resid 42 through 52 removed outlier: 4.691A pdb=" N LEU n 71 " --> pdb=" O PRO n 43 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N ARG n 5 " --> pdb=" O GLY n 103 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 30 through 36 Processing sheet with id= 63, first strand: chain 'p' and resid 29 through 33 removed outlier: 5.257A pdb=" N LEU p 81 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N HIS p 96 " --> pdb=" O ARG p 83 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 36 through 41 removed outlier: 5.122A pdb=" N LYS p 51 " --> pdb=" O ILE p 67 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 't' and resid 4 through 10 removed outlier: 4.191A pdb=" N PHE t 16 " --> pdb=" O HIS t 9 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N GLY t 49 " --> pdb=" O ASN t 40 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 7 through 11 removed outlier: 7.233A pdb=" N GLU u 60 " --> pdb=" O VAL u 76 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N SER u 72 " --> pdb=" O CYS u 64 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'u' and resid 19 through 30 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.295A pdb=" N LEU w 47 " --> pdb=" O VAL w 62 " (cutoff:3.500A) 1970 hydrogen bonds defined for protein. 5820 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3997 hydrogen bonds 6280 hydrogen bond angles 0 basepair planarities 1587 basepair parallelities 2710 stacking parallelities Total time for adding SS restraints: 273.91 Time building geometry restraints manager: 65.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 11742 1.28 - 1.41: 59281 1.41 - 1.54: 76707 1.54 - 1.68: 9329 1.68 - 1.81: 265 Bond restraints: 157324 Sorted by residual: bond pdb=" C5 5MU z 69 " pdb=" C6 5MU z 69 " ideal model delta sigma weight residual 1.155 1.732 -0.577 2.00e-02 2.50e+03 8.33e+02 bond pdb=" C4 5MU z 69 " pdb=" C5 5MU z 69 " ideal model delta sigma weight residual 1.802 1.278 0.524 2.00e-02 2.50e+03 6.86e+02 bond pdb=" N3 5MU z 69 " pdb=" C4 5MU z 69 " ideal model delta sigma weight residual 1.182 1.513 -0.331 2.00e-02 2.50e+03 2.74e+02 bond pdb=" C4 5MU z 71 " pdb=" C5 5MU z 71 " ideal model delta sigma weight residual 1.802 1.477 0.325 2.00e-02 2.50e+03 2.63e+02 bond pdb=" C4 5MU z 39 " pdb=" C5 5MU z 39 " ideal model delta sigma weight residual 1.802 1.481 0.321 2.00e-02 2.50e+03 2.57e+02 ... (remaining 157319 not shown) Histogram of bond angle deviations from ideal: 21.76 - 46.86: 2 46.86 - 71.97: 1 71.97 - 97.07: 37 97.07 - 122.17: 201252 122.17 - 147.28: 34139 Bond angle restraints: 235431 Sorted by residual: angle pdb=" C4 5MU z 69 " pdb=" C5 5MU z 69 " pdb=" C6 5MU z 69 " ideal model delta sigma weight residual 111.01 21.76 89.25 3.00e+00 1.11e-01 8.85e+02 angle pdb=" N3 5MU z 69 " pdb=" C4 5MU z 69 " pdb=" C5 5MU z 69 " ideal model delta sigma weight residual 118.02 40.98 77.04 3.00e+00 1.11e-01 6.60e+02 angle pdb=" OP2 5MU z 64 " pdb=" P 5MU z 64 " pdb=" O5' 5MU z 64 " ideal model delta sigma weight residual 108.00 64.85 43.15 3.00e+00 1.11e-01 2.07e+02 angle pdb=" OP1 5MU z 64 " pdb=" P 5MU z 64 " pdb=" OP2 5MU z 64 " ideal model delta sigma weight residual 119.60 79.82 39.78 3.00e+00 1.11e-01 1.76e+02 angle pdb=" OP2 5MU z 40 " pdb=" P 5MU z 40 " pdb=" O5' 5MU z 40 " ideal model delta sigma weight residual 108.00 72.09 35.91 3.00e+00 1.11e-01 1.43e+02 ... (remaining 235426 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.59: 88580 35.59 - 71.19: 10935 71.19 - 106.78: 1041 106.78 - 142.37: 20 142.37 - 177.97: 39 Dihedral angle restraints: 100615 sinusoidal: 84239 harmonic: 16376 Sorted by residual: 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 35.69 164.31 1 1.50e+01 4.44e-03 8.37e+01 dihedral pdb=" O4' U 1 138 " pdb=" C1' U 1 138 " pdb=" N1 U 1 138 " pdb=" C2 U 1 138 " ideal model delta sinusoidal sigma weight residual 200.00 42.88 157.12 1 1.50e+01 4.44e-03 8.20e+01 dihedral pdb=" O4' U 1 102 " pdb=" C1' U 1 102 " pdb=" N1 U 1 102 " pdb=" C2 U 1 102 " ideal model delta sinusoidal sigma weight residual 200.00 43.82 156.18 1 1.50e+01 4.44e-03 8.17e+01 ... (remaining 100612 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.219: 29634 0.219 - 0.437: 307 0.437 - 0.656: 0 0.656 - 0.875: 1 0.875 - 1.093: 2 Chirality restraints: 29944 Sorted by residual: 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 -1.32 1.09 2.00e-01 2.50e+01 2.99e+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 1.66 0.88 2.00e-01 2.50e+01 1.95e+01 chirality pdb=" C1* PSU 12457 " pdb=" O4* PSU 12457 " pdb=" C2* PSU 12457 " pdb=" C5 PSU 12457 " both_signs ideal model delta sigma weight residual False 2.55 1.87 0.68 2.00e-01 2.50e+01 1.15e+01 ... (remaining 29941 not shown) Planarity restraints: 12569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU z 63 " 0.135 2.00e-02 2.50e+03 7.19e-01 1.16e+04 pdb=" C4' 5MU z 63 " 0.552 2.00e-02 2.50e+03 pdb=" O4' 5MU z 63 " 0.603 2.00e-02 2.50e+03 pdb=" C3' 5MU z 63 " -0.480 2.00e-02 2.50e+03 pdb=" O3' 5MU z 63 " -0.885 2.00e-02 2.50e+03 pdb=" C2' 5MU z 63 " -0.061 2.00e-02 2.50e+03 pdb=" O2' 5MU z 63 " 1.210 2.00e-02 2.50e+03 pdb=" C1' 5MU z 63 " 0.138 2.00e-02 2.50e+03 pdb=" N1 5MU z 63 " -1.212 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.097 2.00e-02 2.50e+03 6.50e-01 9.50e+03 pdb=" C4' 2MG 21516 " -0.480 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.767 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.692 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.178 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -1.000 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.158 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 1.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.076 2.00e-02 2.50e+03 6.25e-01 8.78e+03 pdb=" C4' OMC 12498 " -0.423 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.622 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.624 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.697 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.135 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -1.052 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.225 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.943 2.00e-02 2.50e+03 ... (remaining 12566 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.19: 459 2.19 - 2.87: 48263 2.87 - 3.55: 211203 3.55 - 4.22: 478379 4.22 - 4.90: 626412 Nonbonded interactions: 1364716 Sorted by model distance: nonbonded pdb=" N3 5MU z 69 " pdb=" C6 5MU z 69 " model vdw 1.514 2.680 nonbonded pdb=" OP2 G 12588 " pdb="MG MG 13057 " model vdw 1.701 2.170 nonbonded pdb=" OP2 G 12544 " pdb="MG MG 13149 " model vdw 1.702 2.170 nonbonded pdb=" O3' G 1 535 " pdb="MG MG 13250 " model vdw 1.711 2.170 nonbonded pdb=" O2 U 11375 " pdb="MG MG 13255 " model vdw 1.712 2.170 ... (remaining 1364711 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: 5.260 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: 0.170 Extract box with map and model: 19.240 Check model and map are aligned: 1.720 Set scattering table: 1.050 Process input model: 599.570 Find NCS groups from input model: 2.660 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:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 641.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 : 0.017 0.577 157324 Z= 1.029 Angle : 1.199 89.253 235431 Z= 0.603 Chirality : 0.073 1.093 29944 Planarity : 0.027 0.719 12569 Dihedral : 22.796 177.966 90053 Min Nonbonded Distance : 1.514 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.59 % Favored : 96.23 % Rotamer: Outliers : 0.23 % Allowed : 2.92 % Favored : 96.84 % 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: -3.84 (0.09), residues: 5651 helix: -3.57 (0.06), residues: 1928 sheet: -1.92 (0.14), residues: 1126 loop : -1.83 (0.10), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP E 78 HIS 0.033 0.005 HIS C 53 PHE 0.082 0.004 PHE M 80 TYR 0.053 0.005 TYR N 36 ARG 0.054 0.003 ARG c 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1985 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1974 time to evaluate : 5.918 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: C 96 TYR cc_start: 0.8293 (m-80) cc_final: 0.8031 (m-80) REVERT: D 58 ASN cc_start: 0.7644 (p0) cc_final: 0.7419 (p0) REVERT: E 136 GLN cc_start: 0.7238 (tp-100) cc_final: 0.6747 (tp-100) REVERT: F 159 THR cc_start: 0.8965 (p) cc_final: 0.8335 (t) REVERT: H 2 GLN cc_start: 0.8365 (mm-40) cc_final: 0.7859 (mp10) REVERT: H 4 ILE cc_start: 0.7970 (tp) cc_final: 0.7725 (tp) REVERT: H 20 ASN cc_start: 0.8153 (t0) cc_final: 0.7915 (t0) REVERT: H 129 GLU cc_start: 0.7323 (pt0) cc_final: 0.6759 (tm-30) REVERT: H 130 VAL cc_start: 0.8048 (p) cc_final: 0.7058 (p) REVERT: I 31 GLU cc_start: 0.6792 (tp30) cc_final: 0.6460 (tp30) REVERT: Q 95 ASP cc_start: 0.7310 (m-30) cc_final: 0.7030 (m-30) REVERT: U 90 ASP cc_start: 0.6960 (m-30) cc_final: 0.4685 (m-30) REVERT: X 45 GLN cc_start: 0.7415 (mt0) cc_final: 0.6929 (mt0) REVERT: b 43 VAL cc_start: 0.8252 (t) cc_final: 0.7604 (m) REVERT: f 56 GLU cc_start: 0.7814 (tp30) cc_final: 0.7597 (tp30) REVERT: g 83 ASP cc_start: 0.6118 (m-30) cc_final: 0.5803 (m-30) REVERT: i 105 ILE cc_start: 0.8744 (mt) cc_final: 0.8368 (mm) REVERT: j 61 LEU cc_start: 0.8626 (tp) cc_final: 0.8150 (tp) REVERT: k 12 ILE cc_start: 0.8530 (tt) cc_final: 0.8041 (tp) REVERT: m 25 ASN cc_start: 0.7707 (OUTLIER) cc_final: 0.7038 (p0) REVERT: m 64 TYR cc_start: 0.7537 (t80) cc_final: 0.6831 (t80) REVERT: n 14 ASP cc_start: 0.7440 (t0) cc_final: 0.7161 (t0) REVERT: o 18 ASP cc_start: 0.6235 (p0) cc_final: 0.5655 (p0) REVERT: o 72 ASP cc_start: 0.7237 (t0) cc_final: 0.6684 (t0) REVERT: r 42 TRP cc_start: 0.7930 (t-100) cc_final: 0.7669 (t-100) REVERT: t 80 LYS cc_start: 0.7145 (mmtt) cc_final: 0.6935 (mmtt) REVERT: v 26 ILE cc_start: 0.7673 (mt) cc_final: 0.7405 (mp) outliers start: 11 outliers final: 6 residues processed: 1981 average time/residue: 2.1642 time to fit residues: 6096.7317 Evaluate side-chains 1323 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1316 time to evaluate : 6.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain g residue 118 ASP Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain m residue 25 ASN Chi-restraints excluded: chain n residue 87 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 856 optimal weight: 5.9990 chunk 768 optimal weight: 4.9990 chunk 426 optimal weight: 0.9990 chunk 262 optimal weight: 0.9980 chunk 518 optimal weight: 6.9990 chunk 410 optimal weight: 0.9990 chunk 794 optimal weight: 0.0770 chunk 307 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 chunk 591 optimal weight: 5.9990 chunk 920 optimal weight: 20.0000 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 153 GLN D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN E 92 HIS E 94 GLN E 195 GLN F 81 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 128 GLN H 33 GLN I 67 ASN J 82 ASN K 93 ASN L 22 GLN M 9 GLN M 18 GLN N 38 GLN N 61 GLN O 66 ASN P 59 GLN P 72 ASN Q 11 GLN Q 86 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN X 20 ASN X 58 ASN a 6 ASN c 6 GLN c 13 ASN e 37 GLN f 170 HIS g 8 ASN h 71 GLN h 196 ASN i 70 ASN j 58 HIS k 68 ASN k 130 ASN ** l 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** m 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 64 GLN o 40 ASN q 8 ASN r 66 GLN s 62 GLN t 9 HIS t 26 ASN v 52 GLN w 69 HIS Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.279 157324 Z= 0.186 Angle : 0.769 90.873 235431 Z= 0.397 Chirality : 0.034 0.552 29944 Planarity : 0.008 0.249 12569 Dihedral : 23.796 179.542 78774 Min Nonbonded Distance : 1.296 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.11 % Favored : 96.85 % Rotamer: Outliers : 3.48 % Allowed : 20.78 % Favored : 75.75 % 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: -1.68 (0.10), residues: 5651 helix: -0.57 (0.11), residues: 1947 sheet: -1.33 (0.15), residues: 1105 loop : -1.34 (0.11), residues: 2599 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 11 HIS 0.009 0.001 HIS o 118 PHE 0.034 0.002 PHE Z 43 TYR 0.023 0.002 TYR F 7 ARG 0.013 0.001 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1839 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1676 time to evaluate : 6.626 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: C 96 TYR cc_start: 0.8154 (m-80) cc_final: 0.7696 (m-80) REVERT: C 185 GLU cc_start: 0.7078 (tm-30) cc_final: 0.6762 (tp30) REVERT: C 187 ASP cc_start: 0.7637 (m-30) cc_final: 0.7136 (m-30) REVERT: E 94 GLN cc_start: 0.7558 (mt0) cc_final: 0.7252 (mt0) REVERT: H 2 GLN cc_start: 0.8427 (mm-40) cc_final: 0.7965 (mp10) REVERT: H 20 ASN cc_start: 0.8118 (t0) cc_final: 0.7730 (t0) REVERT: K 1 MET cc_start: 0.6481 (ttp) cc_final: 0.6256 (ttp) REVERT: O 110 ILE cc_start: 0.8487 (OUTLIER) cc_final: 0.8281 (pt) REVERT: P 87 SER cc_start: 0.8451 (OUTLIER) cc_final: 0.7977 (p) REVERT: Q 78 ARG cc_start: 0.8127 (tpp80) cc_final: 0.7733 (tpp80) REVERT: S 87 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.7784 (mt) REVERT: U 41 GLU cc_start: 0.6674 (pp20) cc_final: 0.6243 (pp20) REVERT: U 76 ASP cc_start: 0.6496 (p0) cc_final: 0.5616 (p0) REVERT: X 54 LYS cc_start: 0.8420 (mttm) cc_final: 0.8142 (mttm) REVERT: e 24 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7481 (mtp180) REVERT: k 31 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.7551 (ptp) REVERT: m 64 TYR cc_start: 0.7303 (t80) cc_final: 0.7014 (t80) REVERT: o 18 ASP cc_start: 0.6752 (p0) cc_final: 0.6447 (p0) REVERT: q 54 ASP cc_start: 0.7166 (t0) cc_final: 0.6871 (t0) REVERT: u 38 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8397 (pt) REVERT: w 16 LEU cc_start: 0.8508 (tp) cc_final: 0.7996 (tt) outliers start: 163 outliers final: 60 residues processed: 1734 average time/residue: 1.9541 time to fit residues: 4965.4918 Evaluate side-chains 1494 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1428 time to evaluate : 6.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 30 GLU Chi-restraints excluded: chain D residue 181 ASP Chi-restraints excluded: chain F residue 26 MET Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 146 VAL Chi-restraints excluded: chain I residue 12 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 128 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 65 VAL Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Z residue 4 ASP Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain b residue 7 GLU Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 38 THR Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 126 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 70 ASN Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 31 MET Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain o residue 58 SER Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain t residue 42 ILE Chi-restraints excluded: chain u residue 38 ILE Chi-restraints excluded: chain v residue 66 SER Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain v residue 72 ASP Chi-restraints excluded: chain w residue 48 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 511 optimal weight: 6.9990 chunk 285 optimal weight: 10.0000 chunk 766 optimal weight: 3.9990 chunk 627 optimal weight: 9.9990 chunk 254 optimal weight: 10.0000 chunk 922 optimal weight: 10.0000 chunk 996 optimal weight: 10.0000 chunk 821 optimal weight: 10.0000 chunk 914 optimal weight: 0.3980 chunk 314 optimal weight: 10.0000 chunk 740 optimal weight: 20.0000 overall best weight: 6.2790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 62 GLN E 90 GLN E 195 GLN F 27 GLN F 52 ASN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN L 22 GLN M 107 ASN N 38 GLN P 37 GLN P 59 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 ASN f 170 HIS ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 100 GLN h 54 GLN h 71 GLN h 196 ASN i 61 GLN ** i 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN ** m 110 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 6 GLN q 8 ASN r 66 GLN s 62 GLN t 9 HIS t 26 ASN t 29 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.355 157324 Z= 0.338 Angle : 0.748 90.483 235431 Z= 0.392 Chirality : 0.037 0.474 29944 Planarity : 0.008 0.135 12569 Dihedral : 23.538 179.768 78763 Min Nonbonded Distance : 1.247 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.13 % Favored : 96.81 % Rotamer: Outliers : 5.33 % Allowed : 22.40 % Favored : 72.27 % 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: -0.70 (0.11), residues: 5651 helix: 0.55 (0.11), residues: 1970 sheet: -0.90 (0.15), residues: 1121 loop : -0.97 (0.12), residues: 2560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP g 201 HIS 0.009 0.001 HIS L 13 PHE 0.095 0.002 PHE f 126 TYR 0.021 0.002 TYR o 77 ARG 0.013 0.001 ARG c 41 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1770 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1520 time to evaluate : 6.640 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: C 187 ASP cc_start: 0.7848 (m-30) cc_final: 0.7482 (m-30) REVERT: G 22 GLN cc_start: 0.8542 (mm110) cc_final: 0.8223 (mm-40) REVERT: G 153 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7279 (mtp85) REVERT: H 2 GLN cc_start: 0.8497 (mm-40) cc_final: 0.8189 (mp10) REVERT: H 20 ASN cc_start: 0.8276 (t0) cc_final: 0.7859 (t0) REVERT: H 44 ILE cc_start: 0.8774 (mt) cc_final: 0.8466 (mt) REVERT: I 16 TYR cc_start: 0.7990 (m-80) cc_final: 0.7486 (m-80) REVERT: J 104 THR cc_start: 0.8381 (OUTLIER) cc_final: 0.8071 (t) REVERT: L 75 GLU cc_start: 0.5949 (pp20) cc_final: 0.4021 (pp20) REVERT: Q 78 ARG cc_start: 0.8210 (tpp80) cc_final: 0.7867 (tpp80) REVERT: U 11 GLU cc_start: 0.6273 (pt0) cc_final: 0.5690 (pt0) REVERT: U 41 GLU cc_start: 0.7017 (pp20) cc_final: 0.6767 (pp20) REVERT: W 56 MET cc_start: 0.6480 (ttp) cc_final: 0.6147 (ttm) REVERT: X 54 LYS cc_start: 0.8645 (mttm) cc_final: 0.8436 (mttm) REVERT: a 32 LYS cc_start: 0.7649 (ptpp) cc_final: 0.7436 (ptpp) REVERT: e 24 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.7033 (mtp180) REVERT: e 36 ARG cc_start: 0.8187 (tmm160) cc_final: 0.7527 (ttp80) REVERT: g 31 ASP cc_start: 0.7361 (OUTLIER) cc_final: 0.7150 (p0) REVERT: h 4 TYR cc_start: 0.8281 (t80) cc_final: 0.8018 (t80) REVERT: h 36 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7392 (tt0) REVERT: j 13 ASP cc_start: 0.7932 (p0) cc_final: 0.7719 (p0) REVERT: k 31 MET cc_start: 0.8071 (OUTLIER) cc_final: 0.7646 (ptp) REVERT: l 111 MET cc_start: 0.7990 (OUTLIER) cc_final: 0.7709 (ptp) REVERT: n 5 ARG cc_start: 0.6036 (OUTLIER) cc_final: 0.5791 (ptt90) REVERT: s 73 LYS cc_start: 0.7804 (OUTLIER) cc_final: 0.7512 (ttmm) REVERT: t 35 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7825 (tmm-80) REVERT: u 27 ARG cc_start: 0.8063 (OUTLIER) cc_final: 0.7535 (ptm-80) REVERT: u 38 ILE cc_start: 0.8643 (OUTLIER) cc_final: 0.8439 (pt) outliers start: 250 outliers final: 84 residues processed: 1612 average time/residue: 1.9851 time to fit residues: 4690.9873 Evaluate side-chains 1466 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 1370 time to evaluate : 6.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 112 LYS Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain P residue 109 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 62 LYS Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 7 GLU Chi-restraints excluded: chain b residue 23 THR Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 153 ASP Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 36 GLN Chi-restraints excluded: chain h residue 50 ASP Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain j residue 89 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 31 MET Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 146 GLU Chi-restraints excluded: chain l residue 111 MET Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 94 LEU Chi-restraints excluded: chain n residue 5 ARG Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 50 THR Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 32 SER Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain u residue 14 SER Chi-restraints excluded: chain u residue 27 ARG Chi-restraints excluded: chain u residue 38 ILE Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain w residue 48 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 63 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 911 optimal weight: 20.0000 chunk 693 optimal weight: 8.9990 chunk 478 optimal weight: 0.9990 chunk 102 optimal weight: 10.0000 chunk 440 optimal weight: 10.0000 chunk 619 optimal weight: 7.9990 chunk 925 optimal weight: 6.9990 chunk 980 optimal weight: 10.0000 chunk 483 optimal weight: 5.9990 chunk 877 optimal weight: 4.9990 chunk 264 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 70 ASN D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 90 GLN E 94 GLN E 195 GLN F 27 GLN G 20 ASN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN H 33 GLN I 67 ASN L 22 GLN N 38 GLN P 59 GLN Q 82 HIS Q 86 GLN R 31 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN W 17 ASN X 31 GLN X 38 GLN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 40 GLN h 54 GLN h 71 GLN h 196 ASN i 61 GLN i 70 ASN i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 118 GLN m 50 GLN m 75 GLN q 8 ASN r 66 GLN s 62 GLN t 26 ASN x 3 ASN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.363 157324 Z= 0.286 Angle : 0.734 91.428 235431 Z= 0.385 Chirality : 0.035 0.482 29944 Planarity : 0.007 0.163 12569 Dihedral : 23.515 179.925 78763 Min Nonbonded Distance : 1.260 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 4.84 % Allowed : 24.83 % Favored : 70.33 % Cbeta Deviations : 0.02 % 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: -0.30 (0.11), residues: 5651 helix: 0.90 (0.12), residues: 1966 sheet: -0.62 (0.15), residues: 1070 loop : -0.80 (0.12), residues: 2615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 11 HIS 0.007 0.001 HIS o 118 PHE 0.023 0.002 PHE Z 64 TYR 0.046 0.002 TYR f 213 ARG 0.013 0.001 ARG V 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1736 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 227 poor density : 1509 time to evaluate : 6.709 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: D 151 THR cc_start: 0.6764 (OUTLIER) cc_final: 0.6472 (t) REVERT: G 22 GLN cc_start: 0.8517 (mm110) cc_final: 0.8156 (mm-40) REVERT: G 153 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.7296 (mtp85) REVERT: H 43 ASN cc_start: 0.8647 (m110) cc_final: 0.8430 (m110) REVERT: I 108 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8287 (mtt) REVERT: J 7 MET cc_start: 0.8050 (mmm) cc_final: 0.7668 (mmp) REVERT: J 106 GLU cc_start: 0.6547 (mp0) cc_final: 0.6344 (mp0) REVERT: N 17 LYS cc_start: 0.8736 (tppp) cc_final: 0.8337 (tppp) REVERT: O 3 ASN cc_start: 0.7635 (m110) cc_final: 0.7392 (m-40) REVERT: Q 78 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7902 (tpp80) REVERT: X 54 LYS cc_start: 0.8668 (mttm) cc_final: 0.8426 (mttm) REVERT: e 24 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7090 (mtp180) REVERT: e 36 ARG cc_start: 0.8100 (tmm160) cc_final: 0.7459 (ttp80) REVERT: i 61 GLN cc_start: 0.7370 (tp-100) cc_final: 0.6850 (tp40) REVERT: l 111 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7745 (ptp) REVERT: q 47 GLU cc_start: 0.7598 (pp20) cc_final: 0.5987 (pp20) REVERT: q 72 GLU cc_start: 0.6921 (pp20) cc_final: 0.6578 (pp20) REVERT: s 73 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7507 (ttmm) REVERT: u 27 ARG cc_start: 0.8077 (OUTLIER) cc_final: 0.7596 (ptm-80) REVERT: u 38 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8500 (pt) REVERT: v 50 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8126 (ttmt) REVERT: y 20 LYS cc_start: 0.8107 (ptmm) cc_final: 0.7888 (pptt) outliers start: 227 outliers final: 98 residues processed: 1593 average time/residue: 2.0052 time to fit residues: 4692.5370 Evaluate side-chains 1483 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 1376 time to evaluate : 6.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 97 LEU Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 44 LYS Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 146 GLU Chi-restraints excluded: chain l residue 111 MET Chi-restraints excluded: chain m residue 65 ILE Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 71 LEU Chi-restraints excluded: chain n residue 77 VAL Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 55 ASP Chi-restraints excluded: chain u residue 27 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 38 ILE Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 50 LYS Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 48 THR Chi-restraints excluded: chain w residue 67 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 816 optimal weight: 7.9990 chunk 556 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 729 optimal weight: 3.9990 chunk 404 optimal weight: 20.0000 chunk 836 optimal weight: 20.0000 chunk 677 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 500 optimal weight: 7.9990 chunk 879 optimal weight: 7.9990 chunk 247 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN D 167 ASN E 9 GLN E 115 GLN E 195 GLN F 52 ASN F 81 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN H 33 GLN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN L 22 GLN N 38 GLN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 66 ASN P 71 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 ASN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN X 38 GLN a 5 GLN ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 170 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 54 GLN h 196 ASN i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 68 GLN ** k 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN p 5 ASN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 GLN r 66 GLN s 37 ASN s 62 GLN t 26 ASN t 79 ASN v 54 GLN x 3 ASN y 64 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.360 157324 Z= 0.364 Angle : 0.757 91.391 235431 Z= 0.395 Chirality : 0.037 0.452 29944 Planarity : 0.007 0.133 12569 Dihedral : 23.474 179.641 78763 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 5.20 % Allowed : 26.60 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: -0.20 (0.11), residues: 5651 helix: 0.95 (0.12), residues: 1975 sheet: -0.55 (0.15), residues: 1079 loop : -0.72 (0.12), residues: 2597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 11 HIS 0.007 0.001 HIS j 37 PHE 0.023 0.002 PHE Z 64 TYR 0.046 0.002 TYR f 213 ARG 0.015 0.001 ARG u 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1702 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 244 poor density : 1458 time to evaluate : 6.771 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: D 167 ASN cc_start: 0.8236 (OUTLIER) cc_final: 0.7971 (t0) REVERT: G 22 GLN cc_start: 0.8608 (mm110) cc_final: 0.8274 (mm-40) REVERT: G 153 ARG cc_start: 0.7533 (OUTLIER) cc_final: 0.7247 (mtp85) REVERT: H 20 ASN cc_start: 0.8415 (t0) cc_final: 0.8139 (t0) REVERT: I 16 TYR cc_start: 0.7816 (m-80) cc_final: 0.7593 (m-80) REVERT: I 108 MET cc_start: 0.8781 (OUTLIER) cc_final: 0.8261 (mtt) REVERT: N 17 LYS cc_start: 0.8733 (tppp) cc_final: 0.8261 (tppp) REVERT: N 88 LYS cc_start: 0.7450 (tptt) cc_final: 0.6356 (tptt) REVERT: P 100 VAL cc_start: 0.9108 (t) cc_final: 0.8866 (t) REVERT: Q 1 MET cc_start: 0.6487 (tpp) cc_final: 0.6243 (tpt) REVERT: Q 78 ARG cc_start: 0.8287 (tpp80) cc_final: 0.8021 (tpp-160) REVERT: S 72 GLN cc_start: 0.6677 (OUTLIER) cc_final: 0.6407 (mm110) REVERT: U 41 GLU cc_start: 0.6224 (pp20) cc_final: 0.5866 (pp20) REVERT: d 54 ASP cc_start: 0.5831 (OUTLIER) cc_final: 0.5600 (p0) REVERT: e 24 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.7082 (mtp180) REVERT: e 36 ARG cc_start: 0.8194 (tmm160) cc_final: 0.7579 (ttp80) REVERT: k 31 MET cc_start: 0.8207 (ttp) cc_final: 0.7741 (ptp) REVERT: q 47 GLU cc_start: 0.7527 (pp20) cc_final: 0.5770 (pp20) REVERT: q 69 LEU cc_start: 0.9109 (tp) cc_final: 0.8765 (tp) REVERT: s 73 LYS cc_start: 0.8006 (OUTLIER) cc_final: 0.7642 (ttmm) REVERT: t 35 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7794 (tmm-80) REVERT: u 27 ARG cc_start: 0.8160 (OUTLIER) cc_final: 0.7913 (ptm-80) REVERT: u 38 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8484 (pt) REVERT: w 17 LYS cc_start: 0.8492 (mmmm) cc_final: 0.8137 (mmmm) REVERT: y 20 LYS cc_start: 0.8014 (ptmm) cc_final: 0.7125 (pptt) outliers start: 244 outliers final: 128 residues processed: 1568 average time/residue: 1.9747 time to fit residues: 4556.0575 Evaluate side-chains 1498 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1360 time to evaluate : 6.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 167 ASN Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 199 MET Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 15 SER Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 71 GLN Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 52 LEU Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 20 ASN Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 50 ASP Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 96 MET Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 SER Chi-restraints excluded: chain k residue 29 ILE Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain l residue 74 SER Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 53 GLU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 27 GLU Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 71 LEU Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 19 LEU 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 45 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain u residue 27 ARG Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 38 ILE Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 55 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 27 ASP Chi-restraints excluded: chain w residue 39 THR Chi-restraints excluded: chain w residue 48 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 43 THR Chi-restraints excluded: chain y residue 51 SER Chi-restraints excluded: chain B residue 6 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 329 optimal weight: 10.0000 chunk 882 optimal weight: 20.0000 chunk 193 optimal weight: 9.9990 chunk 575 optimal weight: 9.9990 chunk 241 optimal weight: 10.0000 chunk 981 optimal weight: 7.9990 chunk 814 optimal weight: 9.9990 chunk 454 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 324 optimal weight: 10.0000 chunk 515 optimal weight: 10.0000 overall best weight: 9.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN D 149 ASN E 9 GLN E 94 GLN E 195 GLN F 27 GLN F 52 ASN F 81 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN H 33 GLN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 89 ASN L 22 GLN N 38 GLN ** N 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN X 38 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 5 GLN ** f 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 40 GLN h 196 ASN i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 68 GLN ** k 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 50 GLN o 101 ASN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN s 62 GLN t 26 ASN v 54 GLN x 70 ASN y 64 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.358 157324 Z= 0.460 Angle : 0.804 91.472 235431 Z= 0.417 Chirality : 0.040 0.439 29944 Planarity : 0.008 0.144 12569 Dihedral : 23.472 178.853 78763 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.29 % Allowed : 27.56 % Favored : 67.15 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % Twisted General : 0.04 % 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: -0.27 (0.11), residues: 5651 helix: 0.87 (0.12), residues: 1973 sheet: -0.54 (0.15), residues: 1092 loop : -0.76 (0.12), residues: 2586 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 11 HIS 0.008 0.002 HIS j 37 PHE 0.029 0.002 PHE Z 64 TYR 0.039 0.002 TYR f 213 ARG 0.031 0.001 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1676 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 1428 time to evaluate : 6.676 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: C 264 ASP cc_start: 0.7634 (OUTLIER) cc_final: 0.7430 (m-30) REVERT: G 22 GLN cc_start: 0.8612 (mm110) cc_final: 0.8246 (mm-40) REVERT: G 153 ARG cc_start: 0.7557 (OUTLIER) cc_final: 0.7265 (mtp85) REVERT: H 112 LYS cc_start: 0.5537 (pttt) cc_final: 0.5211 (pttt) REVERT: H 129 GLU cc_start: 0.7623 (pt0) cc_final: 0.6785 (tp30) REVERT: I 108 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8240 (mtt) REVERT: J 20 MET cc_start: 0.7369 (OUTLIER) cc_final: 0.6975 (ttt) REVERT: K 116 VAL cc_start: 0.8819 (m) cc_final: 0.8577 (p) REVERT: N 17 LYS cc_start: 0.8713 (tppp) cc_final: 0.8261 (tppp) REVERT: Q 78 ARG cc_start: 0.8295 (tpp80) cc_final: 0.8017 (tpp-160) REVERT: S 72 GLN cc_start: 0.6787 (OUTLIER) cc_final: 0.5107 (mp10) REVERT: T 60 GLU cc_start: 0.7355 (tm-30) cc_final: 0.7145 (tm-30) REVERT: U 10 LYS cc_start: 0.7370 (OUTLIER) cc_final: 0.6905 (tmmt) REVERT: U 11 GLU cc_start: 0.6409 (pt0) cc_final: 0.6076 (pm20) REVERT: a 4 GLN cc_start: 0.8025 (OUTLIER) cc_final: 0.7581 (pt0) REVERT: d 54 ASP cc_start: 0.5928 (OUTLIER) cc_final: 0.5673 (p0) REVERT: e 24 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.7170 (mtp180) REVERT: e 36 ARG cc_start: 0.8182 (tmm160) cc_final: 0.7706 (ttm170) REVERT: h 36 GLN cc_start: 0.7689 (OUTLIER) cc_final: 0.7465 (tt0) REVERT: l 126 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8515 (mp) REVERT: o 72 ASP cc_start: 0.7359 (t0) cc_final: 0.7111 (t0) REVERT: r 39 GLU cc_start: 0.7501 (tp30) cc_final: 0.7125 (tp30) REVERT: s 73 LYS cc_start: 0.8071 (OUTLIER) cc_final: 0.7698 (ttmm) REVERT: s 89 ARG cc_start: 0.6709 (ttp-170) cc_final: 0.6447 (ttp-170) REVERT: t 35 ARG cc_start: 0.8136 (OUTLIER) cc_final: 0.7820 (tmm-80) outliers start: 248 outliers final: 143 residues processed: 1540 average time/residue: 1.9649 time to fit residues: 4460.6801 Evaluate side-chains 1520 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1364 time to evaluate : 6.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 19 ILE Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 103 ILE Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 14 SER Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 91 SER Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain M residue 48 VAL Chi-restraints excluded: chain M residue 95 THR Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 9 ILE Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 59 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain T residue 93 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 90 ASP Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 7 VAL Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 20 ASN Chi-restraints excluded: chain Z residue 27 THR Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 4 GLN Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 165 THR Chi-restraints excluded: chain h residue 36 GLN Chi-restraints excluded: chain h residue 50 ASP Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 96 MET Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain i residue 164 ILE Chi-restraints excluded: chain j residue 62 MET Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 35 LEU Chi-restraints excluded: chain m residue 53 GLU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain p residue 18 LYS Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 58 ASP Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain q residue 95 LEU Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain t residue 55 ASP Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain y residue 51 SER Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 945 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 558 optimal weight: 6.9990 chunk 716 optimal weight: 4.9990 chunk 555 optimal weight: 10.0000 chunk 825 optimal weight: 6.9990 chunk 547 optimal weight: 9.9990 chunk 977 optimal weight: 10.0000 chunk 611 optimal weight: 9.9990 chunk 595 optimal weight: 0.7980 chunk 451 optimal weight: 10.0000 overall best weight: 5.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN D 149 ASN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 94 GLN E 195 GLN F 81 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN I 67 ASN J 89 ASN L 13 HIS L 22 GLN N 38 GLN P 59 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN X 38 GLN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 33 ASN f 109 GLN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 40 GLN h 196 ASN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 67 GLN l 118 GLN m 50 GLN m 75 GLN p 5 ASN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 GLN r 66 GLN s 62 GLN t 26 ASN v 54 GLN x 13 GLN x 70 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.361 157324 Z= 0.309 Angle : 0.759 91.524 235431 Z= 0.396 Chirality : 0.036 0.466 29944 Planarity : 0.007 0.210 12569 Dihedral : 23.518 179.528 78763 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.37 % Allowed : 29.29 % Favored : 66.34 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % Twisted General : 0.04 % 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: -0.18 (0.11), residues: 5651 helix: 0.91 (0.12), residues: 1969 sheet: -0.46 (0.15), residues: 1092 loop : -0.69 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 11 HIS 0.006 0.001 HIS j 58 PHE 0.030 0.002 PHE Z 64 TYR 0.039 0.002 TYR f 213 ARG 0.039 0.001 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1669 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 1464 time to evaluate : 6.784 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: C 264 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.7304 (m-30) REVERT: G 22 GLN cc_start: 0.8605 (mm110) cc_final: 0.8306 (mm-40) REVERT: G 153 ARG cc_start: 0.7523 (OUTLIER) cc_final: 0.7232 (mtp85) REVERT: H 112 LYS cc_start: 0.5593 (pttt) cc_final: 0.5286 (pttt) REVERT: H 122 LEU cc_start: 0.7969 (OUTLIER) cc_final: 0.7682 (tm) REVERT: H 129 GLU cc_start: 0.7558 (pt0) cc_final: 0.6799 (tp30) REVERT: H 143 ILE cc_start: 0.7897 (OUTLIER) cc_final: 0.7614 (tp) REVERT: I 108 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8240 (mtt) REVERT: N 3 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: N 88 LYS cc_start: 0.7889 (tptp) cc_final: 0.7132 (tppt) REVERT: Q 78 ARG cc_start: 0.8229 (tpp80) cc_final: 0.8004 (tpp-160) REVERT: S 72 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6252 (mm110) REVERT: U 7 GLU cc_start: 0.6127 (pm20) cc_final: 0.5793 (pm20) REVERT: U 10 LYS cc_start: 0.7363 (OUTLIER) cc_final: 0.6884 (tmmt) REVERT: U 11 GLU cc_start: 0.6396 (pt0) cc_final: 0.6015 (pm20) REVERT: U 41 GLU cc_start: 0.6568 (pp20) cc_final: 0.6362 (pp20) REVERT: V 37 ILE cc_start: 0.8623 (mp) cc_final: 0.8404 (mp) REVERT: d 54 ASP cc_start: 0.5916 (OUTLIER) cc_final: 0.5660 (p0) REVERT: e 24 ARG cc_start: 0.8578 (OUTLIER) cc_final: 0.7136 (mtp180) REVERT: e 36 ARG cc_start: 0.8121 (tmm160) cc_final: 0.7681 (ttm170) REVERT: h 36 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: i 61 GLN cc_start: 0.7401 (tp-100) cc_final: 0.7180 (tp-100) REVERT: l 111 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.7756 (ptp) REVERT: n 14 ASP cc_start: 0.7753 (t0) cc_final: 0.7497 (t0) REVERT: r 39 GLU cc_start: 0.7357 (tp30) cc_final: 0.7145 (tp30) REVERT: s 73 LYS cc_start: 0.8003 (OUTLIER) cc_final: 0.7703 (ttmm) REVERT: s 89 ARG cc_start: 0.6597 (ttp-170) cc_final: 0.6337 (ttp-170) REVERT: t 9 HIS cc_start: 0.7587 (m90) cc_final: 0.7278 (m90) REVERT: t 35 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7823 (tmm-80) outliers start: 205 outliers final: 128 residues processed: 1554 average time/residue: 1.9488 time to fit residues: 4458.0269 Evaluate side-chains 1527 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1385 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 2 ARG Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 3 LYS Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 36 GLN Chi-restraints excluded: chain h residue 50 ASP Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 96 MET Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 SER Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 146 GLU Chi-restraints excluded: chain k residue 148 ASN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 111 MET Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 53 GLU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 27 GLU Chi-restraints excluded: chain n residue 42 LEU Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain t residue 55 ASP Chi-restraints excluded: chain u residue 14 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 54 MET Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 604 optimal weight: 20.0000 chunk 390 optimal weight: 30.0000 chunk 583 optimal weight: 5.9990 chunk 294 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 189 optimal weight: 10.0000 chunk 621 optimal weight: 5.9990 chunk 665 optimal weight: 10.0000 chunk 483 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 768 optimal weight: 9.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN E 195 GLN F 27 GLN F 81 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 HIS G 128 GLN H 33 GLN I 67 ASN J 89 ASN N 38 GLN P 59 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** i 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 118 GLN m 50 GLN p 5 ASN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN s 62 GLN t 26 ASN v 54 GLN x 70 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.361 157324 Z= 0.374 Angle : 0.780 91.570 235431 Z= 0.406 Chirality : 0.038 0.448 29944 Planarity : 0.007 0.133 12569 Dihedral : 23.486 179.077 78763 Min Nonbonded Distance : 1.256 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 4.86 % Allowed : 29.46 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.20 (0.11), residues: 5651 helix: 0.90 (0.12), residues: 1963 sheet: -0.45 (0.15), residues: 1115 loop : -0.72 (0.12), residues: 2573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 11 HIS 0.007 0.001 HIS j 3 PHE 0.031 0.002 PHE Z 64 TYR 0.046 0.002 TYR f 213 ARG 0.014 0.001 ARG G 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1653 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 1425 time to evaluate : 6.769 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: C 264 ASP cc_start: 0.7556 (OUTLIER) cc_final: 0.7313 (m-30) REVERT: E 136 GLN cc_start: 0.7242 (tp40) cc_final: 0.7035 (tp40) REVERT: G 22 GLN cc_start: 0.8583 (mm110) cc_final: 0.8300 (mm-40) REVERT: G 153 ARG cc_start: 0.7549 (OUTLIER) cc_final: 0.7263 (mtp85) REVERT: H 112 LYS cc_start: 0.6339 (pttt) cc_final: 0.6047 (pttt) REVERT: H 122 LEU cc_start: 0.8050 (OUTLIER) cc_final: 0.7772 (tm) REVERT: H 129 GLU cc_start: 0.7580 (pt0) cc_final: 0.6868 (tp30) REVERT: H 143 ILE cc_start: 0.7876 (OUTLIER) cc_final: 0.7622 (tp) REVERT: I 108 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8252 (mtt) REVERT: J 7 MET cc_start: 0.8023 (mmm) cc_final: 0.7764 (mmp) REVERT: L 75 GLU cc_start: 0.6946 (pm20) cc_final: 0.6597 (pm20) REVERT: N 17 LYS cc_start: 0.8822 (tppp) cc_final: 0.8508 (tppp) REVERT: N 112 GLU cc_start: 0.7314 (pp20) cc_final: 0.6992 (pp20) REVERT: O 112 GLU cc_start: 0.7172 (tm-30) cc_final: 0.6971 (tp30) REVERT: Q 78 ARG cc_start: 0.8254 (tpp80) cc_final: 0.8030 (tpp-160) REVERT: S 72 GLN cc_start: 0.6656 (OUTLIER) cc_final: 0.6287 (mm110) REVERT: U 10 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6937 (tmmt) REVERT: U 11 GLU cc_start: 0.6438 (pt0) cc_final: 0.6070 (pm20) REVERT: d 54 ASP cc_start: 0.5950 (OUTLIER) cc_final: 0.5694 (p0) REVERT: e 24 ARG cc_start: 0.8591 (OUTLIER) cc_final: 0.7022 (mtp180) REVERT: e 36 ARG cc_start: 0.8135 (tmm160) cc_final: 0.7687 (ttm170) REVERT: h 36 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7405 (tt0) REVERT: l 111 MET cc_start: 0.7979 (OUTLIER) cc_final: 0.7729 (ptp) REVERT: l 126 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8452 (mp) REVERT: m 48 VAL cc_start: 0.8925 (m) cc_final: 0.8605 (t) REVERT: n 64 GLN cc_start: 0.7993 (mt0) cc_final: 0.7562 (mt0) REVERT: r 39 GLU cc_start: 0.7447 (tp30) cc_final: 0.7233 (tp30) REVERT: s 73 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7768 (ttmm) REVERT: t 35 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7846 (tmm-80) REVERT: v 16 GLU cc_start: 0.7141 (OUTLIER) cc_final: 0.6653 (pp20) outliers start: 228 outliers final: 139 residues processed: 1527 average time/residue: 1.9567 time to fit residues: 4407.9322 Evaluate side-chains 1517 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1363 time to evaluate : 6.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 151 THR Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain I residue 131 ASN Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 127 LYS Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 2 ARG Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 103 VAL Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain O residue 110 ILE Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 4 ILE Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 2 SER Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain b residue 42 VAL Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 33 LEU Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 36 GLN Chi-restraints excluded: chain h residue 50 ASP Chi-restraints excluded: chain h residue 99 ASP Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 96 MET Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 62 MET Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 SER Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain k residue 148 ASN Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 111 MET Chi-restraints excluded: chain l residue 126 ILE Chi-restraints excluded: chain m residue 14 SER Chi-restraints excluded: chain m residue 53 GLU Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 16 VAL Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 87 LYS Chi-restraints excluded: chain p residue 18 LYS Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 64 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain t residue 55 ASP Chi-restraints excluded: chain u residue 14 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 57 ASP Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 889 optimal weight: 10.0000 chunk 936 optimal weight: 5.9990 chunk 854 optimal weight: 8.9990 chunk 910 optimal weight: 5.9990 chunk 548 optimal weight: 1.9990 chunk 396 optimal weight: 10.0000 chunk 715 optimal weight: 6.9990 chunk 279 optimal weight: 20.0000 chunk 822 optimal weight: 0.9980 chunk 861 optimal weight: 10.0000 chunk 907 optimal weight: 9.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN F 81 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN H 33 GLN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 89 ASN N 38 GLN Q 86 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 ASN V 76 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** i 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 67 GLN l 118 GLN m 50 GLN m 126 GLN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 49 GLN r 66 GLN s 62 GLN t 26 ASN v 54 GLN x 70 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.363 157324 Z= 0.262 Angle : 0.760 91.578 235431 Z= 0.397 Chirality : 0.035 0.471 29944 Planarity : 0.007 0.142 12569 Dihedral : 23.514 179.743 78763 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.56 % Allowed : 31.38 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.08 % 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: -0.14 (0.11), residues: 5651 helix: 0.91 (0.12), residues: 1965 sheet: -0.41 (0.15), residues: 1099 loop : -0.65 (0.12), residues: 2587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 11 HIS 0.008 0.001 HIS j 58 PHE 0.030 0.002 PHE Z 64 TYR 0.046 0.002 TYR f 213 ARG 0.018 0.001 ARG R 95 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1625 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1458 time to evaluate : 6.725 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: C 264 ASP cc_start: 0.7497 (OUTLIER) cc_final: 0.7241 (m-30) REVERT: E 136 GLN cc_start: 0.7165 (tp40) cc_final: 0.6944 (tp40) REVERT: G 22 GLN cc_start: 0.8511 (mm110) cc_final: 0.8233 (mm-40) REVERT: G 153 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.7238 (mtp85) REVERT: H 112 LYS cc_start: 0.6314 (pttt) cc_final: 0.6053 (pttt) REVERT: H 122 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7725 (tm) REVERT: H 129 GLU cc_start: 0.7480 (pt0) cc_final: 0.6870 (tp30) REVERT: H 143 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7545 (tp) REVERT: I 108 MET cc_start: 0.8741 (OUTLIER) cc_final: 0.8192 (mtt) REVERT: J 7 MET cc_start: 0.7975 (mmm) cc_final: 0.7689 (mmp) REVERT: R 1 MET cc_start: 0.5512 (ptt) cc_final: 0.5130 (ttp) REVERT: S 72 GLN cc_start: 0.6427 (OUTLIER) cc_final: 0.6051 (mm110) REVERT: U 7 GLU cc_start: 0.6133 (pm20) cc_final: 0.5861 (pm20) REVERT: U 10 LYS cc_start: 0.7415 (OUTLIER) cc_final: 0.6920 (tmmt) REVERT: U 11 GLU cc_start: 0.6388 (pt0) cc_final: 0.6032 (pm20) REVERT: V 37 ILE cc_start: 0.8510 (mp) cc_final: 0.8242 (mp) REVERT: d 54 ASP cc_start: 0.5888 (OUTLIER) cc_final: 0.5636 (p0) REVERT: e 24 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.6920 (mtp180) REVERT: e 36 ARG cc_start: 0.8025 (tmm160) cc_final: 0.7416 (ttp80) REVERT: f 74 ARG cc_start: 0.7116 (tmm160) cc_final: 0.6915 (ttp80) REVERT: h 36 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7387 (tt0) REVERT: i 61 GLN cc_start: 0.7395 (tp-100) cc_final: 0.7064 (tp40) REVERT: j 5 GLU cc_start: 0.7342 (tp30) cc_final: 0.7057 (tp30) REVERT: l 88 ARG cc_start: 0.7779 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: l 111 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7724 (ptp) REVERT: m 48 VAL cc_start: 0.8851 (m) cc_final: 0.8543 (t) REVERT: s 73 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7729 (ttmm) REVERT: t 35 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7829 (tmm-80) REVERT: v 16 GLU cc_start: 0.7161 (OUTLIER) cc_final: 0.6655 (pp20) REVERT: w 10 PHE cc_start: 0.8105 (t80) cc_final: 0.7858 (t80) outliers start: 167 outliers final: 114 residues processed: 1535 average time/residue: 1.9412 time to fit residues: 4420.9545 Evaluate side-chains 1514 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 1386 time to evaluate : 6.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 118 SER Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain D residue 202 ILE Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain G residue 166 ASP Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 1 MET Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 40 ARG Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 2 ARG Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain P residue 102 ASP Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 101 ILE Chi-restraints excluded: chain R residue 51 LEU Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain T residue 68 SER Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain b residue 35 GLU Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 36 GLN Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 96 MET Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 16 GLU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 87 SER Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 111 MET Chi-restraints excluded: chain l residue 118 GLN Chi-restraints excluded: chain m residue 53 GLU Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 19 LEU Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain t residue 55 ASP Chi-restraints excluded: chain u residue 14 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 65 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain y residue 13 ASP Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 598 optimal weight: 7.9990 chunk 963 optimal weight: 5.9990 chunk 587 optimal weight: 4.9990 chunk 456 optimal weight: 0.7980 chunk 669 optimal weight: 0.3980 chunk 1010 optimal weight: 10.0000 chunk 929 optimal weight: 10.0000 chunk 804 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 621 optimal weight: 5.9990 chunk 493 optimal weight: 7.9990 overall best weight: 3.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 130 GLN ** D 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 195 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 GLN H 33 GLN ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN J 89 ASN N 38 GLN P 59 GLN Q 86 GLN R 15 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 170 HIS ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** i 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 118 GLN ** o 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 75 GLN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN s 20 ASN s 62 GLN t 26 ASN v 54 GLN x 70 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.364 157324 Z= 0.241 Angle : 0.762 91.580 235431 Z= 0.398 Chirality : 0.035 0.478 29944 Planarity : 0.007 0.126 12569 Dihedral : 23.483 179.721 78763 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.46 % Allowed : 31.98 % Favored : 64.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: -0.16 (0.11), residues: 5651 helix: 0.86 (0.12), residues: 1965 sheet: -0.40 (0.15), residues: 1088 loop : -0.64 (0.12), residues: 2598 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP B 11 HIS 0.007 0.001 HIS j 3 PHE 0.032 0.002 PHE Z 64 TYR 0.045 0.002 TYR f 213 ARG 0.017 0.001 ARG G 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11302 Ramachandran restraints generated. 5651 Oldfield, 0 Emsley, 5651 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1600 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1438 time to evaluate : 6.654 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: C 264 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.7261 (m-30) REVERT: E 1 MET cc_start: 0.6260 (ptp) cc_final: 0.5998 (ptt) REVERT: E 136 GLN cc_start: 0.7144 (tp40) cc_final: 0.6910 (tp40) REVERT: G 22 GLN cc_start: 0.8459 (mm110) cc_final: 0.8162 (mm-40) REVERT: G 153 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7246 (mtp85) REVERT: H 112 LYS cc_start: 0.6305 (pttt) cc_final: 0.6075 (pttt) REVERT: H 122 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7701 (tm) REVERT: H 129 GLU cc_start: 0.7457 (pt0) cc_final: 0.6780 (tp30) REVERT: H 143 ILE cc_start: 0.7827 (OUTLIER) cc_final: 0.7523 (tp) REVERT: I 108 MET cc_start: 0.8734 (OUTLIER) cc_final: 0.8173 (mtt) REVERT: J 7 MET cc_start: 0.7965 (mmm) cc_final: 0.7674 (mmp) REVERT: L 75 GLU cc_start: 0.7053 (pm20) cc_final: 0.6836 (pm20) REVERT: N 112 GLU cc_start: 0.7420 (pp20) cc_final: 0.6921 (pp20) REVERT: R 1 MET cc_start: 0.5588 (ptt) cc_final: 0.5173 (ttp) REVERT: S 72 GLN cc_start: 0.6281 (OUTLIER) cc_final: 0.5960 (mm110) REVERT: U 10 LYS cc_start: 0.7310 (OUTLIER) cc_final: 0.6809 (tmmt) REVERT: U 11 GLU cc_start: 0.6338 (pt0) cc_final: 0.5978 (pm20) REVERT: d 54 ASP cc_start: 0.5810 (OUTLIER) cc_final: 0.5596 (p0) REVERT: e 24 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.6925 (mtp180) REVERT: e 36 ARG cc_start: 0.7989 (tmm160) cc_final: 0.7356 (ttt-90) REVERT: h 36 GLN cc_start: 0.7617 (OUTLIER) cc_final: 0.7400 (tt0) REVERT: j 1 MET cc_start: 0.4483 (ptt) cc_final: 0.3583 (ppp) REVERT: m 48 VAL cc_start: 0.8765 (m) cc_final: 0.8496 (t) REVERT: o 72 ASP cc_start: 0.7455 (t0) cc_final: 0.7031 (t0) REVERT: s 73 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7676 (ttmm) REVERT: t 35 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7827 (tmm-80) REVERT: v 16 GLU cc_start: 0.7194 (OUTLIER) cc_final: 0.6693 (pp20) REVERT: w 10 PHE cc_start: 0.8213 (t80) cc_final: 0.7887 (t80) outliers start: 162 outliers final: 105 residues processed: 1510 average time/residue: 1.9428 time to fit residues: 4334.3896 Evaluate side-chains 1499 residues out of total 4700 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 1381 time to evaluate : 6.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 72 SER Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain G residue 153 ARG Chi-restraints excluded: chain H residue 40 THR Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 143 ILE Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 108 MET Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 89 ASN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain K residue 103 ILE Chi-restraints excluded: chain K residue 111 ILE Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 5 LYS Chi-restraints excluded: chain L residue 7 THR Chi-restraints excluded: chain L residue 42 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 132 THR Chi-restraints excluded: chain M residue 2 ARG Chi-restraints excluded: chain M residue 6 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 48 LEU Chi-restraints excluded: chain N residue 69 ASP Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 60 THR Chi-restraints excluded: chain O residue 83 SER Chi-restraints excluded: chain O residue 104 THR Chi-restraints excluded: chain P residue 4 VAL Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 101 SER Chi-restraints excluded: chain S residue 25 GLU Chi-restraints excluded: chain S residue 72 GLN Chi-restraints excluded: chain S residue 78 SER Chi-restraints excluded: chain T residue 28 VAL Chi-restraints excluded: chain U residue 10 LYS Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain W residue 25 THR Chi-restraints excluded: chain W residue 48 THR Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain Y residue 9 GLN Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 58 ASP Chi-restraints excluded: chain Z residue 59 ARG Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain c residue 8 SER Chi-restraints excluded: chain c residue 44 VAL Chi-restraints excluded: chain d residue 4 ILE Chi-restraints excluded: chain d residue 29 LEU Chi-restraints excluded: chain d residue 54 ASP Chi-restraints excluded: chain e residue 16 ILE Chi-restraints excluded: chain e residue 17 VAL Chi-restraints excluded: chain e residue 24 ARG Chi-restraints excluded: chain f residue 123 ASP Chi-restraints excluded: chain f residue 184 PHE Chi-restraints excluded: chain f residue 223 GLU Chi-restraints excluded: chain f residue 226 SER Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 41 GLN Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 63 SER Chi-restraints excluded: chain g residue 121 THR Chi-restraints excluded: chain h residue 36 GLN Chi-restraints excluded: chain h residue 151 LYS Chi-restraints excluded: chain h residue 205 SER Chi-restraints excluded: chain i residue 22 SER Chi-restraints excluded: chain i residue 144 LEU Chi-restraints excluded: chain j residue 87 SER Chi-restraints excluded: chain k residue 49 THR Chi-restraints excluded: chain k residue 80 VAL Chi-restraints excluded: chain k residue 113 ASP Chi-restraints excluded: chain k residue 135 VAL Chi-restraints excluded: chain l residue 58 GLU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 53 GLU Chi-restraints excluded: chain n residue 96 VAL Chi-restraints excluded: chain o residue 111 THR Chi-restraints excluded: chain p residue 35 THR Chi-restraints excluded: chain p residue 41 THR Chi-restraints excluded: chain p residue 105 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 68 ASP Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 48 LEU Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 20 ASN Chi-restraints excluded: chain s residue 73 LYS Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 35 ARG Chi-restraints excluded: chain t residue 55 ASP Chi-restraints excluded: chain u residue 14 SER Chi-restraints excluded: chain u residue 29 VAL Chi-restraints excluded: chain v residue 14 THR Chi-restraints excluded: chain v residue 16 GLU Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 60 VAL Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain B residue 6 THR Chi-restraints excluded: chain B residue 22 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1014 random chunks: chunk 638 optimal weight: 4.9990 chunk 856 optimal weight: 7.9990 chunk 246 optimal weight: 10.0000 chunk 741 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 223 optimal weight: 10.0000 chunk 805 optimal weight: 0.7980 chunk 337 optimal weight: 20.0000 chunk 827 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 148 optimal weight: 20.0000 overall best weight: 6.3590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN E 195 GLN ** G 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 128 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 67 ASN L 3 GLN N 19 GLN N 38 GLN P 59 GLN Q 86 GLN R 15 GLN ** R 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 76 ASN X 20 ASN ** X 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 20 ASN a 6 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 196 ASN ** i 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** j 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 118 GLN ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 66 GLN s 62 GLN t 26 ASN v 54 GLN ** x 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.050027 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.040390 restraints weight = 733448.932| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 1.44 r_work: 0.2594 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2499 r_free = 0.2499 target_work(ls_wunit_k1) = 0.035 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.361 157324 Z= 0.335 Angle : 0.782 91.591 235431 Z= 0.407 Chirality : 0.037 0.445 29944 Planarity : 0.007 0.131 12569 Dihedral : 23.436 179.891 78762 Min Nonbonded Distance : 1.257 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.28 % Allowed : 32.21 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.54 % 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: -0.20 (0.11), residues: 5651 helix: 0.83 (0.12), residues: 1965 sheet: -0.43 (0.15), residues: 1108 loop : -0.66 (0.12), residues: 2578 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP B 11 HIS 0.007 0.001 HIS j 3 PHE 0.058 0.002 PHE Z 64 TYR 0.043 0.002 TYR f 213 ARG 0.014 0.001 ARG H 51 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 61373.31 seconds wall clock time: 1059 minutes 4.72 seconds (63544.72 seconds total)