Starting phenix.real_space_refine on Tue Apr 16 23:17:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ot5_13055/04_2024/7ot5_13055_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4648 5.49 5 Mg 394 5.21 5 S 149 5.16 5 C 72827 2.51 5 N 27011 2.21 5 O 40334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 52": "NH1" <-> "NH2" Residue "C ARG 63": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 167": "NH1" <-> "NH2" Residue "C ARG 177": "NH1" <-> "NH2" Residue "C ARG 182": "NH1" <-> "NH2" Residue "C ARG 212": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "D ARG 13": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 59": "NH1" <-> "NH2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D ARG 169": "NH1" <-> "NH2" Residue "D ARG 184": "NH1" <-> "NH2" Residue "E ARG 21": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 162": "NH1" <-> "NH2" Residue "E ARG 170": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 71": "NH1" <-> "NH2" Residue "F ARG 92": "NH1" <-> "NH2" Residue "F ARG 102": "NH1" <-> "NH2" Residue "F ARG 110": "NH1" <-> "NH2" Residue "F ARG 112": "NH1" <-> "NH2" Residue "F ARG 115": "NH1" <-> "NH2" Residue "F ARG 148": "NH1" <-> "NH2" Residue "G ARG 3": "NH1" <-> "NH2" Residue "G ARG 152": "NH1" <-> "NH2" Residue "G ARG 153": "NH1" <-> "NH2" Residue "G ARG 163": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "H ARG 50": "NH1" <-> "NH2" Residue "H ARG 51": "NH1" <-> "NH2" Residue "H GLU 55": "OE1" <-> "OE2" Residue "H ARG 68": "NH1" <-> "NH2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 127": "OE1" <-> "OE2" Residue "H GLU 137": "OE1" <-> "OE2" 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 GLU 4": "OE1" <-> "OE2" Residue "J ARG 17": "NH1" <-> "NH2" Residue "J ARG 18": "NH1" <-> "NH2" Residue "K ARG 21": "NH1" <-> "NH2" Residue "K ARG 33": "NH1" <-> "NH2" Residue "K ARG 41": "NH1" <-> "NH2" Residue "K ARG 47": "NH1" <-> "NH2" Residue "K TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 ARG 114": "NH1" <-> "NH2" Residue "M ARG 8": "NH1" <-> "NH2" Residue "M ARG 12": "NH1" <-> "NH2" Residue "M ARG 17": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "M ARG 46": "NH1" <-> "NH2" Residue "M ARG 63": "NH1" <-> "NH2" Residue "M ARG 64": "NH1" <-> "NH2" Residue "M ARG 69": "NH1" <-> "NH2" Residue "M ARG 96": "NH1" <-> "NH2" Residue "M ARG 118": "NH1" <-> "NH2" Residue "N ARG 10": "NH1" <-> "NH2" Residue "N ARG 13": "NH1" <-> "NH2" Residue "N ARG 16": "NH1" <-> "NH2" Residue "N ARG 25": "NH1" <-> "NH2" Residue "N ARG 81": "NH1" <-> "NH2" Residue "N ARG 94": "NH1" <-> "NH2" Residue "N ARG 102": "NH1" <-> "NH2" Residue "N ARG 111": "NH1" <-> "NH2" Residue "O ARG 21": "NH1" <-> "NH2" Residue "O ARG 62": "NH1" <-> "NH2" Residue "O ARG 89": "NH1" <-> "NH2" Residue "O ARG 101": "NH1" <-> "NH2" Residue "O ARG 109": "NH1" <-> "NH2" Residue "P ARG 3": "NH1" <-> "NH2" Residue "P ARG 6": "NH1" <-> "NH2" Residue "P ARG 13": "NH1" <-> "NH2" Residue "P ARG 33": "NH1" <-> "NH2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 70": "NH1" <-> "NH2" Residue "Q ARG 21": "NH1" <-> "NH2" Residue "Q ARG 68": "NH1" <-> "NH2" Residue "Q ARG 78": "NH1" <-> "NH2" Residue "Q ARG 79": "NH1" <-> "NH2" Residue "Q ARG 84": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "R ARG 88": "NH1" <-> "NH2" Residue "R ARG 92": "NH1" <-> "NH2" Residue "R ARG 110": "NH1" <-> "NH2" Residue "S ARG 3": "NH1" <-> "NH2" Residue "S ARG 6": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T ARG 82": "NH1" <-> "NH2" Residue "T ARG 86": "NH1" <-> "NH2" Residue "T ARG 94": "NH1" <-> "NH2" Residue "U ARG 19": "NH1" <-> "NH2" Residue "W ARG 3": "NH1" <-> "NH2" Residue "W ARG 18": "NH1" <-> "NH2" Residue "W ARG 37": "NH1" <-> "NH2" Residue "W ARG 45": "NH1" <-> "NH2" Residue "W ARG 50": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "X ARG 29": "NH1" <-> "NH2" Residue "X ARG 47": "NH1" <-> "NH2" Residue "X ARG 52": "NH1" <-> "NH2" Residue "Y ARG 11": "NH1" <-> "NH2" Residue "Y ARG 30": "NH1" <-> "NH2" Residue "Y ARG 45": "NH1" <-> "NH2" Residue "Z ARG 56": "NH1" <-> "NH2" Residue "Z ARG 63": "NH1" <-> "NH2" Residue "a ARG 10": "NH1" <-> "NH2" Residue "a ARG 16": "NH1" <-> "NH2" Residue "a ARG 52": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 44": "NH1" <-> "NH2" Residue "c ARG 3": "NH1" <-> "NH2" Residue "c ARG 14": "NH1" <-> "NH2" Residue "c ARG 19": "NH1" <-> "NH2" Residue "c ARG 21": "NH1" <-> "NH2" Residue "c ARG 33": "NH1" <-> "NH2" Residue "c ARG 41": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 30": "NH1" <-> "NH2" Residue "d ARG 40": "NH1" <-> "NH2" Residue "d ARG 42": "NH1" <-> "NH2" Residue "e ARG 24": "NH1" <-> "NH2" Residue "f ARG 63": "NH1" <-> "NH2" Residue "f ARG 74": "NH1" <-> "NH2" Residue "f ARG 208": "NH1" <-> "NH2" Residue "f ARG 225": "NH1" <-> "NH2" Residue "g ARG 54": "NH1" <-> "NH2" Residue "g ARG 72": "NH1" <-> "NH2" Residue "g ARG 88": "NH1" <-> "NH2" Residue "g ARG 127": "NH1" <-> "NH2" Residue "g ARG 131": "NH1" <-> "NH2" Residue "g ARG 132": "NH1" <-> "NH2" Residue "g ARG 164": "NH1" <-> "NH2" Residue "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 ARG 157": "NH1" <-> "NH2" Residue "j PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 4": "NH1" <-> "NH2" Residue "k GLU 48": "OE1" <-> "OE2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "k ARG 78": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ARG 92": "NH1" <-> "NH2" Residue "m ARG 11": "NH1" <-> "NH2" Residue "m ARG 41": "NH1" <-> "NH2" Residue "m ARG 130": "NH1" <-> "NH2" Residue "n ARG 5": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 89": "NH1" <-> "NH2" Residue "o ARG 37": "NH1" <-> "NH2" Residue "o ARG 69": "NH1" <-> "NH2" Residue "o ARG 93": "NH1" <-> "NH2" Residue "o ARG 106": "NH1" <-> "NH2" Residue "p ARG 9": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 50": "NH1" <-> "NH2" Residue "p 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 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" Residue "B GLU 56": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 145365 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': 289, 'rna2p_pyr': 166, 'rna3p': 16, 'rna3p_pur': 1378, 'rna3p_pyr': 1048} Link IDs: {'rna2p': 460, 'rna3p': 2442} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 206, 'rna3p': 1327} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "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: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 610 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} 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': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p': 11, 'rna3p_pur': 35, 'rna3p_pyr': 25} Link IDs: {'rna2p': 13, 'rna3p': 71} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 12 Chain: "B" Number of atoms: 496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 496 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "1" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 261 Unusual residues: {' MG': 261} Classifications: {'undetermined': 261} Link IDs: {None: 260} Chain: "2" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 113 Unusual residues: {' MG': 113} Classifications: {'undetermined': 113} Link IDs: {None: 112} 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" 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: "z" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0G8Q SG CYS Z 16 64.839 59.292 105.180 1.00 87.76 S ATOM A0G92 SG CYS Z 18 62.833 57.937 101.831 1.00 91.18 S ATOM A0GD0 SG CYS Z 37 65.671 58.210 101.367 1.00 86.64 S ATOM A0GDL SG CYS Z 40 64.165 61.255 101.770 1.00 88.44 S ATOM A0HYM SG CYS e 11 143.084 115.729 48.092 1.00 52.56 S ATOM A0HZB SG CYS e 14 145.794 113.950 49.479 1.00 51.38 S ATOM A0I26 SG CYS e 27 145.657 117.900 47.859 1.00 53.06 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb="MG MG 13141 " occ=0.50 Time building chain proxies: 56.32, per 1000 atoms: 0.39 Number of scatterers: 145365 At special positions: 0 Unit cell: (276.06, 266.43, 230.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 149 16.00 P 4648 15.00 Mg 394 11.99 O 40334 8.00 N 27011 7.00 C 72827 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 59.02 Conformation dependent library (CDL) restraints added in 6.6 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 40 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 16 " pdb="ZN ZN Z 101 " - pdb=" SG CYS Z 18 " pdb=" ZN e 101 " pdb="ZN ZN e 101 " - pdb=" ND1 HIS e 33 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 11 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 27 " pdb="ZN ZN e 101 " - pdb=" SG CYS e 14 " Number of angles added : 9 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10606 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: 177 helices and 74 sheets defined 39.3% alpha, 19.3% beta 1586 base pairs and 2647 stacking pairs defined. Time for finding SS restraints: 74.89 Creating SS restraints... Processing helix chain 'C' and resid 10 through 16 removed outlier: 7.497A pdb=" N HIS C 15 " --> pdb=" O PRO C 11 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N VAL C 16 " --> pdb=" O GLY C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 removed outlier: 3.818A pdb=" N LEU C 34 " --> pdb=" O PHE C 30 " (cutoff:3.500A) removed outlier: 5.666A 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: 4.034A pdb=" N ALA C 211 " --> pdb=" O LYS C 207 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ARG C 214 " --> pdb=" O ALA C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 226 removed outlier: 4.442A pdb=" N MET C 225 " --> pdb=" O ARG C 221 " (cutoff:3.500A) removed outlier: 5.412A 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: 4.024A pdb=" N ASP C 264 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N LYS C 265 " --> pdb=" O LYS C 261 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 5.557A 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: 6.006A pdb=" N THR D 61 " --> pdb=" O ALA D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 72 removed outlier: 3.737A pdb=" N ALA D 71 " --> pdb=" O HIS D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 98 through 103 removed outlier: 4.043A pdb=" N ALA D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) removed outlier: 5.070A 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: 3.668A pdb=" N ARG E 40 " --> pdb=" O ALA E 36 " (cutoff:3.500A) removed outlier: 5.691A pdb=" N GLN E 41 " --> pdb=" O ALA E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 53 removed outlier: 6.530A 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: 4.555A pdb=" N ASN E 163 " --> pdb=" O LEU E 159 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 184 removed outlier: 6.375A 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: 5.260A pdb=" N VAL F 13 " --> pdb=" O LYS F 9 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N LYS F 14 " --> pdb=" O ASP F 10 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 47 removed outlier: 3.958A pdb=" N ASP F 46 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.850A 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: 3.835A pdb=" N GLY F 62 " --> pdb=" O ALA F 58 " (cutoff:3.500A) Processing helix chain 'F' and resid 93 through 111 removed outlier: 5.477A 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: 5.510A pdb=" N ASP F 147 " --> pdb=" O TYR F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 174 removed outlier: 4.495A pdb=" N GLY F 166 " --> pdb=" O SER F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 134 through 139 removed outlier: 3.745A 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: 3.927A 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: 3.661A pdb=" N TYR G 151 " --> pdb=" O ASP G 147 " (cutoff:3.500A) removed outlier: 4.502A 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: 4.567A pdb=" N ALA H 49 " --> pdb=" O GLU H 45 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N ARG H 50 " --> pdb=" O PHE H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 51 through 74 removed outlier: 4.597A pdb=" N ALA H 56 " --> pdb=" O ALA H 52 " (cutoff:3.500A) removed outlier: 4.285A 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: 4.150A 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: 4.458A 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: 3.848A pdb=" N LYS I 121 " --> pdb=" O ALA I 117 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU I 122 " --> pdb=" O MET I 118 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS I 123 " --> pdb=" O PHE I 119 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 4.498A pdb=" N LYS I 72 " --> pdb=" O ASN I 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 67 through 72' Processing helix chain 'J' and resid 112 through 119 Processing helix chain 'K' and resid 37 through 42 removed outlier: 4.159A pdb=" N ARG K 41 " --> pdb=" O GLY K 37 " (cutoff:3.500A) removed outlier: 5.645A 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: 4.054A pdb=" N ALA K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE K 73 " --> pdb=" O ARG K 69 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ALA K 75 " --> pdb=" O ALA K 71 " (cutoff:3.500A) Processing helix chain 'K' and resid 78 through 85 removed outlier: 4.033A pdb=" N LEU K 82 " --> pdb=" O ARG K 78 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LYS K 84 " --> pdb=" O SER K 80 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 78 through 85' Processing helix chain 'K' and resid 91 through 99 Processing helix chain 'K' and resid 128 through 139 Processing helix chain 'L' and resid 42 through 58 Processing helix chain 'L' and resid 109 through 125 removed outlier: 4.025A pdb=" N LYS L 123 " --> pdb=" O LEU L 119 " (cutoff:3.500A) removed outlier: 3.615A 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: 4.296A pdb=" N ARG M 46 " --> pdb=" O LYS M 42 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL M 47 " --> pdb=" O GLU M 43 " (cutoff:3.500A) Proline residue: M 50 - end of helix removed outlier: 4.559A 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: 3.735A pdb=" N LEU M 83 " --> pdb=" O LEU M 79 " (cutoff:3.500A) removed outlier: 4.846A 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: 4.541A pdb=" N ARG N 13 " --> pdb=" O ARG N 9 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N ALA N 14 " --> pdb=" O ARG N 10 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG N 16 " --> pdb=" O THR N 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 63 removed outlier: 4.897A pdb=" N GLN N 61 " --> pdb=" O ALA N 57 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LEU N 62 " --> pdb=" O ILE N 58 " (cutoff:3.500A) removed outlier: 5.333A 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: 3.655A pdb=" N GLU O 11 " --> pdb=" O GLN O 7 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLN O 12 " --> pdb=" O LEU O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 104 removed outlier: 3.951A pdb=" N ARG O 103 " --> pdb=" O TYR O 99 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N THR O 104 " --> pdb=" O LEU O 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 104' Processing helix chain 'P' and resid 6 through 22 removed outlier: 3.769A pdb=" N ILE P 17 " --> pdb=" O ARG P 13 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN P 20 " --> pdb=" O LYS P 16 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS P 22 " --> pdb=" O LEU P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 26 through 31 removed outlier: 3.794A pdb=" N ARG P 30 " --> pdb=" O GLY P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 39 through 73 removed outlier: 3.967A pdb=" N ARG P 51 " --> pdb=" O TYR P 47 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N LYS P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 3.784A 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: 3.689A pdb=" N LEU R 19 " --> pdb=" O GLN R 15 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL R 20 " --> pdb=" O LYS R 16 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N LEU R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ILE R 24 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 3.890A 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: 3.751A pdb=" N VAL R 45 " --> pdb=" O LYS R 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 3 through 11 removed outlier: 4.438A pdb=" N LEU S 11 " --> pdb=" O LEU S 7 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 27 Processing helix chain 'S' and resid 39 through 50 Processing helix chain 'T' and resid 66 through 71 removed outlier: 3.781A pdb=" N VAL T 70 " --> pdb=" O GLN T 66 " (cutoff:3.500A) removed outlier: 5.028A 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: 3.901A pdb=" N ALA U 52 " --> pdb=" O MET U 48 " (cutoff:3.500A) removed outlier: 4.661A 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: 3.713A pdb=" N GLU X 8 " --> pdb=" O LYS X 4 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS X 9 " --> pdb=" O GLU X 5 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N SER X 10 " --> pdb=" O LEU X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 11 through 35 removed outlier: 4.205A pdb=" N GLY X 35 " --> pdb=" O GLN X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 39 through 62 removed outlier: 4.793A pdb=" N LEU X 43 " --> pdb=" O GLN X 39 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N LYS X 44 " --> pdb=" O SER X 40 " (cutoff:3.500A) removed outlier: 4.932A 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: 5.634A pdb=" N GLN Z 48 " --> pdb=" O PHE Z 44 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL Z 51 " --> pdb=" O LYS Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 55 through 65 removed outlier: 4.123A pdb=" N PHE Z 64 " --> pdb=" O PHE Z 60 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N ASN Z 65 " --> pdb=" O ASN Z 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 9 through 21 removed outlier: 4.775A pdb=" N HIS a 19 " --> pdb=" O MET a 15 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ASP a 20 " --> pdb=" O ARG a 16 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA a 21 " --> pdb=" O ARG a 17 " (cutoff:3.500A) Processing helix chain 'b' and resid 26 through 31 Proline residue: b 31 - end of helix Processing helix chain 'c' and resid 8 through 16 Processing helix chain 'c' and resid 17 through 25 removed outlier: 4.390A pdb=" N THR c 24 " --> pdb=" O ALA c 20 " (cutoff:3.500A) removed outlier: 5.424A 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: 4.636A pdb=" N LYS d 36 " --> pdb=" O ILE d 32 " (cutoff:3.500A) removed outlier: 5.849A 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: 4.667A pdb=" N GLY d 56 " --> pdb=" O LYS d 52 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU d 57 " --> pdb=" O GLY d 53 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL d 58 " --> pdb=" O ASP d 54 " (cutoff:3.500A) Proline residue: d 63 - end of helix Processing helix chain 'f' and resid 5 through 13 Processing helix chain 'f' and resid 42 through 64 Proline residue: f 48 - end of helix Processing helix chain 'f' and resid 73 through 88 removed outlier: 6.352A pdb=" N SER f 77 " --> pdb=" O LYS f 73 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N GLU f 78 " --> pdb=" O ARG f 74 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA f 79 " --> pdb=" O ALA f 75 " (cutoff:3.500A) Processing helix chain 'f' and resid 103 through 122 removed outlier: 4.389A pdb=" N GLN f 109 " --> pdb=" O LYS f 105 " (cutoff:3.500A) removed outlier: 3.901A 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: 4.240A pdb=" N VAL g 76 " --> pdb=" O ARG g 72 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 96 removed outlier: 3.709A pdb=" N VAL g 90 " --> pdb=" O LYS g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 108 through 113 removed outlier: 4.330A pdb=" N ASP g 112 " --> pdb=" O LYS g 108 " (cutoff:3.500A) removed outlier: 5.953A 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: 4.128A 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: 5.160A pdb=" N LYS h 83 " --> pdb=" O ALA h 79 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 97 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: 4.023A pdb=" N LYS h 156 " --> pdb=" O GLN h 152 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N GLU h 166 " --> pdb=" O ALA h 162 " (cutoff:3.500A) Processing helix chain 'h' and resid 187 through 192 removed outlier: 4.783A pdb=" N SER h 192 " --> pdb=" O ARG h 188 " (cutoff:3.500A) Processing helix chain 'h' and resid 196 through 206 removed outlier: 3.958A pdb=" N ILE h 200 " --> pdb=" O ASN h 196 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS h 206 " --> pdb=" O GLU h 202 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 71 removed outlier: 3.717A pdb=" N ARG i 69 " --> pdb=" O GLU i 65 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASN i 70 " --> pdb=" O LYS i 66 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N MET i 71 " --> pdb=" O ALA i 67 " (cutoff:3.500A) Processing helix chain 'i' and resid 109 through 119 removed outlier: 3.780A 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: 3.825A pdb=" N SER j 15 " --> pdb=" O HIS j 11 " (cutoff:3.500A) removed outlier: 5.511A 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 82 removed outlier: 3.600A pdb=" N ILE j 71 " --> pdb=" O PRO j 67 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASP j 82 " --> pdb=" O PHE j 78 " (cutoff:3.500A) Processing helix chain 'k' and resid 20 through 31 removed outlier: 3.618A pdb=" N ALA k 24 " --> pdb=" O SER k 20 " (cutoff:3.500A) Processing helix chain 'k' and resid 35 through 55 removed outlier: 3.764A pdb=" N ALA k 39 " --> pdb=" O LYS k 35 " (cutoff:3.500A) Processing helix chain 'k' and resid 57 through 70 removed outlier: 3.726A pdb=" N VAL k 69 " --> pdb=" O ALA k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 112 removed outlier: 6.170A 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: 3.741A pdb=" N ARG m 49 " --> pdb=" O ARG m 45 " (cutoff:3.500A) Proline residue: m 51 - end of helix removed outlier: 4.378A 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: 4.134A 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: 5.121A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 46 through 51 removed outlier: 4.238A pdb=" N GLY o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 54 through 59 removed outlier: 3.862A pdb=" N SER o 58 " --> pdb=" O GLY o 54 " (cutoff:3.500A) removed outlier: 4.686A 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: 5.086A pdb=" N ILE o 97 " --> pdb=" O ARG o 93 " (cutoff:3.500A) removed outlier: 4.372A 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: 3.775A pdb=" N TYR p 117 " --> pdb=" O ALA p 113 " (cutoff:3.500A) Processing helix chain 'q' and resid 14 through 22 removed outlier: 4.348A 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: 4.068A pdb=" N PHE q 63 " --> pdb=" O GLU q 59 " (cutoff:3.500A) removed outlier: 5.008A 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: 3.835A 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: 4.035A pdb=" N GLN r 60 " --> pdb=" O SER r 56 " (cutoff:3.500A) removed outlier: 5.680A 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: 4.651A pdb=" N GLY s 41 " --> pdb=" O ASN s 37 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N HIS s 42 " --> pdb=" O HIS s 38 " (cutoff:3.500A) Processing helix chain 's' and resid 49 through 74 removed outlier: 3.881A 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: 5.716A pdb=" N THR v 34 " --> pdb=" O LYS v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 41 through 46 removed outlier: 3.672A pdb=" N THR v 45 " --> pdb=" O PRO v 41 " (cutoff:3.500A) Processing helix chain 'v' and resid 48 through 66 removed outlier: 3.762A 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: 4.451A pdb=" N PHE w 74 " --> pdb=" O LYS w 70 " (cutoff:3.500A) removed outlier: 3.919A 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: 4.427A pdb=" N GLY w 68 " --> pdb=" O GLU w 65 " (cutoff:3.500A) removed outlier: 4.127A 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: 4.819A 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: 4.985A pdb=" N PHE y 37 " --> pdb=" O ARG y 33 " (cutoff:3.500A) Processing helix chain 'y' and resid 40 through 69 removed outlier: 3.987A pdb=" N ARG y 67 " --> pdb=" O GLU y 63 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N THR y 68 " --> pdb=" O ASN y 64 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N ARG y 69 " --> pdb=" O ALA y 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 53 Processing helix chain 'B' and resid 63 through 70 removed outlier: 4.299A pdb=" N VAL B 67 " --> pdb=" O ALA B 63 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 70 " --> pdb=" O ASN B 66 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 2 through 5 Processing sheet with id= 2, first strand: chain 'C' and resid 80 through 83 removed outlier: 6.603A pdb=" N LEU C 93 " --> pdb=" O GLU C 79 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ILE C 74 " --> pdb=" O SER C 118 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER C 118 " --> pdb=" O ILE C 74 " (cutoff:3.500A) removed outlier: 4.460A 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: 4.211A pdb=" N SER C 139 " --> pdb=" O ILE C 164 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR C 173 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 4.118A 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: 5.445A 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 6 removed outlier: 4.169A 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: 3.768A pdb=" N GLY D 10 " --> pdb=" O VAL D 26 " (cutoff:3.500A) removed outlier: 4.473A 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: 3.772A pdb=" N LEU D 40 " --> pdb=" O TYR D 45 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TYR D 45 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N GLN D 49 " --> pdb=" O THR D 35 " (cutoff:3.500A) removed outlier: 4.705A 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: 5.718A 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: 6.116A 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: 4.222A 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: 4.911A pdb=" N ILE F 85 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLY F 39 " --> pdb=" O GLY F 151 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N GLY F 151 " --> pdb=" O GLY F 39 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU F 152 " --> pdb=" O VAL F 132 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'F' and resid 72 through 75 removed outlier: 5.305A pdb=" N SER F 73 " --> pdb=" O ARG F 80 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG F 80 " --> pdb=" O SER F 73 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N ALA F 75 " --> pdb=" O LYS F 78 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'G' and resid 16 through 19 Processing sheet with id= 15, first strand: chain 'G' and resid 41 through 45 Processing sheet with id= 16, first strand: chain 'G' and resid 82 through 89 removed outlier: 5.836A pdb=" N THR G 129 " --> pdb=" O LEU G 89 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 94 through 98 Processing sheet with id= 18, first strand: chain 'H' and resid 2 through 5 removed outlier: 4.466A pdb=" N ASP H 17 " --> pdb=" O LEU H 5 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 76 through 81 Processing sheet with id= 20, first strand: chain 'H' and resid 114 through 117 removed outlier: 6.042A pdb=" N GLU H 114 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'I' and resid 52 through 57 removed outlier: 4.871A pdb=" N ASP I 19 " --> pdb=" O LEU I 140 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 74 through 78 removed outlier: 7.114A pdb=" N GLY I 83 " --> pdb=" O THR I 78 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 18 through 21 removed outlier: 4.053A pdb=" N THR J 6 " --> pdb=" O CYS J 21 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ASN J 82 " --> pdb=" O MET J 7 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 38 through 41 Processing sheet with id= 25, first strand: chain 'J' and resid 68 through 71 removed outlier: 3.787A pdb=" N SER J 75 " --> pdb=" O ARG J 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 37 through 40 No H-bonds generated for sheet with id= 26 Processing sheet with id= 27, first strand: chain 'L' and resid 62 through 65 removed outlier: 3.625A pdb=" N TYR L 103 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N LEU L 33 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS L 100 " --> pdb=" O ALA L 35 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 73 through 76 removed outlier: 6.926A pdb=" N ILE L 73 " --> pdb=" O GLU L 90 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'L' and resid 30 through 36 removed outlier: 7.915A pdb=" N SER L 30 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LYS L 127 " --> pdb=" O VAL L 36 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'M' and resid 33 through 37 removed outlier: 5.175A pdb=" N ARG M 103 " --> pdb=" O ASN M 107 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N GLY M 101 " --> pdb=" O PRO M 109 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ALA M 111 " --> pdb=" O LYS M 99 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N LYS M 99 " --> pdb=" O ALA M 111 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE M 113 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ILE M 97 " --> pdb=" O ILE M 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N LEU M 115 " --> pdb=" O THR M 95 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N THR M 95 " --> pdb=" O LEU M 115 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 49 through 52 removed outlier: 3.921A pdb=" N VAL N 49 " --> pdb=" O VAL N 39 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 38 through 45 removed outlier: 6.728A pdb=" N THR O 25 " --> pdb=" O LYS O 87 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'O' and resid 49 through 53 removed outlier: 3.811A pdb=" N ALA O 49 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG O 53 " --> pdb=" O HIS O 56 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER O 57 " --> pdb=" O THR O 76 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'Q' and resid 11 through 15 removed outlier: 6.800A pdb=" N LEU Q 39 " --> pdb=" O GLY Q 50 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN Q 43 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU Q 46 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'Q' and resid 18 through 23 removed outlier: 4.663A pdb=" N GLN Q 18 " --> pdb=" O ILE Q 98 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ASP Q 95 " --> pdb=" O VAL Q 64 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LYS Q 60 " --> pdb=" O THR Q 99 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N GLU Q 31 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 57 through 60 Processing sheet with id= 37, first strand: chain 'Q' and resid 65 through 77 removed outlier: 5.032A pdb=" N GLN Q 91 " --> pdb=" O GLY Q 69 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LYS Q 71 " --> pdb=" O HIS Q 89 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N HIS Q 89 " --> pdb=" O LYS Q 71 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS Q 73 " --> pdb=" O GLN Q 87 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN Q 87 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N VAL Q 75 " --> pdb=" O LYS Q 85 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N LYS Q 85 " --> pdb=" O VAL Q 75 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N PHE Q 77 " --> pdb=" O TYR Q 83 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TYR Q 83 " --> pdb=" O PHE Q 77 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'R' and resid 2 through 8 removed outlier: 6.876A pdb=" N VAL R 106 " --> pdb=" O THR R 72 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'R' and resid 80 through 88 removed outlier: 3.852A pdb=" N THR R 100 " --> pdb=" O PRO R 80 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET R 82 " --> pdb=" O LYS R 98 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG R 92 " --> pdb=" O ARG R 88 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'S' and resid 12 through 15 removed outlier: 5.176A pdb=" N VAL S 31 " --> pdb=" O HIS S 15 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ASN S 28 " --> pdb=" O LEU S 87 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N LYS S 81 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LYS S 66 " --> pdb=" O ARG S 77 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP S 79 " --> pdb=" O LYS S 64 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N LYS S 64 " --> pdb=" O ASP S 79 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LYS S 81 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL S 62 " --> pdb=" O LYS S 81 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ALA S 83 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N THR S 60 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL S 85 " --> pdb=" O VAL S 58 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N VAL S 58 " --> pdb=" O VAL S 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 40 through 45 removed outlier: 4.955A pdb=" N ASN T 40 " --> pdb=" O ALA T 63 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'T' and resid 83 through 86 Processing sheet with id= 43, first strand: chain 'U' and resid 69 through 72 removed outlier: 6.700A pdb=" N ALA U 39 " --> pdb=" O ARG U 9 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE U 89 " --> pdb=" O PRO U 27 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 51 through 54 removed outlier: 4.411A pdb=" N THR V 58 " --> pdb=" O GLY V 54 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 12 through 19 removed outlier: 4.531A pdb=" N ASN W 23 " --> pdb=" O SER W 19 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 35 through 41 Processing sheet with id= 47, first strand: chain 'Y' and resid 33 through 39 removed outlier: 4.117A pdb=" N HIS Y 34 " --> pdb=" O GLN Y 9 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N MET Y 54 " --> pdb=" O THR Y 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Z' and resid 20 through 25 removed outlier: 4.153A pdb=" N ASN Z 20 " --> pdb=" O CYS Z 16 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'a' and resid 29 through 32 removed outlier: 4.373A pdb=" N GLU a 36 " --> pdb=" O ASP a 31 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'b' and resid 19 through 25 removed outlier: 6.079A pdb=" N HIS b 19 " --> pdb=" O SER b 13 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE b 48 " --> pdb=" O SER b 14 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LEU b 34 " --> pdb=" O GLU b 51 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'd' and resid 22 through 25 removed outlier: 5.579A pdb=" N PHE d 22 " --> pdb=" O VAL d 50 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 89 through 93 Processing sheet with id= 53, first strand: chain 'g' and resid 53 through 59 removed outlier: 3.614A pdb=" N ARG g 54 " --> pdb=" O HIS g 69 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 164 through 169 removed outlier: 6.053A pdb=" N ARG g 164 " --> pdb=" O GLY g 155 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ASP g 181 " --> pdb=" O LYS g 204 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'h' and resid 141 through 145 removed outlier: 6.452A pdb=" N MET h 178 " --> pdb=" O ILE h 145 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'i' and resid 11 through 16 removed outlier: 7.152A pdb=" N LEU i 36 " --> pdb=" O ILE i 16 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 84 through 88 removed outlier: 3.660A pdb=" N ALA i 99 " --> pdb=" O ASN i 122 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASN i 122 " --> pdb=" O ALA i 99 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'i' and resid 33 through 41 removed outlier: 6.707A pdb=" N ARG i 45 " --> pdb=" O ASP i 41 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 38 through 43 removed outlier: 5.538A pdb=" N TYR j 59 " --> pdb=" O TRP j 42 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS j 3 " --> pdb=" O THR j 92 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 44 through 47 removed outlier: 7.246A pdb=" N HIS j 55 " --> pdb=" O LEU j 47 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 72 through 79 removed outlier: 6.087A pdb=" N THR k 72 " --> pdb=" O VAL k 91 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N TYR k 85 " --> pdb=" O ARG k 78 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 23 through 29 removed outlier: 6.894A pdb=" N ALA l 23 " --> pdb=" O LEU l 63 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASP l 48 " --> pdb=" O THR l 62 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'l' and resid 74 through 77 removed outlier: 3.642A pdb=" N CYS l 127 " --> pdb=" O VAL l 103 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL l 103 " --> pdb=" O ILE l 126 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 5 through 11 Processing sheet with id= 65, first strand: chain 'n' and resid 35 through 38 removed outlier: 7.577A pdb=" N GLN n 35 " --> pdb=" O VAL n 77 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ASP n 75 " --> pdb=" O ARG n 37 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N ARG n 5 " --> pdb=" O GLY n 103 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'n' and resid 42 through 52 removed outlier: 4.727A pdb=" N LEU n 71 " --> pdb=" O PRO n 43 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'o' and resid 42 through 45 Processing sheet with id= 68, first strand: chain 'p' and resid 29 through 33 removed outlier: 5.366A pdb=" N LEU p 81 " --> pdb=" O VAL p 98 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N HIS p 96 " --> pdb=" O ARG p 83 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'p' and resid 36 through 41 removed outlier: 5.117A pdb=" N LYS p 51 " --> pdb=" O ILE p 67 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE p 61 " --> pdb=" O LEU p 57 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 't' and resid 4 through 10 removed outlier: 4.208A pdb=" N PHE t 16 " --> pdb=" O HIS t 9 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N GLY t 49 " --> pdb=" O ASN t 40 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 7 through 11 removed outlier: 7.289A pdb=" N GLU u 60 " --> pdb=" O VAL u 76 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'u' and resid 19 through 30 No H-bonds generated for sheet with id= 72 Processing sheet with id= 73, first strand: chain 'w' and resid 30 through 33 removed outlier: 4.591A pdb=" N LEU w 47 " --> pdb=" O VAL w 62 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'B' and resid 10 through 13 1990 hydrogen bonds defined for protein. 5871 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3993 hydrogen bonds 6264 hydrogen bond angles 0 basepair planarities 1586 basepair parallelities 2647 stacking parallelities Total time for adding SS restraints: 296.63 Time building geometry restraints manager: 64.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 11774 1.28 - 1.41: 58989 1.41 - 1.55: 77205 1.55 - 1.68: 9317 1.68 - 1.81: 266 Bond restraints: 157551 Sorted by residual: bond pdb=" C4 5MU z 69 " pdb=" C5 5MU z 69 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.59e+02 bond pdb=" C4 5MU z 64 " pdb=" C5 5MU z 64 " ideal model delta sigma weight residual 1.802 1.480 0.322 2.00e-02 2.50e+03 2.59e+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 bond pdb=" C4 5MU z 40 " pdb=" C5 5MU z 40 " ideal model delta sigma weight residual 1.802 1.484 0.318 2.00e-02 2.50e+03 2.54e+02 bond pdb=" C4 5MU z 76 " pdb=" C5 5MU z 76 " ideal model delta sigma weight residual 1.802 1.484 0.318 2.00e-02 2.50e+03 2.53e+02 ... (remaining 157546 not shown) Histogram of bond angle deviations from ideal: 72.04 - 86.99: 11 86.99 - 101.93: 4956 101.93 - 116.88: 137536 116.88 - 131.82: 92451 131.82 - 146.77: 779 Bond angle restraints: 235733 Sorted by residual: angle pdb=" OP2 5MU z 76 " pdb=" P 5MU z 76 " pdb=" O5' 5MU z 76 " ideal model delta sigma weight residual 108.00 72.04 35.96 3.00e+00 1.11e-01 1.44e+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 72.31 35.69 3.00e+00 1.11e-01 1.42e+02 angle pdb=" OP1 5MU z 71 " pdb=" P 5MU z 71 " pdb=" O5' 5MU z 71 " ideal model delta sigma weight residual 108.00 72.75 35.25 3.00e+00 1.11e-01 1.38e+02 angle pdb=" OP2 5MU z 71 " pdb=" P 5MU z 71 " pdb=" O5' 5MU z 71 " ideal model delta sigma weight residual 108.00 75.17 32.83 3.00e+00 1.11e-01 1.20e+02 angle pdb=" OP1 5MU z 76 " pdb=" P 5MU z 76 " pdb=" O5' 5MU z 76 " ideal model delta sigma weight residual 108.00 75.54 32.46 3.00e+00 1.11e-01 1.17e+02 ... (remaining 235728 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 88761 35.82 - 71.63: 11078 71.63 - 107.45: 862 107.45 - 143.26: 13 143.26 - 179.08: 40 Dihedral angle restraints: 100754 sinusoidal: 84309 harmonic: 16445 Sorted by residual: dihedral pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" C2' C 12146 " pdb=" C1' C 12146 " ideal model delta sinusoidal sigma weight residual -35.00 33.49 -68.49 1 8.00e+00 1.56e-02 9.50e+01 dihedral pdb=" C5' C 12146 " pdb=" C4' C 12146 " pdb=" C3' C 12146 " pdb=" O3' C 12146 " ideal model delta sinusoidal sigma weight residual 147.00 79.10 67.90 1 8.00e+00 1.56e-02 9.36e+01 dihedral pdb=" O4' U z 34 " pdb=" C1' U z 34 " pdb=" N1 U z 34 " pdb=" C2 U z 34 " ideal model delta sinusoidal sigma weight residual 200.00 38.51 161.49 1 1.50e+01 4.44e-03 8.31e+01 ... (remaining 100751 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.242: 29915 0.242 - 0.484: 56 0.484 - 0.726: 2 0.726 - 0.967: 1 0.967 - 1.209: 1 Chirality restraints: 29975 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 -1.20 1.21 2.00e-01 2.50e+01 3.66e+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 1.77 0.78 2.00e-01 2.50e+01 1.53e+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 2.00 0.55 2.00e-01 2.50e+01 7.59e+00 ... (remaining 29972 not shown) Planarity restraints: 12607 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.080 2.00e-02 2.50e+03 6.37e-01 9.12e+03 pdb=" C4' 2MG 21516 " -0.483 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.773 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.581 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.664 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.196 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.957 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.171 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 1.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC 12498 " -0.083 2.00e-02 2.50e+03 6.19e-01 8.63e+03 pdb=" C4' OMC 12498 " -0.438 2.00e-02 2.50e+03 pdb=" O4' OMC 12498 " -0.630 2.00e-02 2.50e+03 pdb=" C3' OMC 12498 " 0.610 2.00e-02 2.50e+03 pdb=" O3' OMC 12498 " 0.685 2.00e-02 2.50e+03 pdb=" C2' OMC 12498 " 0.151 2.00e-02 2.50e+03 pdb=" O2' OMC 12498 " -1.023 2.00e-02 2.50e+03 pdb=" C1' OMC 12498 " -0.219 2.00e-02 2.50e+03 pdb=" N1 OMC 12498 " 0.948 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU z 42 " -0.086 2.00e-02 2.50e+03 6.07e-01 8.29e+03 pdb=" C4' 5MU z 42 " -0.421 2.00e-02 2.50e+03 pdb=" O4' 5MU z 42 " -0.559 2.00e-02 2.50e+03 pdb=" C3' 5MU z 42 " 0.608 2.00e-02 2.50e+03 pdb=" O3' 5MU z 42 " 0.679 2.00e-02 2.50e+03 pdb=" C2' 5MU z 42 " 0.140 2.00e-02 2.50e+03 pdb=" O2' 5MU z 42 " -1.044 2.00e-02 2.50e+03 pdb=" C1' 5MU z 42 " -0.226 2.00e-02 2.50e+03 pdb=" N1 5MU z 42 " 0.909 2.00e-02 2.50e+03 ... (remaining 12604 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 359 2.15 - 2.83: 43068 2.83 - 3.52: 200754 3.52 - 4.21: 482387 4.21 - 4.90: 632105 Nonbonded interactions: 1358673 Sorted by model distance: nonbonded pdb=" O3' A z 85 " pdb=" C LEU B 70 " model vdw 1.457 3.270 nonbonded pdb=" OP2 A 12748 " pdb="MG MG 13191 " model vdw 1.721 2.170 nonbonded pdb=" OP2 U 1 963 " pdb="MG MG 13024 " model vdw 1.728 2.170 nonbonded pdb=" OP1 G 1 446 " pdb="MG MG 13155 " model vdw 1.762 2.170 nonbonded pdb=" N ARG h 81 " pdb="MG MG h 301 " model vdw 1.765 2.250 ... (remaining 1358668 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: 5.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.140 Extract box with map and model: 18.300 Check model and map are aligned: 1.600 Set scattering table: 1.000 Process input model: 612.380 Find NCS groups from input model: 2.980 Set up NCS constraints: 0.390 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:9.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 651.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 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 : 0.010 0.322 157551 Z= 0.617 Angle : 0.945 35.959 235733 Z= 0.502 Chirality : 0.056 1.209 29975 Planarity : 0.025 0.637 12607 Dihedral : 22.780 179.079 90148 Min Nonbonded Distance : 1.457 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.61 % Favored : 96.21 % Rotamer: Outliers : 0.23 % Allowed : 2.65 % Favored : 97.12 % Cbeta Deviations : 0.04 % 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: -3.87 (0.09), residues: 5675 helix: -3.60 (0.06), residues: 1949 sheet: -1.92 (0.14), residues: 1120 loop : -1.84 (0.10), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 78 HIS 0.024 0.003 HIS C 53 PHE 0.065 0.003 PHE M 80 TYR 0.034 0.003 TYR b 49 ARG 0.028 0.002 ARG M 71 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2065 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 2054 time to evaluate : 6.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 ASP cc_start: 0.6303 (m-30) cc_final: 0.5556 (m-30) REVERT: G 58 TYR cc_start: 0.8214 (m-80) cc_final: 0.7849 (m-80) REVERT: H 11 ASN cc_start: 0.8421 (t0) cc_final: 0.8162 (t0) REVERT: I 69 ARG cc_start: 0.7348 (ttm-80) cc_final: 0.7143 (ttt-90) REVERT: J 53 LYS cc_start: 0.7940 (mmtm) cc_final: 0.7579 (tppt) REVERT: T 54 GLN cc_start: 0.6190 (mt0) cc_final: 0.5920 (mt0) REVERT: W 71 LEU cc_start: 0.8313 (mt) cc_final: 0.8075 (mt) REVERT: X 16 THR cc_start: 0.8310 (m) cc_final: 0.8072 (p) REVERT: g 187 SER cc_start: 0.8668 (t) cc_final: 0.6832 (t) REVERT: i 130 SER cc_start: 0.8450 (t) cc_final: 0.8249 (p) REVERT: m 64 TYR cc_start: 0.7545 (t80) cc_final: 0.7095 (t80) REVERT: m 79 ILE cc_start: 0.9011 (mt) cc_final: 0.8799 (mm) REVERT: n 53 ILE cc_start: 0.8955 (pt) cc_final: 0.8686 (pt) REVERT: x 48 GLN cc_start: 0.7946 (tp40) cc_final: 0.7535 (tp-100) outliers start: 11 outliers final: 7 residues processed: 2061 average time/residue: 2.1915 time to fit residues: 6374.1811 Evaluate side-chains 1405 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1398 time to evaluate : 6.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 93 ASN Chi-restraints excluded: chain O residue 11 GLU Chi-restraints excluded: chain S residue 2 ILE Chi-restraints excluded: chain i residue 30 ILE Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain o residue 79 ILE Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 858 optimal weight: 0.0020 chunk 770 optimal weight: 8.9990 chunk 427 optimal weight: 10.0000 chunk 263 optimal weight: 10.0000 chunk 519 optimal weight: 4.9990 chunk 411 optimal weight: 10.0000 chunk 797 optimal weight: 5.9990 chunk 308 optimal weight: 20.0000 chunk 484 optimal weight: 4.9990 chunk 593 optimal weight: 30.0000 chunk 923 optimal weight: 3.9990 overall best weight: 3.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 60 GLN C 117 GLN D 164 GLN E 94 GLN F 23 ASN F 81 GLN G 38 ASN G 104 ASN H 33 GLN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 73 ASN H 119 ASN I 138 GLN N 38 GLN O 56 HIS P 20 GLN P 37 GLN P 44 GLN P 56 GLN P 72 ASN Q 11 GLN Q 87 GLN ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 40 ASN T 46 GLN T 66 GLN ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 17 ASN W 23 ASN Y 9 GLN Z 33 ASN a 42 HIS c 6 GLN ** c 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 13 ASN e 37 GLN ** f 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 41 GLN ** g 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 71 GLN h 89 ASN ** h 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 152 GLN ** j 14 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 52 ASN k 28 ASN k 97 ASN k 130 ASN m 50 GLN m 126 GLN o 29 ASN o 40 ASN p 5 ASN p 6 GLN p 112 GLN q 8 ASN q 14 HIS r 49 GLN r 62 ASN r 66 GLN s 37 ASN ** s 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 59 HIS x 13 GLN ** x 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 61 GLN x 78 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 49 GLN Total number of N/Q/H flips: 59 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 157551 Z= 0.231 Angle : 0.715 16.158 235733 Z= 0.386 Chirality : 0.035 0.510 29975 Planarity : 0.007 0.129 12607 Dihedral : 23.693 179.451 78801 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.78 % Favored : 97.18 % Rotamer: Outliers : 4.11 % Allowed : 19.67 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.10), residues: 5675 helix: -0.53 (0.11), residues: 1958 sheet: -1.27 (0.15), residues: 1080 loop : -1.23 (0.11), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 11 HIS 0.009 0.001 HIS L 13 PHE 0.025 0.002 PHE F 100 TYR 0.028 0.002 TYR B 42 ARG 0.012 0.001 ARG L 59 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1868 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1674 time to evaluate : 6.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 13 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7827 (ptm160) REVERT: H 11 ASN cc_start: 0.8318 (t0) cc_final: 0.8020 (t0) REVERT: H 42 LYS cc_start: 0.8102 (tptp) cc_final: 0.7866 (tptp) REVERT: J 86 LEU cc_start: 0.8952 (mp) cc_final: 0.8743 (mp) REVERT: N 76 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7896 (ttmm) REVERT: O 114 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.7195 (pp) REVERT: Q 60 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7623 (mmmm) REVERT: S 79 ASP cc_start: 0.7123 (m-30) cc_final: 0.6866 (m-30) REVERT: i 36 LEU cc_start: 0.8601 (tp) cc_final: 0.8374 (tp) REVERT: i 60 ILE cc_start: 0.8488 (pp) cc_final: 0.7922 (pp) REVERT: i 130 SER cc_start: 0.8607 (t) cc_final: 0.8206 (p) REVERT: j 88 MET cc_start: 0.7803 (ttm) cc_final: 0.7571 (ttm) REVERT: m 62 ASP cc_start: 0.6884 (m-30) cc_final: 0.6217 (m-30) REVERT: v 25 ASP cc_start: 0.7171 (t0) cc_final: 0.6856 (t0) REVERT: v 28 THR cc_start: 0.7886 (m) cc_final: 0.7594 (m) REVERT: B 11 TRP cc_start: 0.2960 (p-90) cc_final: 0.2623 (p-90) outliers start: 194 outliers final: 56 residues processed: 1742 average time/residue: 2.0048 time to fit residues: 5044.1450 Evaluate side-chains 1520 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1460 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 79 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain O residue 114 LEU Chi-restraints excluded: chain Q residue 60 LYS Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 62 ASP Chi-restraints excluded: chain T residue 53 ASN Chi-restraints excluded: chain W residue 22 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain f residue 151 ILE Chi-restraints excluded: chain g residue 31 ASP Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 142 ASP Chi-restraints excluded: chain j residue 26 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 39 LEU Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 103 VAL Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 91 ASP Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 64 THR Chi-restraints excluded: chain q residue 21 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 r residue 82 ILE Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 69 ASP Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 81 LYS Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain x residue 14 SER Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 513 optimal weight: 10.0000 chunk 286 optimal weight: 10.0000 chunk 768 optimal weight: 7.9990 chunk 628 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 925 optimal weight: 7.9990 chunk 999 optimal weight: 2.9990 chunk 823 optimal weight: 8.9990 chunk 917 optimal weight: 6.9990 chunk 315 optimal weight: 10.0000 chunk 742 optimal weight: 9.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN D 136 ASN E 62 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN F 81 GLN G 22 GLN ** G 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN ** H 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 138 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 23 ASN N 38 GLN P 44 GLN P 56 GLN P 59 GLN Q 82 HIS ** T 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 ASN Z 33 ASN e 13 ASN e 37 GLN ** f 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 51 ASN f 177 ASN ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 100 GLN g 102 ASN h 54 GLN h 71 GLN ** h 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 116 GLN m 32 GLN m 126 GLN p 112 GLN r 66 GLN ** s 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 61 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 157551 Z= 0.334 Angle : 0.709 14.723 235733 Z= 0.383 Chirality : 0.037 0.472 29975 Planarity : 0.007 0.136 12607 Dihedral : 23.534 179.430 78788 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 4.57 % Allowed : 21.86 % Favored : 73.57 % 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: -0.68 (0.11), residues: 5675 helix: 0.51 (0.11), residues: 1963 sheet: -0.93 (0.15), residues: 1106 loop : -0.88 (0.12), residues: 2606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 11 HIS 0.009 0.001 HIS L 13 PHE 0.025 0.002 PHE F 100 TYR 0.025 0.002 TYR B 42 ARG 0.023 0.001 ARG u 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1783 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1567 time to evaluate : 6.231 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: D 13 ARG cc_start: 0.8173 (OUTLIER) cc_final: 0.7918 (ptm160) REVERT: E 94 GLN cc_start: 0.8235 (mt0) cc_final: 0.7960 (mt0) REVERT: H 11 ASN cc_start: 0.8313 (t0) cc_final: 0.8111 (t0) REVERT: H 55 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7344 (tp30) REVERT: L 110 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7101 (tt0) REVERT: S 25 GLU cc_start: 0.6914 (pp20) cc_final: 0.6611 (pp20) REVERT: T 88 GLU cc_start: 0.6277 (tm-30) cc_final: 0.5574 (tm-30) REVERT: e 8 LYS cc_start: 0.8466 (OUTLIER) cc_final: 0.8215 (mtpp) REVERT: g 25 ASN cc_start: 0.7392 (p0) cc_final: 0.7151 (p0) REVERT: i 36 LEU cc_start: 0.8635 (tp) cc_final: 0.8407 (tp) REVERT: i 130 SER cc_start: 0.8712 (t) cc_final: 0.8214 (p) REVERT: j 88 MET cc_start: 0.7833 (ttm) cc_final: 0.7577 (ttm) REVERT: k 140 ASP cc_start: 0.7555 (m-30) cc_final: 0.7306 (m-30) REVERT: m 42 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6570 (mm-30) REVERT: m 62 ASP cc_start: 0.7069 (m-30) cc_final: 0.6456 (m-30) REVERT: o 40 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7422 (m-40) REVERT: o 85 MET cc_start: 0.7648 (mmp) cc_final: 0.7336 (mmp) REVERT: p 14 ARG cc_start: 0.7536 (OUTLIER) cc_final: 0.7315 (ptp-110) REVERT: q 58 ASP cc_start: 0.7988 (m-30) cc_final: 0.7687 (m-30) REVERT: q 68 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7324 (m-30) REVERT: s 18 ASP cc_start: 0.6950 (OUTLIER) cc_final: 0.6744 (t0) REVERT: w 17 LYS cc_start: 0.8589 (mmmm) cc_final: 0.8281 (mmmt) outliers start: 216 outliers final: 95 residues processed: 1646 average time/residue: 2.0257 time to fit residues: 4837.0382 Evaluate side-chains 1512 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1408 time to evaluate : 6.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 74 SER Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 45 GLU Chi-restraints excluded: chain H residue 55 GLU Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain H residue 142 VAL Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain J residue 104 THR Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain P residue 17 ILE Chi-restraints excluded: chain Q residue 15 SER Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain S residue 21 SER Chi-restraints excluded: chain T residue 53 ASN Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Z residue 34 LEU Chi-restraints excluded: chain Z residue 65 ASN Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 54 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain e residue 8 LYS Chi-restraints excluded: chain e residue 20 ASP Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 132 ILE Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain j residue 26 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 56 LYS Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 97 THR Chi-restraints excluded: chain j residue 103 VAL Chi-restraints excluded: chain l residue 9 ASP Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 111 MET Chi-restraints excluded: chain l residue 125 ILE Chi-restraints excluded: chain m residue 42 GLU Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 128 SER Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 40 ASN Chi-restraints excluded: chain p residue 14 ARG Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain q residue 21 SER 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 67 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 18 ASP Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 42 ILE Chi-restraints excluded: chain t residue 69 ASP Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 22 ASP Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 57 ILE Chi-restraints excluded: chain y residue 4 ILE Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 914 optimal weight: 10.0000 chunk 695 optimal weight: 20.0000 chunk 480 optimal weight: 9.9990 chunk 102 optimal weight: 10.0000 chunk 441 optimal weight: 10.0000 chunk 621 optimal weight: 6.9990 chunk 928 optimal weight: 5.9990 chunk 983 optimal weight: 10.0000 chunk 485 optimal weight: 9.9990 chunk 880 optimal weight: 8.9990 chunk 264 optimal weight: 10.0000 overall best weight: 8.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 117 GLN D 130 GLN E 62 GLN ** E 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 ASN F 81 GLN H 20 ASN H 43 ASN J 3 GLN L 3 GLN L 22 GLN M 9 GLN N 38 GLN P 44 GLN P 56 GLN P 59 GLN Q 86 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN Z 33 ASN e 13 ASN e 37 GLN ** f 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 19 ASN ** g 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 71 GLN i 132 ASN ** k 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 126 GLN p 112 GLN r 66 GLN ** s 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 78 ASN ** B 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 157551 Z= 0.403 Angle : 0.738 15.257 235733 Z= 0.396 Chirality : 0.039 0.436 29975 Planarity : 0.007 0.135 12607 Dihedral : 23.501 179.897 78788 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 5.40 % Allowed : 23.17 % Favored : 71.43 % 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: -0.36 (0.11), residues: 5675 helix: 0.83 (0.12), residues: 1962 sheet: -0.78 (0.15), residues: 1117 loop : -0.74 (0.12), residues: 2596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 11 HIS 0.009 0.002 HIS L 13 PHE 0.027 0.002 PHE s 15 TYR 0.023 0.002 TYR B 42 ARG 0.012 0.001 ARG g 107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1748 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 255 poor density : 1493 time to evaluate : 6.233 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: J 12 ASP cc_start: 0.8111 (OUTLIER) cc_final: 0.7713 (p0) REVERT: L 110 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.7163 (tt0) REVERT: M 75 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8010 (mp) REVERT: e 8 LYS cc_start: 0.8615 (OUTLIER) cc_final: 0.8361 (mtpp) REVERT: g 25 ASN cc_start: 0.7775 (p0) cc_final: 0.7500 (p0) REVERT: h 105 MET cc_start: 0.8063 (OUTLIER) cc_final: 0.7587 (mtm) REVERT: i 130 SER cc_start: 0.8749 (t) cc_final: 0.8237 (p) REVERT: j 14 GLN cc_start: 0.8089 (mm-40) cc_final: 0.7569 (mm-40) REVERT: j 24 ARG cc_start: 0.7727 (ptt-90) cc_final: 0.7411 (ptt-90) REVERT: j 88 MET cc_start: 0.7876 (ttm) cc_final: 0.7629 (ttm) REVERT: m 42 GLU cc_start: 0.6887 (OUTLIER) cc_final: 0.6601 (mm-30) REVERT: m 62 ASP cc_start: 0.7298 (m-30) cc_final: 0.6989 (m-30) REVERT: n 78 GLU cc_start: 0.7037 (mp0) cc_final: 0.5949 (mp0) REVERT: o 72 ASP cc_start: 0.7679 (p0) cc_final: 0.7386 (p0) REVERT: o 75 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8038 (ptpp) REVERT: r 65 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7263 (mtm180) REVERT: w 17 LYS cc_start: 0.8638 (mmmm) cc_final: 0.8428 (mmmt) REVERT: y 70 LEU cc_start: 0.8226 (mt) cc_final: 0.7949 (mt) outliers start: 255 outliers final: 116 residues processed: 1594 average time/residue: 2.0184 time to fit residues: 4689.3494 Evaluate side-chains 1498 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1374 time to evaluate : 6.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 LEU Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 193 VAL Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 6 ASP Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 158 THR Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 48 ASN Chi-restraints excluded: chain H residue 35 LYS Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 88 ASN Chi-restraints excluded: chain J residue 113 MET Chi-restraints excluded: chain K residue 81 ASP Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 110 GLU Chi-restraints excluded: chain M residue 1 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 75 ILE Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 8 ILE Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 91 SER Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain O residue 40 LEU Chi-restraints excluded: chain P residue 87 SER Chi-restraints excluded: chain P residue 100 VAL Chi-restraints excluded: chain Q residue 22 LEU Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain R residue 82 MET Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 53 ASN Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 66 ASP Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain W residue 65 ASP Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Z residue 65 ASN Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain b residue 43 VAL Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain c residue 25 LYS Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 52 LYS Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain e residue 8 LYS Chi-restraints excluded: chain e residue 10 LEU Chi-restraints excluded: chain f residue 157 LEU Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain g residue 208 LEU Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain h residue 132 ILE Chi-restraints excluded: chain i residue 15 LEU Chi-restraints excluded: chain i residue 26 LYS Chi-restraints excluded: chain i residue 115 LEU Chi-restraints excluded: chain j residue 26 THR Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 70 VAL Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 97 THR Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 42 GLU Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 46 THR Chi-restraints excluded: chain o residue 75 LYS Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 78 SER Chi-restraints excluded: chain q residue 21 SER Chi-restraints excluded: chain q residue 27 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain r residue 34 VAL Chi-restraints excluded: chain r residue 65 ARG Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 69 ASP Chi-restraints excluded: chain t residue 71 VAL Chi-restraints excluded: chain u residue 50 ASN Chi-restraints excluded: chain u residue 67 LEU Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 28 THR Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 57 ILE Chi-restraints excluded: chain y residue 44 GLU Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 818 optimal weight: 0.8980 chunk 558 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 731 optimal weight: 6.9990 chunk 405 optimal weight: 20.0000 chunk 838 optimal weight: 0.8980 chunk 679 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 501 optimal weight: 20.0000 chunk 882 optimal weight: 0.0570 chunk 248 optimal weight: 10.0000 overall best weight: 1.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN D 130 GLN E 62 GLN E 156 ASN F 23 ASN ** H 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 20 ASN I 80 HIS L 3 GLN M 3 HIS M 9 GLN N 38 GLN P 44 GLN P 56 GLN P 59 GLN ** Q 18 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** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 6 GLN W 16 ASN Z 33 ASN e 13 ASN e 37 GLN f 15 HIS g 3 GLN g 19 ASN g 102 ASN h 54 GLN h 71 GLN h 116 GLN k 68 ASN n 20 GLN o 40 ASN p 112 GLN r 62 ASN ** s 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 9 HIS x 61 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 157551 Z= 0.155 Angle : 0.675 13.905 235733 Z= 0.367 Chirality : 0.033 0.502 29975 Planarity : 0.007 0.123 12607 Dihedral : 23.524 178.624 78788 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 4.02 % Allowed : 25.86 % Favored : 70.12 % 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: -0.17 (0.11), residues: 5675 helix: 0.97 (0.12), residues: 1962 sheet: -0.58 (0.15), residues: 1058 loop : -0.66 (0.12), residues: 2655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 11 HIS 0.005 0.001 HIS o 118 PHE 0.030 0.001 PHE B 31 TYR 0.029 0.001 TYR B 42 ARG 0.015 0.001 ARG g 107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1747 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 190 poor density : 1557 time to evaluate : 6.393 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 98 ASP cc_start: 0.7526 (OUTLIER) cc_final: 0.7305 (p0) REVERT: D 1 MET cc_start: 0.7527 (tmt) cc_final: 0.7309 (tmt) REVERT: D 13 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7852 (ptm160) REVERT: J 45 GLU cc_start: 0.6344 (pp20) cc_final: 0.5830 (pm20) REVERT: S 12 ARG cc_start: 0.8490 (OUTLIER) cc_final: 0.7923 (mmp80) REVERT: U 7 GLU cc_start: 0.6290 (mm-30) cc_final: 0.6046 (mm-30) REVERT: Y 47 MET cc_start: 0.7143 (mtp) cc_final: 0.6789 (mtm) REVERT: Z 31 ASP cc_start: 0.6998 (t0) cc_final: 0.6729 (t0) REVERT: e 4 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7401 (mtp85) REVERT: e 8 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8220 (mtpp) REVERT: g 25 ASN cc_start: 0.7669 (p0) cc_final: 0.7441 (p0) REVERT: h 105 MET cc_start: 0.7972 (OUTLIER) cc_final: 0.7498 (mtm) REVERT: i 64 MET cc_start: 0.7775 (mmt) cc_final: 0.7427 (mmt) REVERT: i 130 SER cc_start: 0.8646 (t) cc_final: 0.8211 (p) REVERT: j 9 MET cc_start: 0.7022 (mtp) cc_final: 0.6754 (mtm) REVERT: j 24 ARG cc_start: 0.7726 (ptt-90) cc_final: 0.7505 (ptt-90) REVERT: k 140 ASP cc_start: 0.7674 (m-30) cc_final: 0.7443 (m-30) REVERT: l 3 MET cc_start: 0.7215 (tpp) cc_final: 0.6921 (tpp) REVERT: p 62 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6606 (mm-30) REVERT: v 25 ASP cc_start: 0.7549 (t0) cc_final: 0.7142 (t0) REVERT: y 31 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6536 (mm-30) REVERT: y 70 LEU cc_start: 0.8358 (mt) cc_final: 0.8117 (mt) outliers start: 190 outliers final: 77 residues processed: 1623 average time/residue: 2.0492 time to fit residues: 4834.1279 Evaluate side-chains 1496 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 1414 time to evaluate : 6.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 98 ASP Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 229 ASP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 90 ASN Chi-restraints excluded: chain J residue 107 LEU Chi-restraints excluded: chain J residue 113 MET Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain S residue 12 ARG Chi-restraints excluded: chain T residue 9 ASP Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain V residue 66 LYS Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain f residue 15 HIS Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain l residue 9 ASP Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain l residue 96 MET Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain n residue 76 ILE Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain o residue 81 ASN Chi-restraints excluded: chain o residue 94 GLU Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 20 ASN Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 33 ILE Chi-restraints excluded: chain t residue 69 ASP Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 76 VAL Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 5 LEU Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 57 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 66 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 330 optimal weight: 20.0000 chunk 885 optimal weight: 8.9990 chunk 194 optimal weight: 10.0000 chunk 577 optimal weight: 7.9990 chunk 242 optimal weight: 10.0000 chunk 983 optimal weight: 6.9990 chunk 816 optimal weight: 20.0000 chunk 455 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 325 optimal weight: 10.0000 chunk 516 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 153 GLN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 9 GLN E 62 GLN G 45 HIS H 20 ASN H 33 GLN ** J 29 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN L 60 GLN M 9 GLN N 38 GLN P 44 GLN P 56 GLN P 59 GLN ** Q 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 86 GLN R 15 GLN ** S 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 16 ASN W 23 ASN Z 33 ASN e 13 ASN e 37 GLN f 15 HIS f 51 ASN g 3 GLN g 19 ASN ** g 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 54 GLN h 71 GLN ** h 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 97 GLN ** m 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 112 GLN ** s 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** x 78 ASN ** B 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 157551 Z= 0.376 Angle : 0.725 14.874 235733 Z= 0.390 Chirality : 0.038 0.439 29975 Planarity : 0.007 0.136 12607 Dihedral : 23.406 179.980 78788 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.68 % Allowed : 27.68 % Favored : 67.64 % 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: -0.13 (0.11), residues: 5675 helix: 1.00 (0.12), residues: 1961 sheet: -0.60 (0.15), residues: 1103 loop : -0.60 (0.12), residues: 2611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 11 HIS 0.031 0.002 HIS f 15 PHE 0.027 0.002 PHE Z 60 TYR 0.029 0.002 TYR q 86 ARG 0.018 0.001 ARG s 58 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11350 Ramachandran restraints generated. 5675 Oldfield, 0 Emsley, 5675 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1665 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1444 time to evaluate : 6.360 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: D 13 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.8011 (ptm160) REVERT: J 12 ASP cc_start: 0.8013 (OUTLIER) cc_final: 0.7612 (p0) REVERT: L 106 ASP cc_start: 0.6925 (p0) cc_final: 0.6618 (p0) REVERT: S 4 GLU cc_start: 0.6894 (pm20) cc_final: 0.6676 (pm20) REVERT: Y 6 LYS cc_start: 0.8152 (mmpt) cc_final: 0.7933 (mmpt) REVERT: Z 31 ASP cc_start: 0.7046 (t0) cc_final: 0.6789 (t0) REVERT: e 4 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7424 (mtp85) REVERT: e 8 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8248 (mtpp) REVERT: g 25 ASN cc_start: 0.7836 (p0) cc_final: 0.7594 (p0) REVERT: h 105 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.7567 (mtm) REVERT: i 130 SER cc_start: 0.8704 (t) cc_final: 0.8260 (p) REVERT: j 14 GLN cc_start: 0.8092 (mm-40) cc_final: 0.7696 (mm-40) REVERT: j 88 MET cc_start: 0.7872 (ttm) cc_final: 0.7621 (ttm) REVERT: m 62 ASP cc_start: 0.7231 (m-30) cc_final: 0.6979 (t0) REVERT: t 70 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8284 (mmt-90) REVERT: y 70 LEU cc_start: 0.8230 (mt) cc_final: 0.8000 (mt) REVERT: B 11 TRP cc_start: 0.3859 (p-90) cc_final: 0.2700 (p-90) outliers start: 221 outliers final: 115 residues processed: 1530 average time/residue: 2.0355 time to fit residues: 4515.7686 Evaluate side-chains 1510 residues out of total 4722 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 1389 time to evaluate : 5.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 180 GLU Chi-restraints excluded: chain C residue 228 VAL Chi-restraints excluded: chain C residue 264 ASP Chi-restraints excluded: chain D residue 13 ARG Chi-restraints excluded: chain D residue 18 ASP Chi-restraints excluded: chain D residue 137 SER Chi-restraints excluded: chain D residue 139 SER Chi-restraints excluded: chain D residue 170 VAL Chi-restraints excluded: chain D residue 174 SER Chi-restraints excluded: chain D residue 177 VAL Chi-restraints excluded: chain E residue 7 ASP Chi-restraints excluded: chain E residue 25 GLU Chi-restraints excluded: chain E residue 65 THR Chi-restraints excluded: chain F residue 21 ASN Chi-restraints excluded: chain F residue 175 PHE Chi-restraints excluded: chain G residue 10 VAL Chi-restraints excluded: chain G residue 11 VAL Chi-restraints excluded: chain G residue 16 ASP Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 127 THR Chi-restraints excluded: chain H residue 47 PHE Chi-restraints excluded: chain H residue 75 LEU Chi-restraints excluded: chain I residue 14 ASP Chi-restraints excluded: chain I residue 86 GLN Chi-restraints excluded: chain I residue 101 ILE Chi-restraints excluded: chain J residue 12 ASP Chi-restraints excluded: chain J residue 14 SER Chi-restraints excluded: chain J residue 113 MET Chi-restraints excluded: chain K residue 85 VAL Chi-restraints excluded: chain K residue 91 ASP Chi-restraints excluded: chain K residue 116 VAL Chi-restraints excluded: chain K residue 118 THR Chi-restraints excluded: chain K residue 136 GLU Chi-restraints excluded: chain L residue 2 LEU Chi-restraints excluded: chain L residue 74 THR Chi-restraints excluded: chain L residue 88 ASN Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain M residue 97 ILE Chi-restraints excluded: chain N residue 5 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 49 VAL Chi-restraints excluded: chain N residue 76 LYS Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain P residue 88 VAL Chi-restraints excluded: chain Q residue 29 THR Chi-restraints excluded: chain Q residue 96 VAL Chi-restraints excluded: chain R residue 53 SER Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 87 LEU Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 65 ILE Chi-restraints excluded: chain U residue 42 LEU Chi-restraints excluded: chain U residue 61 LEU Chi-restraints excluded: chain U residue 77 VAL Chi-restraints excluded: chain U residue 79 ARG Chi-restraints excluded: chain W residue 71 LEU Chi-restraints excluded: chain Y residue 17 LEU Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Z residue 64 PHE Chi-restraints excluded: chain a residue 11 SER Chi-restraints excluded: chain a residue 26 THR Chi-restraints excluded: chain a residue 33 THR Chi-restraints excluded: chain b residue 9 ILE Chi-restraints excluded: chain b residue 48 ILE Chi-restraints excluded: chain d residue 51 SER Chi-restraints excluded: chain d residue 58 VAL Chi-restraints excluded: chain e residue 4 ARG Chi-restraints excluded: chain e residue 8 LYS Chi-restraints excluded: chain f residue 130 THR Chi-restraints excluded: chain f residue 157 LEU Chi-restraints excluded: chain g residue 52 VAL Chi-restraints excluded: chain g residue 76 VAL Chi-restraints excluded: chain g residue 128 VAL Chi-restraints excluded: chain h residue 105 MET Chi-restraints excluded: chain j residue 30 THR Chi-restraints excluded: chain j residue 56 LYS Chi-restraints excluded: chain j residue 84 VAL Chi-restraints excluded: chain j residue 96 VAL Chi-restraints excluded: chain j residue 97 THR Chi-restraints excluded: chain k residue 54 SER Chi-restraints excluded: chain k residue 104 ILE Chi-restraints excluded: chain k residue 148 ASN Chi-restraints excluded: chain l residue 9 ASP Chi-restraints excluded: chain l residue 51 VAL Chi-restraints excluded: chain l residue 61 LEU Chi-restraints excluded: chain l residue 90 ASP Chi-restraints excluded: chain m residue 46 MET Chi-restraints excluded: chain m residue 56 ASP Chi-restraints excluded: chain m residue 58 VAL Chi-restraints excluded: chain m residue 72 ILE Chi-restraints excluded: chain m residue 73 SER Chi-restraints excluded: chain m residue 79 ILE Chi-restraints excluded: chain n residue 76 ILE Chi-restraints excluded: chain n residue 102 LEU Chi-restraints excluded: chain o residue 33 THR Chi-restraints excluded: chain p residue 19 SER Chi-restraints excluded: chain p residue 97 THR Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain r residue 45 VAL Chi-restraints excluded: chain r residue 67 THR Chi-restraints excluded: chain r residue 80 SER Chi-restraints excluded: chain s residue 25 THR Chi-restraints excluded: chain t residue 2 VAL Chi-restraints excluded: chain t residue 3 THR Chi-restraints excluded: chain t residue 19 VAL Chi-restraints excluded: chain t residue 23 ASP Chi-restraints excluded: chain t residue 69 ASP Chi-restraints excluded: chain t residue 70 ARG Chi-restraints excluded: chain u residue 7 THR Chi-restraints excluded: chain u residue 79 VAL Chi-restraints excluded: chain v residue 42 SER Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 71 THR Chi-restraints excluded: chain w residue 79 THR Chi-restraints excluded: chain x residue 12 ILE Chi-restraints excluded: chain x residue 57 ILE Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 25 ASP Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 54 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1017 random chunks: chunk 948 optimal weight: 6.9990 chunk 110 optimal weight: 30.0000 chunk 560 optimal weight: 6.9990 chunk 718 optimal weight: 9.9990 chunk 556 optimal weight: 6.9990 chunk 828 optimal weight: 0.7980 chunk 549 optimal weight: 3.9990 chunk 980 optimal weight: 8.9990 chunk 613 optimal weight: 10.0000 chunk 597 optimal weight: 7.9990 chunk 452 optimal weight: 10.0000 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: