Starting phenix.real_space_refine on Tue Feb 13 16:11:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/02_2024/5x8r_6710.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/02_2024/5x8r_6710.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/02_2024/5x8r_6710.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/02_2024/5x8r_6710.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/02_2024/5x8r_6710.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5x8r_6710/02_2024/5x8r_6710.pdb" } resolution = 3.7 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= 0.001 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1480 5.49 5 S 89 5.16 5 C 29036 2.51 5 N 10368 2.21 5 O 14439 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "b ARG 25": "NH1" <-> "NH2" Residue "b ARG 30": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "b ARG 67": "NH1" <-> "NH2" Residue "b ARG 86": "NH1" <-> "NH2" Residue "b ARG 90": "NH1" <-> "NH2" Residue "b ARG 92": "NH1" <-> "NH2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 119": "NH1" <-> "NH2" Residue "b ARG 122": "NH1" <-> "NH2" Residue "b ARG 129": "NH1" <-> "NH2" Residue "b ARG 132": "NH1" <-> "NH2" Residue "b ARG 136": "NH1" <-> "NH2" Residue "b ARG 143": "NH1" <-> "NH2" Residue "b ARG 178": "NH1" <-> "NH2" Residue "b ASP 209": "OD1" <-> "OD2" Residue "b ARG 215": "NH1" <-> "NH2" Residue "b ARG 229": "NH1" <-> "NH2" Residue "c ARG 11": "NH1" <-> "NH2" Residue "c ARG 40": "NH1" <-> "NH2" Residue "c ARG 88": "NH1" <-> "NH2" Residue "c ARG 108": "NH1" <-> "NH2" Residue "c ARG 116": "NH1" <-> "NH2" Residue "c ARG 167": "NH1" <-> "NH2" Residue "c ARG 175": "NH1" <-> "NH2" Residue "c ARG 183": "NH1" <-> "NH2" Residue "c ARG 190": "NH1" <-> "NH2" Residue "c ARG 201": "NH1" <-> "NH2" Residue "e TYR 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ARG 226": "NH1" <-> "NH2" Residue "e ARG 280": "NH1" <-> "NH2" Residue "e ARG 290": "NH1" <-> "NH2" Residue "e ARG 299": "NH1" <-> "NH2" Residue "f ARG 106": "NH1" <-> "NH2" Residue "f ARG 115": "NH1" <-> "NH2" Residue "f ARG 147": "NH1" <-> "NH2" Residue "f ARG 158": "NH1" <-> "NH2" Residue "f ARG 200": "NH1" <-> "NH2" Residue "g ARG 21": "NH1" <-> "NH2" Residue "g ARG 78": "NH1" <-> "NH2" Residue "g ARG 79": "NH1" <-> "NH2" Residue "g ARG 102": "NH1" <-> "NH2" Residue "g ARG 111": "NH1" <-> "NH2" Residue "g ARG 143": "NH1" <-> "NH2" Residue "h ARG 20": "NH1" <-> "NH2" Residue "h ARG 64": "NH1" <-> "NH2" Residue "h TYR 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i ARG 77": "NH1" <-> "NH2" Residue "i ARG 99": "NH1" <-> "NH2" Residue "i ARG 152": "NH1" <-> "NH2" Residue "i ARG 173": "NH1" <-> "NH2" Residue "i ARG 176": "NH1" <-> "NH2" Residue "i ARG 189": "NH1" <-> "NH2" Residue "j ARG 155": "NH1" <-> "NH2" Residue "k PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 137": "NH1" <-> "NH2" Residue "l ARG 12": "NH1" <-> "NH2" Residue "l ARG 30": "NH1" <-> "NH2" Residue "l ARG 31": "NH1" <-> "NH2" Residue "l ARG 36": "NH1" <-> "NH2" Residue "l ARG 50": "NH1" <-> "NH2" Residue "l ARG 54": "NH1" <-> "NH2" Residue "l ARG 56": "NH1" <-> "NH2" Residue "l ARG 83": "NH1" <-> "NH2" Residue "l ARG 94": "NH1" <-> "NH2" Residue "l ARG 99": "NH1" <-> "NH2" Residue "l ARG 110": "NH1" <-> "NH2" Residue "l ARG 114": "NH1" <-> "NH2" Residue "m ARG 108": "NH1" <-> "NH2" Residue "m ARG 118": "NH1" <-> "NH2" Residue "m ARG 135": "NH1" <-> "NH2" Residue "o ARG 34": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 51": "NH1" <-> "NH2" Residue "o ARG 54": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 74": "NH1" <-> "NH2" Residue "p ARG 5": "NH1" <-> "NH2" Residue "p ARG 8": "NH1" <-> "NH2" Residue "p ARG 14": "NH1" <-> "NH2" Residue "p ARG 18": "NH1" <-> "NH2" Residue "p ARG 25": "NH1" <-> "NH2" Residue "p ARG 28": "NH1" <-> "NH2" Residue "p ARG 31": "NH1" <-> "NH2" Residue "p ARG 73": "NH1" <-> "NH2" Residue "r ARG 27": "NH1" <-> "NH2" Residue "r TYR 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 38": "NH1" <-> "NH2" Residue "r ARG 49": "NH1" <-> "NH2" Residue "r ARG 50": "NH1" <-> "NH2" Residue "r ARG 53": "NH1" <-> "NH2" Residue "r ARG 60": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "s ARG 17": "NH1" <-> "NH2" Residue "s ARG 55": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "t ARG 84": "NH1" <-> "NH2" Residue "t ARG 103": "NH1" <-> "NH2" Residue "t ARG 105": "NH1" <-> "NH2" Residue "t ARG 150": "NH1" <-> "NH2" Residue "t ARG 162": "NH1" <-> "NH2" Residue "u ARG 104": "NH1" <-> "NH2" Residue "u ARG 109": "NH1" <-> "NH2" Residue "u ARG 120": "NH1" <-> "NH2" Residue "y ARG 91": "NH1" <-> "NH2" Residue "y ARG 110": "NH1" <-> "NH2" Residue "y ARG 115": "NH1" <-> "NH2" Residue "y ARG 130": "NH1" <-> "NH2" Residue "y ARG 131": "NH1" <-> "NH2" Residue "y ARG 140": "NH1" <-> "NH2" Residue "y ARG 166": "NH1" <-> "NH2" Residue "w ARG 98": "NH1" <-> "NH2" Residue "w GLU 107": "OE1" <-> "OE2" Residue "w ASP 115": "OD1" <-> "OD2" Residue "w ARG 134": "NH1" <-> "NH2" Residue "w ASP 136": "OD1" <-> "OD2" Residue "w GLU 140": "OE1" <-> "OE2" Residue "w GLU 146": "OE1" <-> "OE2" Residue "w ASP 165": "OD1" <-> "OD2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 13": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 25": "NH1" <-> "NH2" Residue "d ARG 45": "NH1" <-> "NH2" Residue "d ARG 47": "NH1" <-> "NH2" Residue "d ARG 55": "NH1" <-> "NH2" Residue "d ARG 63": "NH1" <-> "NH2" Residue "d ARG 70": "NH1" <-> "NH2" Residue "d ARG 97": "NH1" <-> "NH2" Residue "d ARG 108": "NH1" <-> "NH2" Residue "d ARG 114": "NH1" <-> "NH2" Residue "d ARG 121": "NH1" <-> "NH2" Residue "d ARG 129": "NH1" <-> "NH2" Residue "d ARG 139": "NH1" <-> "NH2" Residue "d ARG 157": "NH1" <-> "NH2" Residue "d TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d GLU 195": "OE1" <-> "OE2" Residue "v ASP 17": "OD1" <-> "OD2" Residue "v ARG 22": "NH1" <-> "NH2" Residue "v ARG 23": "NH1" <-> "NH2" Residue "v ARG 31": "NH1" <-> "NH2" Residue "v ASP 36": "OD1" <-> "OD2" Residue "v ARG 39": "NH1" <-> "NH2" Residue "v GLU 44": "OE1" <-> "OE2" Residue "v GLU 49": "OE1" <-> "OE2" Residue "v ARG 61": "NH1" <-> "NH2" Residue "v ARG 63": "NH1" <-> "NH2" Residue "v ARG 64": "NH1" <-> "NH2" Residue "v GLU 74": "OE1" <-> "OE2" Residue "v ASP 75": "OD1" <-> "OD2" Residue "v GLU 81": "OE1" <-> "OE2" Residue "v ASP 85": "OD1" <-> "OD2" Residue "v GLU 87": "OE1" <-> "OE2" Residue "v ARG 91": "NH1" <-> "NH2" Residue "v GLU 99": "OE1" <-> "OE2" Residue "v ASP 106": "OD1" <-> "OD2" Residue "v GLU 113": "OE1" <-> "OE2" Residue "v ASP 114": "OD1" <-> "OD2" Residue "v GLU 119": "OE1" <-> "OE2" Residue "v GLU 136": "OE1" <-> "OE2" Residue "v ASP 140": "OD1" <-> "OD2" Residue "v GLU 144": "OE1" <-> "OE2" Residue "v ARG 155": "NH1" <-> "NH2" Residue "v GLU 173": "OE1" <-> "OE2" Residue "v GLU 174": "OE1" <-> "OE2" Residue "v GLU 177": "OE1" <-> "OE2" Residue "v GLU 189": "OE1" <-> "OE2" Residue "v ARG 194": "NH1" <-> "NH2" Residue "n ARG 9": "NH1" <-> "NH2" Residue "n ARG 13": "NH1" <-> "NH2" Residue "n ARG 14": "NH1" <-> "NH2" Residue "n TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "n ARG 24": "NH1" <-> "NH2" Residue "n ARG 25": "NH1" <-> "NH2" Residue "n ARG 32": "NH1" <-> "NH2" Residue "n ARG 61": "NH1" <-> "NH2" Residue "n ARG 62": "NH1" <-> "NH2" Residue "n ARG 70": "NH1" <-> "NH2" Residue "n ARG 74": "NH1" <-> "NH2" Residue "n ARG 84": "NH1" <-> "NH2" Residue "x ARG 75": "NH1" <-> "NH2" Residue "x PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 PHE 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "8 GLU 350": "OE1" <-> "OE2" Residue "8 PHE 356": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 55412 Number of models: 1 Model: "" Number of chains: 26 Chain: "b" Number of atoms: 1787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1787 Classifications: {'peptide': 227} Link IDs: {'PTRANS': 7, 'TRANS': 219} Chain: "c" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1719 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 7, 'TRANS': 205} Chain: "e" Number of atoms: 1292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1292 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 5, 'TRANS': 165} Chain: "f" Number of atoms: 886 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 886 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 7, 'TRANS': 103} Chain: "g" Number of atoms: 1161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1161 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 5, 'TRANS': 143} Chain: "h" Number of atoms: 1088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1088 Classifications: {'peptide': 134} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 130} Chain: "i" Number of atoms: 1020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1020 Classifications: {'peptide': 133} Link IDs: {'PTRANS': 6, 'TRANS': 126} Chain: "j" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 796 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 90} Chain: "k" Number of atoms: 887 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 887 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 967 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain: "m" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 898 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "o" Number of atoms: 525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 525 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "p" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 664 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 3, 'TRANS': 76} Chain: "q" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 635 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 5, 'TRANS': 72} Chain: "r" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 518 Classifications: {'peptide': 64} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 62} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "s" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 627 Classifications: {'peptide': 78} Link IDs: {'PTRANS': 4, 'TRANS': 73} Chain: "t" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 832 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 3, 'TRANS': 101} Chain: "u" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 393 Classifications: {'peptide': 44} Link IDs: {'TRANS': 43} Chain: "y" Number of atoms: 845 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 845 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 2, 'TRANS': 105} Chain: "a" Number of atoms: 31777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1480, 31777 Classifications: {'RNA': 1480} Modifications used: {'rna2p_pur': 118, 'rna2p_pyr': 77, 'rna3p_pur': 730, 'rna3p_pyr': 555} Link IDs: {'rna2p': 195, 'rna3p': 1284} Chain breaks: 2 Chain: "w" Number of atoms: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 689 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 6, 'TRANS': 77} Chain: "d" Number of atoms: 1633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1633 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 11, 'TRANS': 187} Chain: "v" Number of atoms: 1464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1464 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "n" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "x" Number of atoms: 289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 289 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 4, 'TRANS': 32} Chain: "8" Number of atoms: 1201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1201 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 7, 'TRANS': 146} Chain breaks: 1 Time building chain proxies: 22.22, per 1000 atoms: 0.40 Number of scatterers: 55412 At special positions: 0 Unit cell: (223.65, 219.45, 187.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 89 16.00 P 1480 15.00 O 14439 8.00 N 10368 7.00 C 29036 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: 23.40 Conformation dependent library (CDL) restraints added in 3.5 seconds 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5508 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 30 sheets defined 39.2% alpha, 16.1% beta 510 base pairs and 824 stacking pairs defined. Time for finding SS restraints: 19.92 Creating SS restraints... Processing helix chain 'b' and resid 9 through 16 removed outlier: 3.859A pdb=" N MET b 13 " --> pdb=" O ASN b 9 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ALA b 16 " --> pdb=" O GLU b 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 28 through 32 Processing helix chain 'b' and resid 46 through 68 removed outlier: 3.696A pdb=" N ALA b 64 " --> pdb=" O LEU b 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 80 through 90 removed outlier: 3.888A pdb=" N VAL b 84 " --> pdb=" O ALA b 80 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA b 85 " --> pdb=" O ALA b 81 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ARG b 90 " --> pdb=" O ARG b 86 " (cutoff:3.500A) Processing helix chain 'b' and resid 107 through 127 removed outlier: 3.518A pdb=" N THR b 111 " --> pdb=" O ASN b 107 " (cutoff:3.500A) Processing helix chain 'b' and resid 134 through 152 Processing helix chain 'b' and resid 173 through 184 Processing helix chain 'b' and resid 210 through 230 Processing helix chain 'c' and resid 6 through 11 Processing helix chain 'c' and resid 25 through 53 Processing helix chain 'c' and resid 80 through 84 Processing helix chain 'c' and resid 89 through 101 removed outlier: 3.608A pdb=" N GLU c 93 " --> pdb=" O PRO c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 140 through 154 Processing helix chain 'c' and resid 188 through 191 Processing helix chain 'e' and resid 196 through 209 Processing helix chain 'e' and resid 250 through 259 Processing helix chain 'e' and resid 275 through 288 removed outlier: 3.715A pdb=" N THR e 288 " --> pdb=" O VAL e 284 " (cutoff:3.500A) Processing helix chain 'e' and resid 292 through 300 Processing helix chain 'f' and resid 124 through 137 Processing helix chain 'f' and resid 185 through 195 removed outlier: 3.722A pdb=" N ASP f 195 " --> pdb=" O ALA f 191 " (cutoff:3.500A) Processing helix chain 'g' and resid 20 through 30 removed outlier: 3.611A pdb=" N MET g 25 " --> pdb=" O ARG g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 35 through 54 removed outlier: 3.658A pdb=" N GLN g 52 " --> pdb=" O LYS g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 57 through 68 removed outlier: 3.744A pdb=" N GLY g 68 " --> pdb=" O GLN g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 92 through 109 Processing helix chain 'g' and resid 115 through 130 Processing helix chain 'g' and resid 133 through 146 removed outlier: 4.003A pdb=" N MET g 144 " --> pdb=" O GLU g 140 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ALA g 145 " --> pdb=" O THR g 141 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 18 removed outlier: 3.876A pdb=" N ILE h 9 " --> pdb=" O THR h 5 " (cutoff:3.500A) Processing helix chain 'h' and resid 29 through 41 removed outlier: 4.019A pdb=" N ARG h 41 " --> pdb=" O LYS h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 98 through 103 removed outlier: 3.964A pdb=" N MET h 103 " --> pdb=" O LEU h 100 " (cutoff:3.500A) Processing helix chain 'h' and resid 116 through 122 Processing helix chain 'i' and resid 101 through 105 Processing helix chain 'i' and resid 109 through 123 removed outlier: 3.988A pdb=" N GLN i 113 " --> pdb=" O PRO i 109 " (cutoff:3.500A) Proline residue: i 118 - end of helix removed outlier: 3.529A pdb=" N LEU i 122 " --> pdb=" O PRO i 118 " (cutoff:3.500A) Processing helix chain 'i' and resid 138 through 156 removed outlier: 3.576A pdb=" N LYS i 156 " --> pdb=" O ARG i 152 " (cutoff:3.500A) Processing helix chain 'i' and resid 157 through 160 removed outlier: 6.583A pdb=" N SER i 160 " --> pdb=" O VAL i 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 157 through 160' Processing helix chain 'i' and resid 161 through 168 removed outlier: 3.609A pdb=" N GLN i 167 " --> pdb=" O ALA i 163 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLU i 168 " --> pdb=" O PRO i 164 " (cutoff:3.500A) Processing helix chain 'j' and resid 107 through 126 Processing helix chain 'j' and resid 173 through 181 Processing helix chain 'k' and resid 68 through 81 Processing helix chain 'k' and resid 82 through 84 No H-bonds generated for 'chain 'k' and resid 82 through 84' Processing helix chain 'k' and resid 101 through 113 removed outlier: 3.745A pdb=" N ALA k 105 " --> pdb=" O GLY k 101 " (cutoff:3.500A) Processing helix chain 'm' and resid 44 through 51 Processing helix chain 'm' and resid 56 through 64 Processing helix chain 'm' and resid 79 through 93 removed outlier: 3.780A pdb=" N SER m 93 " --> pdb=" O THR m 89 " (cutoff:3.500A) Processing helix chain 'm' and resid 95 through 113 removed outlier: 4.116A pdb=" N LEU m 100 " --> pdb=" O GLU m 96 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ARG m 113 " --> pdb=" O VAL m 109 " (cutoff:3.500A) Processing helix chain 'm' and resid 115 through 123 removed outlier: 3.605A pdb=" N ILE m 123 " --> pdb=" O CYS m 119 " (cutoff:3.500A) Processing helix chain 'o' and resid 22 through 41 Processing helix chain 'o' and resid 48 through 71 removed outlier: 3.961A pdb=" N GLY o 52 " --> pdb=" O SER o 48 " (cutoff:3.500A) Processing helix chain 'o' and resid 72 through 82 removed outlier: 3.725A pdb=" N LEU o 82 " --> pdb=" O LEU o 78 " (cutoff:3.500A) Processing helix chain 'p' and resid 49 through 60 Processing helix chain 'p' and resid 64 through 74 removed outlier: 3.504A pdb=" N ALA p 74 " --> pdb=" O ILE p 70 " (cutoff:3.500A) Processing helix chain 'r' and resid 48 through 53 Processing helix chain 'r' and resid 55 through 72 Processing helix chain 's' and resid 12 through 23 Processing helix chain 's' and resid 41 through 45 removed outlier: 3.591A pdb=" N ILE s 45 " --> pdb=" O PRO s 42 " (cutoff:3.500A) Processing helix chain 's' and resid 70 through 74 removed outlier: 3.553A pdb=" N GLU s 73 " --> pdb=" O LYS s 70 " (cutoff:3.500A) Processing helix chain 't' and resid 82 through 120 Processing helix chain 't' and resid 127 through 148 removed outlier: 3.983A pdb=" N LEU t 131 " --> pdb=" O PRO t 127 " (cutoff:3.500A) Processing helix chain 't' and resid 155 through 171 Processing helix chain 'u' and resid 100 through 106 Processing helix chain 'u' and resid 107 through 113 removed outlier: 7.595A pdb=" N ALA u 110 " --> pdb=" O VAL u 107 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLY u 111 " --> pdb=" O MET u 108 " (cutoff:3.500A) Processing helix chain 'u' and resid 122 through 137 removed outlier: 3.688A pdb=" N ALA u 137 " --> pdb=" O HIS u 133 " (cutoff:3.500A) Processing helix chain 'y' and resid 87 through 102 removed outlier: 3.869A pdb=" N ARG y 91 " --> pdb=" O SER y 87 " (cutoff:3.500A) Processing helix chain 'y' and resid 152 through 175 Processing helix chain 'w' and resid 137 through 148 Processing helix chain 'w' and resid 152 through 176 Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 42 through 59 removed outlier: 3.791A pdb=" N HIS d 57 " --> pdb=" O LYS d 53 " (cutoff:3.500A) Processing helix chain 'd' and resid 61 through 75 Processing helix chain 'd' and resid 78 through 87 removed outlier: 4.167A pdb=" N LEU d 84 " --> pdb=" O GLY d 80 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 98 Processing helix chain 'd' and resid 103 through 113 Processing helix chain 'd' and resid 139 through 144 removed outlier: 3.716A pdb=" N LYS d 143 " --> pdb=" O ASP d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 146 through 155 Processing helix chain 'd' and resid 189 through 197 removed outlier: 3.508A pdb=" N VAL d 193 " --> pdb=" O ASN d 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 10 through 20 Processing helix chain 'v' and resid 34 through 44 removed outlier: 3.853A pdb=" N GLU v 44 " --> pdb=" O THR v 40 " (cutoff:3.500A) Processing helix chain 'v' and resid 72 through 84 removed outlier: 3.869A pdb=" N ASN v 84 " --> pdb=" O ILE v 80 " (cutoff:3.500A) Processing helix chain 'v' and resid 105 through 116 Processing helix chain 'v' and resid 134 through 145 Processing helix chain 'v' and resid 172 through 184 Processing helix chain 'n' and resid 3 through 32 removed outlier: 3.877A pdb=" N ILE n 7 " --> pdb=" O ARG n 3 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLN n 8 " --> pdb=" O LYS n 4 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR n 20 " --> pdb=" O LEU n 16 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N LEU n 22 " --> pdb=" O GLN n 18 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ILE n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU n 30 " --> pdb=" O SER n 26 " (cutoff:3.500A) Processing helix chain 'n' and resid 43 through 49 Processing helix chain 'n' and resid 80 through 86 removed outlier: 3.866A pdb=" N ARG n 84 " --> pdb=" O GLY n 80 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLU n 85 " --> pdb=" O HIS n 81 " (cutoff:3.500A) Processing helix chain 'x' and resid 61 through 69 removed outlier: 3.751A pdb=" N LYS x 65 " --> pdb=" O THR x 61 " (cutoff:3.500A) Processing helix chain '8' and resid 51 through 66 Processing helix chain '8' and resid 250 through 257 Processing helix chain '8' and resid 289 through 292 Processing helix chain '8' and resid 319 through 323 removed outlier: 4.123A pdb=" N ARG 8 323 " --> pdb=" O GLU 8 320 " (cutoff:3.500A) Processing helix chain '8' and resid 341 through 359 removed outlier: 3.670A pdb=" N GLU 8 347 " --> pdb=" O LYS 8 343 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'b' and resid 37 through 39 Processing sheet with id=AA2, first strand: chain 'b' and resid 94 through 95 removed outlier: 3.507A pdb=" N ILE b 73 " --> pdb=" O HIS b 94 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU b 72 " --> pdb=" O ILE b 166 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'b' and resid 190 through 191 Processing sheet with id=AA4, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.698A pdb=" N LYS c 67 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG c 62 " --> pdb=" O HIS c 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'c' and resid 20 through 21 removed outlier: 3.698A pdb=" N LYS c 67 " --> pdb=" O LEU c 21 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG c 62 " --> pdb=" O HIS c 77 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N THR c 115 " --> pdb=" O VAL c 74 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ILE c 76 " --> pdb=" O THR c 115 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'c' and resid 177 through 181 Processing sheet with id=AA7, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.517A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN e 158 " --> pdb=" O ILE e 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'e' and resid 153 through 165 removed outlier: 5.517A pdb=" N GLU e 154 " --> pdb=" O GLY e 181 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N GLY e 181 " --> pdb=" O GLU e 154 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N VAL e 156 " --> pdb=" O VAL e 179 " (cutoff:3.500A) removed outlier: 5.618A pdb=" N VAL e 179 " --> pdb=" O VAL e 156 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLN e 158 " --> pdb=" O ILE e 177 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN e 186 " --> pdb=" O ASP e 182 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'e' and resid 227 through 228 removed outlier: 6.767A pdb=" N ILE e 248 " --> pdb=" O GLY e 267 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N GLN e 269 " --> pdb=" O ILE e 248 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'f' and resid 106 through 107 Processing sheet with id=AB2, first strand: chain 'f' and resid 146 through 155 removed outlier: 5.392A pdb=" N ASN f 146 " --> pdb=" O LEU f 175 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU f 175 " --> pdb=" O ASN f 146 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N GLY f 148 " --> pdb=" O TYR f 173 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR f 173 " --> pdb=" O GLY f 148 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE f 150 " --> pdb=" O GLY f 171 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLY f 171 " --> pdb=" O ILE f 150 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N LEU f 169 " --> pdb=" O LEU f 152 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE f 172 " --> pdb=" O LEU f 114 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N VAL f 113 " --> pdb=" O ARG f 200 " (cutoff:3.500A) removed outlier: 5.210A pdb=" N ARG f 200 " --> pdb=" O VAL f 113 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'g' and resid 74 through 75 removed outlier: 3.755A pdb=" N ALA g 74 " --> pdb=" O ILE g 89 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'g' and resid 78 through 80 Processing sheet with id=AB5, first strand: chain 'h' and resid 24 through 27 removed outlier: 6.240A pdb=" N PHE h 58 " --> pdb=" O LYS h 50 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N LYS h 50 " --> pdb=" O PHE h 58 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL h 60 " --> pdb=" O ALA h 48 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ALA h 48 " --> pdb=" O VAL h 60 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N THR h 62 " --> pdb=" O GLU h 46 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'h' and resid 114 through 115 removed outlier: 3.562A pdb=" N LEU h 108 " --> pdb=" O MET h 115 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N ILE h 105 " --> pdb=" O TYR h 132 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR h 132 " --> pdb=" O ILE h 105 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ILE h 107 " --> pdb=" O LEU h 130 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU h 128 " --> pdb=" O SER h 109 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'i' and resid 73 through 78 removed outlier: 3.551A pdb=" N HIS i 135 " --> pdb=" O ILE i 82 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'i' and resid 95 through 96 Processing sheet with id=AB9, first strand: chain 'j' and resid 130 through 134 removed outlier: 4.871A pdb=" N GLY j 131 " --> pdb=" O ASP j 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP j 168 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'j' and resid 130 through 134 removed outlier: 4.871A pdb=" N GLY j 131 " --> pdb=" O ASP j 168 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N ASP j 168 " --> pdb=" O GLY j 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'k' and resid 50 through 55 removed outlier: 6.235A pdb=" N GLY k 28 " --> pdb=" O GLU k 92 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N MET k 94 " --> pdb=" O GLY k 28 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ILE k 30 " --> pdb=" O MET k 94 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N LYS k 96 " --> pdb=" O ILE k 30 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N VAL k 32 " --> pdb=" O LYS k 96 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N ALA k 91 " --> pdb=" O SER k 117 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL k 119 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N VAL k 93 " --> pdb=" O VAL k 119 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N ASP k 121 " --> pdb=" O VAL k 93 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ILE k 95 " --> pdb=" O ASP k 121 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'l' and resid 39 through 40 removed outlier: 4.390A pdb=" N TYR l 95 " --> pdb=" O THR l 64 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ARG l 54 " --> pdb=" O THR l 35 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'p' and resid 2 through 8 removed outlier: 4.042A pdb=" N ILE p 22 " --> pdb=" O LYS p 3 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'q' and resid 61 through 64 removed outlier: 3.793A pdb=" N ASP q 115 " --> pdb=" O LEU q 127 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU q 127 " --> pdb=" O ASP q 115 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N PHE q 126 " --> pdb=" O GLN q 98 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 's' and resid 48 through 52 Processing sheet with id=AC7, first strand: chain 'y' and resid 76 through 82 removed outlier: 6.109A pdb=" N LYS y 76 " --> pdb=" O VAL y 112 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N VAL y 114 " --> pdb=" O LYS y 76 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ILE y 78 " --> pdb=" O VAL y 114 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU y 116 " --> pdb=" O ILE y 78 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N GLN y 80 " --> pdb=" O LEU y 116 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N ALA y 118 " --> pdb=" O GLN y 80 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N ARG y 82 " --> pdb=" O ALA y 118 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'w' and resid 100 through 106 Processing sheet with id=AC9, first strand: chain 'd' and resid 117 through 118 Processing sheet with id=AD1, first strand: chain 'v' and resid 48 through 53 removed outlier: 3.714A pdb=" N THR v 86 " --> pdb=" O ILE v 93 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'v' and resid 148 through 154 removed outlier: 3.923A pdb=" N PHE v 165 " --> pdb=" O GLN v 154 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS v 123 " --> pdb=" O ALA v 198 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '8' and resid 309 through 310 removed outlier: 7.097A pdb=" N PHE 8 277 " --> pdb=" O GLN 8 269 " (cutoff:3.500A) removed outlier: 5.396A pdb=" N LEU 8 271 " --> pdb=" O GLY 8 275 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N GLY 8 275 " --> pdb=" O LEU 8 271 " (cutoff:3.500A) removed outlier: 8.209A pdb=" N LEU 8 326 " --> pdb=" O ASN 8 284 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU 8 286 " --> pdb=" O LEU 8 326 " (cutoff:3.500A) 1015 hydrogen bonds defined for protein. 2910 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 1289 hydrogen bonds 2036 hydrogen bond angles 0 basepair planarities 510 basepair parallelities 824 stacking parallelities Total time for adding SS restraints: 35.44 Time building geometry restraints manager: 25.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.01 - 1.17: 13 1.17 - 1.34: 13199 1.34 - 1.50: 28462 1.50 - 1.66: 17764 1.66 - 1.83: 147 Bond restraints: 59585 Sorted by residual: bond pdb=" CZ ARG h 67 " pdb=" NH2 ARG h 67 " ideal model delta sigma weight residual 1.330 1.127 0.203 1.30e-02 5.92e+03 2.45e+02 bond pdb=" CB ARG h 67 " pdb=" CG ARG h 67 " ideal model delta sigma weight residual 1.520 1.127 0.393 3.00e-02 1.11e+03 1.72e+02 bond pdb=" CE1 PHE v 142 " pdb=" CZ PHE v 142 " ideal model delta sigma weight residual 1.382 1.008 0.374 3.00e-02 1.11e+03 1.55e+02 bond pdb=" CE2 PHE v 142 " pdb=" CZ PHE v 142 " ideal model delta sigma weight residual 1.382 1.030 0.352 3.00e-02 1.11e+03 1.38e+02 bond pdb=" CG ASN b 7 " pdb=" ND2 ASN b 7 " ideal model delta sigma weight residual 1.328 1.084 0.244 2.10e-02 2.27e+03 1.35e+02 ... (remaining 59580 not shown) Histogram of bond angle deviations from ideal: 85.27 - 97.33: 9 97.33 - 109.39: 22095 109.39 - 121.45: 50762 121.45 - 133.51: 14816 133.51 - 145.57: 56 Bond angle restraints: 87738 Sorted by residual: angle pdb=" NE ARG h 67 " pdb=" CZ ARG h 67 " pdb=" NH1 ARG h 67 " ideal model delta sigma weight residual 121.50 145.57 -24.07 1.00e+00 1.00e+00 5.79e+02 angle pdb=" CA ASP b 201 " pdb=" CB ASP b 201 " pdb=" CG ASP b 201 " ideal model delta sigma weight residual 112.60 126.79 -14.19 1.00e+00 1.00e+00 2.01e+02 angle pdb=" NH1 ARG h 67 " pdb=" CZ ARG h 67 " pdb=" NH2 ARG h 67 " ideal model delta sigma weight residual 119.30 101.21 18.09 1.30e+00 5.92e-01 1.94e+02 angle pdb=" CD ARG h 67 " pdb=" NE ARG h 67 " pdb=" CZ ARG h 67 " ideal model delta sigma weight residual 124.40 143.78 -19.38 1.40e+00 5.10e-01 1.92e+02 angle pdb=" CB ARG h 67 " pdb=" CG ARG h 67 " pdb=" CD ARG h 67 " ideal model delta sigma weight residual 111.30 143.04 -31.74 2.30e+00 1.89e-01 1.90e+02 ... (remaining 87733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.46: 34071 35.46 - 70.92: 3532 70.92 - 106.38: 462 106.38 - 141.85: 9 141.85 - 177.31: 5 Dihedral angle restraints: 38079 sinusoidal: 29550 harmonic: 8529 Sorted by residual: dihedral pdb=" CA THR 8 302 " pdb=" C THR 8 302 " pdb=" N VAL 8 303 " pdb=" CA VAL 8 303 " ideal model delta harmonic sigma weight residual 180.00 -103.83 -76.17 0 5.00e+00 4.00e-02 2.32e+02 dihedral pdb=" CA MET 8 72 " pdb=" C MET 8 72 " pdb=" N GLU 8 73 " pdb=" CA GLU 8 73 " ideal model delta harmonic sigma weight residual 180.00 110.70 69.30 0 5.00e+00 4.00e-02 1.92e+02 dihedral pdb=" CA ARG 8 359 " pdb=" C ARG 8 359 " pdb=" N ILE 8 360 " pdb=" CA ILE 8 360 " ideal model delta harmonic sigma weight residual 180.00 120.01 59.99 0 5.00e+00 4.00e-02 1.44e+02 ... (remaining 38076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.238: 10924 0.238 - 0.477: 58 0.477 - 0.715: 9 0.715 - 0.953: 2 0.953 - 1.192: 1 Chirality restraints: 10994 Sorted by residual: chirality pdb=" CB ILE 8 280 " pdb=" CA ILE 8 280 " pdb=" CG1 ILE 8 280 " pdb=" CG2 ILE 8 280 " both_signs ideal model delta sigma weight residual False 2.64 1.45 1.19 2.00e-01 2.50e+01 3.55e+01 chirality pdb=" CG LEU 8 315 " pdb=" CB LEU 8 315 " pdb=" CD1 LEU 8 315 " pdb=" CD2 LEU 8 315 " both_signs ideal model delta sigma weight residual False -2.59 -1.71 -0.88 2.00e-01 2.50e+01 1.92e+01 chirality pdb=" CG LEU b 60 " pdb=" CB LEU b 60 " pdb=" CD1 LEU b 60 " pdb=" CD2 LEU b 60 " both_signs ideal model delta sigma weight residual False -2.59 -1.84 -0.75 2.00e-01 2.50e+01 1.41e+01 ... (remaining 10991 not shown) Planarity restraints: 5617 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE u 103 " -0.122 2.00e-02 2.50e+03 8.62e-02 1.30e+02 pdb=" CG PHE u 103 " 0.085 2.00e-02 2.50e+03 pdb=" CD1 PHE u 103 " 0.047 2.00e-02 2.50e+03 pdb=" CD2 PHE u 103 " 0.078 2.00e-02 2.50e+03 pdb=" CE1 PHE u 103 " 0.036 2.00e-02 2.50e+03 pdb=" CE2 PHE u 103 " 0.017 2.00e-02 2.50e+03 pdb=" CZ PHE u 103 " -0.141 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE 8 346 " -0.034 2.00e-02 2.50e+03 7.76e-02 1.05e+02 pdb=" CG PHE 8 346 " 0.157 2.00e-02 2.50e+03 pdb=" CD1 PHE 8 346 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 PHE 8 346 " -0.108 2.00e-02 2.50e+03 pdb=" CE1 PHE 8 346 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE 8 346 " 0.034 2.00e-02 2.50e+03 pdb=" CZ PHE 8 346 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE v 165 " 0.113 2.00e-02 2.50e+03 7.37e-02 9.50e+01 pdb=" CG PHE v 165 " -0.129 2.00e-02 2.50e+03 pdb=" CD1 PHE v 165 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE v 165 " -0.042 2.00e-02 2.50e+03 pdb=" CE1 PHE v 165 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE v 165 " -0.007 2.00e-02 2.50e+03 pdb=" CZ PHE v 165 " 0.082 2.00e-02 2.50e+03 ... (remaining 5614 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 21 1.98 - 2.71: 5724 2.71 - 3.44: 74922 3.44 - 4.17: 171935 4.17 - 4.90: 237432 Nonbonded interactions: 490034 Sorted by model distance: nonbonded pdb=" ND1 HIS d 163 " pdb=" CD1 ILE d 179 " model vdw 1.255 3.540 nonbonded pdb=" O PHE u 103 " pdb=" CE2 TRP w 138 " model vdw 1.356 3.260 nonbonded pdb=" NZ LYS d 51 " pdb=" OH TYR d 197 " model vdw 1.471 2.520 nonbonded pdb=" OP1 U a 75 " pdb=" CZ ARG v 194 " model vdw 1.522 3.270 nonbonded pdb=" O PHE u 103 " pdb=" CD2 TRP w 138 " model vdw 1.548 3.260 ... (remaining 490029 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.300 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: 0.030 Extract box with map and model: 12.800 Check model and map are aligned: 0.640 Set scattering table: 0.400 Process input model: 143.570 Find NCS groups from input model: 1.130 Set up NCS constraints: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 163.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 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 : 0.012 0.393 59585 Z= 0.719 Angle : 1.321 31.737 87738 Z= 0.674 Chirality : 0.063 1.192 10994 Planarity : 0.011 0.166 5617 Dihedral : 22.251 177.307 32571 Min Nonbonded Distance : 1.255 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 1.10 % Allowed : 12.14 % Favored : 86.77 % Rotamer: Outliers : 1.03 % Allowed : 3.63 % Favored : 95.35 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.83 % Twisted General : 1.56 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.13), residues: 2917 helix: -2.57 (0.12), residues: 1059 sheet: -2.44 (0.21), residues: 443 loop : -3.00 (0.14), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP w 150 HIS 0.035 0.004 HIS 8 294 PHE 0.157 0.009 PHE 8 346 TYR 0.091 0.005 TYR w 130 ARG 0.153 0.002 ARG v 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1218 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1192 time to evaluate : 2.921 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: b 120 ASP cc_start: 0.7758 (m-30) cc_final: 0.7366 (m-30) REVERT: c 31 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8057 (mm-30) REVERT: c 35 GLU cc_start: 0.7924 (mm-30) cc_final: 0.7669 (mm-30) REVERT: c 73 GLN cc_start: 0.8780 (tp40) cc_final: 0.8445 (tm-30) REVERT: c 74 VAL cc_start: 0.9055 (t) cc_final: 0.8820 (t) REVERT: c 78 MET cc_start: 0.7992 (ptp) cc_final: 0.7607 (ptm) REVERT: c 81 PRO cc_start: 0.8659 (Cg_endo) cc_final: 0.8393 (Cg_exo) REVERT: c 98 ASN cc_start: 0.8664 (m-40) cc_final: 0.8102 (p0) REVERT: e 263 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8179 (mm-30) REVERT: e 268 LYS cc_start: 0.8394 (tptt) cc_final: 0.7598 (tttt) REVERT: e 292 PHE cc_start: 0.8274 (m-80) cc_final: 0.7882 (p90) REVERT: e 297 ARG cc_start: 0.8215 (ttp80) cc_final: 0.7969 (tmm-80) REVERT: e 305 GLU cc_start: 0.5927 (OUTLIER) cc_final: 0.5327 (tp30) REVERT: f 174 LEU cc_start: 0.8553 (mt) cc_final: 0.8128 (mp) REVERT: f 176 PHE cc_start: 0.8269 (m-10) cc_final: 0.8068 (m-80) REVERT: f 177 THR cc_start: 0.9002 (m) cc_final: 0.8487 (p) REVERT: f 185 ILE cc_start: 0.8469 (mt) cc_final: 0.8163 (tt) REVERT: g 27 VAL cc_start: 0.8894 (p) cc_final: 0.8641 (p) REVERT: g 37 SER cc_start: 0.9313 (m) cc_final: 0.8971 (p) REVERT: g 110 LYS cc_start: 0.8272 (mmmt) cc_final: 0.7893 (mtmm) REVERT: g 129 LYS cc_start: 0.8485 (mmmt) cc_final: 0.8015 (tmtt) REVERT: h 8 ASP cc_start: 0.8305 (t70) cc_final: 0.8078 (t70) REVERT: h 17 ASP cc_start: 0.8490 (p0) cc_final: 0.8190 (p0) REVERT: h 37 LYS cc_start: 0.9135 (ttpt) cc_final: 0.8892 (ptmt) REVERT: h 67 ARG cc_start: 0.0191 (OUTLIER) cc_final: -0.1024 (ttt180) REVERT: h 92 ASN cc_start: 0.9101 (p0) cc_final: 0.8886 (p0) REVERT: i 116 LYS cc_start: 0.9068 (mmtt) cc_final: 0.8714 (mmmm) REVERT: j 117 GLN cc_start: 0.8924 (pt0) cc_final: 0.8436 (pp30) REVERT: j 181 MET cc_start: 0.7035 (mmt) cc_final: 0.6760 (mmt) REVERT: k 58 THR cc_start: 0.9307 (m) cc_final: 0.9077 (p) REVERT: k 65 LYS cc_start: 0.9001 (mttt) cc_final: 0.8772 (mtpp) REVERT: l 47 SER cc_start: 0.8890 (t) cc_final: 0.8496 (t) REVERT: l 62 GLU cc_start: 0.8311 (mt-10) cc_final: 0.7824 (mt-10) REVERT: m 83 ASN cc_start: 0.9161 (m-40) cc_final: 0.8931 (t0) REVERT: m 86 ASN cc_start: 0.9299 (m-40) cc_final: 0.8951 (m-40) REVERT: m 115 LYS cc_start: 0.8066 (mtpp) cc_final: 0.7525 (pttt) REVERT: o 70 ILE cc_start: 0.8620 (mt) cc_final: 0.8211 (mt) REVERT: o 71 ASN cc_start: 0.7782 (m-40) cc_final: 0.7058 (m-40) REVERT: p 12 LYS cc_start: 0.8860 (ttpt) cc_final: 0.8609 (tttt) REVERT: p 31 ARG cc_start: 0.8569 (ptm-80) cc_final: 0.8234 (ptm160) REVERT: p 34 GLN cc_start: 0.7778 (tp40) cc_final: 0.7521 (tp40) REVERT: p 39 TYR cc_start: 0.9144 (t80) cc_final: 0.8929 (t80) REVERT: q 101 ASP cc_start: 0.7399 (t0) cc_final: 0.7116 (t0) REVERT: q 118 ARG cc_start: 0.8793 (ttp80) cc_final: 0.8067 (ptm-80) REVERT: q 127 LEU cc_start: 0.9256 (pp) cc_final: 0.8845 (pp) REVERT: r 34 SER cc_start: 0.9169 (m) cc_final: 0.8943 (p) REVERT: s 44 MET cc_start: 0.8571 (ttm) cc_final: 0.8277 (tmm) REVERT: s 47 HIS cc_start: 0.8491 (m-70) cc_final: 0.7864 (m90) REVERT: t 91 LEU cc_start: 0.8744 (mt) cc_final: 0.8476 (tp) REVERT: t 115 LYS cc_start: 0.9376 (tttt) cc_final: 0.9171 (tptt) REVERT: t 145 LYS cc_start: 0.8942 (mmpt) cc_final: 0.8648 (mmtt) REVERT: t 164 LYS cc_start: 0.8772 (mmpt) cc_final: 0.8330 (mmmt) REVERT: y 153 LEU cc_start: 0.8573 (mt) cc_final: 0.8082 (mp) REVERT: w 167 ILE cc_start: -0.0032 (OUTLIER) cc_final: -0.0387 (tp) REVERT: d 85 GLN cc_start: 0.8382 (mt0) cc_final: 0.7658 (mt0) REVERT: d 100 MET cc_start: 0.7990 (mmt) cc_final: 0.7676 (mmt) REVERT: d 123 VAL cc_start: 0.9451 (t) cc_final: 0.9041 (m) REVERT: d 124 ASP cc_start: 0.6574 (m-30) cc_final: 0.6239 (m-30) REVERT: d 178 ILE cc_start: 0.8715 (mt) cc_final: 0.8299 (pt) REVERT: d 180 ASP cc_start: 0.7287 (t0) cc_final: 0.6558 (t0) REVERT: 8 251 MET cc_start: 0.0364 (mpt) cc_final: -0.1468 (mpt) REVERT: 8 352 MET cc_start: 0.1359 (mmm) cc_final: 0.0447 (ptt) outliers start: 26 outliers final: 4 residues processed: 1208 average time/residue: 0.6929 time to fit residues: 1313.9371 Evaluate side-chains 886 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 879 time to evaluate : 3.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 201 ASP Chi-restraints excluded: chain e residue 305 GLU Chi-restraints excluded: chain h residue 67 ARG Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain y residue 159 LEU Chi-restraints excluded: chain w residue 167 ILE Chi-restraints excluded: chain d residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 365 optimal weight: 0.8980 chunk 328 optimal weight: 1.9990 chunk 182 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 221 optimal weight: 3.9990 chunk 175 optimal weight: 0.3980 chunk 339 optimal weight: 5.9990 chunk 131 optimal weight: 0.9990 chunk 206 optimal weight: 0.9990 chunk 252 optimal weight: 6.9990 chunk 393 optimal weight: 8.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 34 GLN c 73 GLN c 134 GLN c 187 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 24 ASN g 86 GLN ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 51 HIS h 78 HIS i 127 ASN ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 HIS k 31 HIS k 127 HIS ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 83 ASN m 125 HIS ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 68 GLN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 124 ASN ** u 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 34 ASN d 64 GLN d 93 ASN ** d 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 96 ASN v 135 ASN v 163 ASN n 8 GLN ** n 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8 269 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 59585 Z= 0.193 Angle : 0.731 16.764 87738 Z= 0.373 Chirality : 0.040 0.601 10994 Planarity : 0.006 0.100 5617 Dihedral : 23.603 176.618 26497 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.72 % Allowed : 9.19 % Favored : 90.09 % Rotamer: Outliers : 4.85 % Allowed : 16.64 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.14), residues: 2917 helix: -1.01 (0.14), residues: 1095 sheet: -1.50 (0.24), residues: 456 loop : -3.00 (0.15), residues: 1366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP w 138 HIS 0.014 0.002 HIS d 163 PHE 0.027 0.002 PHE i 94 TYR 0.027 0.002 TYR w 130 ARG 0.014 0.001 ARG p 25 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1093 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 970 time to evaluate : 2.950 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: b 30 ARG cc_start: 0.7088 (OUTLIER) cc_final: 0.6776 (mmm-85) REVERT: b 120 ASP cc_start: 0.7751 (m-30) cc_final: 0.7513 (m-30) REVERT: c 73 GLN cc_start: 0.8612 (tp-100) cc_final: 0.8228 (tm-30) REVERT: c 78 MET cc_start: 0.7901 (ptp) cc_final: 0.7694 (ptm) REVERT: c 93 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7748 (mm-30) REVERT: c 98 ASN cc_start: 0.8509 (m-40) cc_final: 0.8075 (p0) REVERT: c 204 TYR cc_start: 0.6603 (p90) cc_final: 0.6123 (p90) REVERT: e 277 ASN cc_start: 0.9112 (m-40) cc_final: 0.8766 (m-40) REVERT: e 292 PHE cc_start: 0.8258 (m-80) cc_final: 0.7402 (p90) REVERT: f 111 MET cc_start: 0.7431 (tpp) cc_final: 0.7168 (tpp) REVERT: f 177 THR cc_start: 0.8882 (m) cc_final: 0.8511 (p) REVERT: f 200 ARG cc_start: 0.7857 (tpp-160) cc_final: 0.7651 (ttm170) REVERT: f 204 PHE cc_start: 0.8485 (m-80) cc_final: 0.7786 (m-80) REVERT: g 129 LYS cc_start: 0.8535 (mmmt) cc_final: 0.8127 (tmtt) REVERT: h 11 THR cc_start: 0.9172 (OUTLIER) cc_final: 0.8972 (p) REVERT: h 12 CYS cc_start: 0.8842 (m) cc_final: 0.8377 (m) REVERT: h 17 ASP cc_start: 0.8358 (p0) cc_final: 0.7864 (p0) REVERT: h 19 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7759 (p0) REVERT: h 37 LYS cc_start: 0.9210 (ttpt) cc_final: 0.8941 (ptmt) REVERT: h 70 LYS cc_start: 0.5728 (tttp) cc_final: 0.5023 (pttp) REVERT: h 72 PRO cc_start: 0.7894 (Cg_endo) cc_final: 0.7240 (Cg_exo) REVERT: h 108 LEU cc_start: 0.9322 (pp) cc_final: 0.9077 (pt) REVERT: i 98 TYR cc_start: 0.8892 (m-80) cc_final: 0.8612 (m-80) REVERT: i 102 LYS cc_start: 0.9219 (mppt) cc_final: 0.8805 (mppt) REVERT: k 27 LYS cc_start: 0.8889 (ptmt) cc_final: 0.8654 (ptmm) REVERT: k 73 GLN cc_start: 0.9046 (OUTLIER) cc_final: 0.8633 (mm-40) REVERT: k 125 MET cc_start: 0.7202 (tmm) cc_final: 0.6877 (tmm) REVERT: l 47 SER cc_start: 0.8824 (t) cc_final: 0.8396 (t) REVERT: l 59 SER cc_start: 0.9089 (p) cc_final: 0.8865 (p) REVERT: l 77 HIS cc_start: 0.8046 (OUTLIER) cc_final: 0.7659 (t-90) REVERT: m 83 ASN cc_start: 0.9073 (m110) cc_final: 0.8842 (t0) REVERT: m 115 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7661 (mtmt) REVERT: o 56 THR cc_start: 0.8975 (m) cc_final: 0.8548 (p) REVERT: o 67 LEU cc_start: 0.9198 (tp) cc_final: 0.8922 (tt) REVERT: o 70 ILE cc_start: 0.8251 (mt) cc_final: 0.7781 (mt) REVERT: o 71 ASN cc_start: 0.7585 (m-40) cc_final: 0.7183 (m-40) REVERT: p 12 LYS cc_start: 0.8760 (ttpt) cc_final: 0.8385 (tttt) REVERT: p 39 TYR cc_start: 0.8937 (t80) cc_final: 0.8530 (t80) REVERT: r 30 TYR cc_start: 0.8135 (p90) cc_final: 0.7863 (p90) REVERT: r 49 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7273 (ttt-90) REVERT: s 20 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7947 (mm-30) REVERT: s 47 HIS cc_start: 0.8381 (m-70) cc_final: 0.7824 (m90) REVERT: s 62 ILE cc_start: 0.9225 (mm) cc_final: 0.9009 (mm) REVERT: s 70 LYS cc_start: 0.8207 (mttt) cc_final: 0.7946 (mttt) REVERT: t 81 LYS cc_start: 0.7330 (mtpm) cc_final: 0.6958 (mtpm) REVERT: t 92 ARG cc_start: 0.8488 (mtm-85) cc_final: 0.7994 (ttm-80) REVERT: t 101 LYS cc_start: 0.8345 (ttmt) cc_final: 0.7918 (ttmt) REVERT: t 115 LYS cc_start: 0.9401 (tttt) cc_final: 0.9198 (tptt) REVERT: t 164 LYS cc_start: 0.8562 (mmpt) cc_final: 0.8127 (mmmt) REVERT: y 159 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8299 (mt) REVERT: d 60 ILE cc_start: 0.8818 (mm) cc_final: 0.8579 (mm) REVERT: d 89 MET cc_start: 0.7634 (mmm) cc_final: 0.7409 (mmt) REVERT: d 123 VAL cc_start: 0.9403 (t) cc_final: 0.9170 (m) REVERT: d 180 ASP cc_start: 0.8558 (t0) cc_final: 0.8034 (t0) REVERT: v 54 MET cc_start: -0.0973 (OUTLIER) cc_final: -0.1580 (ppp) REVERT: 8 251 MET cc_start: 0.0017 (mpt) cc_final: -0.1950 (mpt) REVERT: 8 269 GLN cc_start: 0.1483 (OUTLIER) cc_final: 0.1056 (tm-30) REVERT: 8 352 MET cc_start: 0.1144 (mmm) cc_final: 0.0452 (ptt) REVERT: 8 366 MET cc_start: 0.4374 (tmm) cc_final: 0.4157 (tmm) REVERT: 8 371 MET cc_start: -0.0615 (mtt) cc_final: -0.2492 (ptm) outliers start: 123 outliers final: 62 residues processed: 1022 average time/residue: 0.6131 time to fit residues: 998.4788 Evaluate side-chains 911 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 840 time to evaluate : 2.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 133 LEU Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 196 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 150 ILE Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 19 ASN Chi-restraints excluded: chain h residue 23 THR Chi-restraints excluded: chain h residue 93 TYR Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 85 VAL Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 160 SER Chi-restraints excluded: chain j residue 112 GLU Chi-restraints excluded: chain j residue 143 CYS Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 73 GLN Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 34 LYS Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain r residue 38 ARG Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 116 LYS Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 109 VAL Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 159 LEU Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 61 THR Chi-restraints excluded: chain d residue 171 TYR Chi-restraints excluded: chain v residue 24 LEU Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 84 ASN Chi-restraints excluded: chain v residue 105 MET Chi-restraints excluded: chain v residue 133 VAL Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain v residue 175 GLU Chi-restraints excluded: chain n residue 44 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain 8 residue 264 VAL Chi-restraints excluded: chain 8 residue 269 GLN Chi-restraints excluded: chain 8 residue 314 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 218 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 267 optimal weight: 7.9990 chunk 108 optimal weight: 0.0770 chunk 393 optimal weight: 8.9990 chunk 425 optimal weight: 30.0000 chunk 350 optimal weight: 10.0000 chunk 390 optimal weight: 9.9990 chunk 134 optimal weight: 2.9990 chunk 316 optimal weight: 6.9990 overall best weight: 4.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 134 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 264 ASN ** e 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 19 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 142 GLN ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN m 68 HIS ** m 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 70 ASN q 75 ASN r 52 ASN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 101 ASN ** u 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 GLN w 168 ASN d 64 GLN ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 135 ASN n 29 GLN 8 58 GLN ** 8 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.102 59585 Z= 0.444 Angle : 0.841 12.504 87738 Z= 0.424 Chirality : 0.043 0.280 10994 Planarity : 0.007 0.097 5617 Dihedral : 23.522 174.796 26483 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 22.14 Ramachandran Plot: Outliers : 0.58 % Allowed : 12.17 % Favored : 87.25 % Rotamer: Outliers : 7.45 % Allowed : 17.78 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.68 (0.15), residues: 2917 helix: -0.59 (0.15), residues: 1113 sheet: -1.68 (0.23), residues: 487 loop : -2.90 (0.15), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP j 107 HIS 0.011 0.003 HIS d 163 PHE 0.026 0.003 PHE 8 346 TYR 0.035 0.003 TYR h 132 ARG 0.009 0.001 ARG p 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1049 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 860 time to evaluate : 2.959 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: b 30 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6641 (mmm-85) REVERT: b 89 ILE cc_start: 0.7978 (mt) cc_final: 0.7768 (mm) REVERT: b 120 ASP cc_start: 0.7786 (m-30) cc_final: 0.7577 (m-30) REVERT: b 156 LYS cc_start: 0.4842 (tttt) cc_final: 0.4544 (tptm) REVERT: b 225 ILE cc_start: 0.8604 (mm) cc_final: 0.8356 (mt) REVERT: c 68 ARG cc_start: 0.8371 (ttp80) cc_final: 0.7913 (ttp80) REVERT: c 98 ASN cc_start: 0.8545 (m-40) cc_final: 0.8214 (p0) REVERT: c 129 GLU cc_start: 0.8161 (tp30) cc_final: 0.7886 (tp30) REVERT: c 141 PHE cc_start: 0.6510 (p90) cc_final: 0.6225 (p90) REVERT: e 186 GLN cc_start: 0.8653 (tp40) cc_final: 0.8289 (tp40) REVERT: e 211 ASN cc_start: 0.8365 (t0) cc_final: 0.7640 (t0) REVERT: e 292 PHE cc_start: 0.8457 (m-80) cc_final: 0.7587 (p90) REVERT: f 177 THR cc_start: 0.9068 (m) cc_final: 0.8587 (p) REVERT: g 129 LYS cc_start: 0.8715 (mmmt) cc_final: 0.8087 (tmtt) REVERT: g 146 GLU cc_start: 0.8819 (tm-30) cc_final: 0.8592 (tp30) REVERT: h 11 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.9053 (p) REVERT: h 12 CYS cc_start: 0.8906 (m) cc_final: 0.8438 (m) REVERT: h 37 LYS cc_start: 0.9176 (ttpt) cc_final: 0.8882 (ptmt) REVERT: h 70 LYS cc_start: 0.5747 (tttp) cc_final: 0.5315 (pttp) REVERT: i 121 THR cc_start: 0.8656 (p) cc_final: 0.8439 (p) REVERT: j 150 VAL cc_start: 0.9160 (p) cc_final: 0.8958 (p) REVERT: j 162 THR cc_start: 0.9160 (m) cc_final: 0.8754 (p) REVERT: j 168 ASP cc_start: 0.8156 (m-30) cc_final: 0.7787 (m-30) REVERT: l 47 SER cc_start: 0.8758 (t) cc_final: 0.8398 (t) REVERT: l 77 HIS cc_start: 0.8138 (OUTLIER) cc_final: 0.7911 (t-90) REVERT: l 103 ASP cc_start: 0.8482 (t0) cc_final: 0.8138 (t0) REVERT: m 90 LYS cc_start: 0.8935 (mtpp) cc_final: 0.8554 (mtpp) REVERT: m 115 LYS cc_start: 0.8309 (mtpp) cc_final: 0.7452 (mtmt) REVERT: m 132 ARG cc_start: 0.6500 (mtt90) cc_final: 0.6270 (mtt90) REVERT: o 56 THR cc_start: 0.8785 (m) cc_final: 0.8407 (t) REVERT: o 71 ASN cc_start: 0.7493 (m-40) cc_final: 0.7263 (m-40) REVERT: p 11 ARG cc_start: 0.8908 (mtm-85) cc_final: 0.8694 (mtm-85) REVERT: q 71 ASP cc_start: 0.8613 (t0) cc_final: 0.8164 (p0) REVERT: q 96 LYS cc_start: 0.9111 (OUTLIER) cc_final: 0.8884 (ptmm) REVERT: q 105 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8449 (pm20) REVERT: r 49 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7727 (ttm-80) REVERT: r 51 VAL cc_start: 0.7190 (t) cc_final: 0.6979 (t) REVERT: s 10 PHE cc_start: 0.8359 (t80) cc_final: 0.8128 (t80) REVERT: s 44 MET cc_start: 0.8487 (tmm) cc_final: 0.8202 (tmm) REVERT: s 47 HIS cc_start: 0.8541 (m-70) cc_final: 0.7877 (m90) REVERT: t 101 LYS cc_start: 0.8696 (ttmt) cc_final: 0.8466 (ttmt) REVERT: t 105 ARG cc_start: 0.8552 (mmt180) cc_final: 0.8149 (mtt-85) REVERT: t 145 LYS cc_start: 0.8927 (mmpt) cc_final: 0.8508 (mmtt) REVERT: t 152 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8478 (p) REVERT: t 155 ARG cc_start: 0.7401 (mtt180) cc_final: 0.7160 (mtt90) REVERT: t 164 LYS cc_start: 0.8657 (mmpt) cc_final: 0.8135 (mmmt) REVERT: t 168 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8268 (tm-30) REVERT: t 173 TRP cc_start: 0.7704 (OUTLIER) cc_final: 0.7339 (t60) REVERT: t 174 TYR cc_start: 0.7409 (m-10) cc_final: 0.6544 (m-10) REVERT: u 126 GLN cc_start: 0.7275 (pp30) cc_final: 0.6917 (pp30) REVERT: y 144 ILE cc_start: 0.8859 (pp) cc_final: 0.8646 (pp) REVERT: d 50 GLU cc_start: 0.7660 (mm-30) cc_final: 0.7160 (mm-30) REVERT: d 123 VAL cc_start: 0.9397 (t) cc_final: 0.9173 (m) REVERT: d 132 PRO cc_start: 0.9201 (Cg_exo) cc_final: 0.8828 (Cg_endo) REVERT: d 188 ILE cc_start: 0.9586 (pt) cc_final: 0.9332 (pt) REVERT: v 54 MET cc_start: -0.1083 (OUTLIER) cc_final: -0.1482 (ppp) REVERT: n 40 LYS cc_start: 0.5980 (tppt) cc_final: 0.5697 (tppt) REVERT: 8 352 MET cc_start: 0.1859 (mmm) cc_final: 0.0995 (ptt) REVERT: 8 371 MET cc_start: -0.1500 (OUTLIER) cc_final: -0.2214 (ptm) outliers start: 189 outliers final: 132 residues processed: 946 average time/residue: 0.6058 time to fit residues: 939.2358 Evaluate side-chains 960 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 818 time to evaluate : 2.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 41 ASP Chi-restraints excluded: chain c residue 47 VAL Chi-restraints excluded: chain c residue 54 SER Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain c residue 196 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 282 THR Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain e residue 303 MET Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 134 LEU Chi-restraints excluded: chain f residue 150 ILE Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain f residue 180 THR Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 121 SER Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 65 HIS Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain h residue 109 SER Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 142 GLN Chi-restraints excluded: chain i residue 165 LEU Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 157 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 130 CYS Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 34 CYS Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 77 HIS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain m residue 139 ASN Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 66 THR Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 96 LYS Chi-restraints excluded: chain q residue 105 GLN Chi-restraints excluded: chain q residue 117 CYS Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 48 SER Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 112 ASP Chi-restraints excluded: chain t residue 125 LEU Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 167 VAL Chi-restraints excluded: chain t residue 173 TRP Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 135 THR Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 159 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 61 THR Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain d residue 171 TYR Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain d residue 193 VAL Chi-restraints excluded: chain d residue 198 SER Chi-restraints excluded: chain v residue 24 LEU Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 84 ASN Chi-restraints excluded: chain v residue 137 LEU Chi-restraints excluded: chain v residue 172 SER Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 61 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 314 ILE Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 341 ASN Chi-restraints excluded: chain 8 residue 370 ASP Chi-restraints excluded: chain 8 residue 371 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 389 optimal weight: 9.9990 chunk 296 optimal weight: 5.9990 chunk 204 optimal weight: 0.9980 chunk 43 optimal weight: 0.0050 chunk 187 optimal weight: 0.8980 chunk 264 optimal weight: 4.9990 chunk 395 optimal weight: 0.9990 chunk 418 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 374 optimal weight: 0.7980 chunk 112 optimal weight: 0.6980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 22 HIS ** c 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 134 GLN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 33 HIS ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 19 ASN h 34 ASN i 127 ASN i 135 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** k 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN o 71 ASN q 62 GLN r 52 ASN r 68 GLN u 114 GLN ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 162 GLN d 85 GLN ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 163 HIS ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 29 GLN n 44 HIS Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 59585 Z= 0.170 Angle : 0.654 12.233 87738 Z= 0.333 Chirality : 0.036 0.281 10994 Planarity : 0.005 0.088 5617 Dihedral : 23.410 175.963 26483 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.36 % Favored : 90.16 % Rotamer: Outliers : 5.80 % Allowed : 21.88 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.15), residues: 2917 helix: -0.09 (0.15), residues: 1109 sheet: -1.08 (0.24), residues: 454 loop : -2.83 (0.15), residues: 1354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP q 111 HIS 0.026 0.001 HIS h 65 PHE 0.025 0.002 PHE i 94 TYR 0.034 0.002 TYR o 75 ARG 0.010 0.001 ARG m 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1012 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 865 time to evaluate : 3.023 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: b 22 HIS cc_start: 0.5058 (OUTLIER) cc_final: 0.4634 (m90) REVERT: b 30 ARG cc_start: 0.6860 (OUTLIER) cc_final: 0.6092 (tpp80) REVERT: b 98 LYS cc_start: 0.8595 (mmmm) cc_final: 0.8316 (mmmm) REVERT: b 120 ASP cc_start: 0.7730 (m-30) cc_final: 0.7507 (m-30) REVERT: b 209 ASP cc_start: 0.6010 (OUTLIER) cc_final: 0.5697 (t0) REVERT: b 225 ILE cc_start: 0.8551 (mm) cc_final: 0.8253 (mt) REVERT: c 31 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7781 (mm-30) REVERT: e 186 GLN cc_start: 0.8583 (tp40) cc_final: 0.8270 (tp40) REVERT: e 211 ASN cc_start: 0.8251 (t0) cc_final: 0.7746 (t0) REVERT: e 258 GLU cc_start: 0.8163 (mt-10) cc_final: 0.7821 (mt-10) REVERT: e 292 PHE cc_start: 0.8329 (m-80) cc_final: 0.7593 (p90) REVERT: f 177 THR cc_start: 0.8892 (m) cc_final: 0.8401 (p) REVERT: g 129 LYS cc_start: 0.8617 (mmmt) cc_final: 0.8153 (tmtt) REVERT: h 11 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8979 (p) REVERT: h 12 CYS cc_start: 0.8814 (m) cc_final: 0.8291 (m) REVERT: h 17 ASP cc_start: 0.8275 (p0) cc_final: 0.7854 (p0) REVERT: h 37 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8872 (ptmt) REVERT: h 70 LYS cc_start: 0.5819 (tttp) cc_final: 0.5335 (pttp) REVERT: h 119 GLU cc_start: 0.8767 (mm-30) cc_final: 0.8065 (mm-30) REVERT: i 121 THR cc_start: 0.8516 (p) cc_final: 0.8266 (p) REVERT: i 165 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9038 (mm) REVERT: j 123 ARG cc_start: 0.8610 (tpm170) cc_final: 0.8267 (tpm170) REVERT: j 150 VAL cc_start: 0.9053 (p) cc_final: 0.8823 (p) REVERT: j 162 THR cc_start: 0.9061 (m) cc_final: 0.8713 (p) REVERT: l 33 THR cc_start: 0.9326 (p) cc_final: 0.8975 (p) REVERT: l 35 THR cc_start: 0.8687 (m) cc_final: 0.8315 (p) REVERT: l 47 SER cc_start: 0.8653 (t) cc_final: 0.8225 (t) REVERT: l 111 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.8371 (mp10) REVERT: m 83 ASN cc_start: 0.9040 (OUTLIER) cc_final: 0.8750 (t0) REVERT: m 116 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8533 (tm-30) REVERT: o 50 GLN cc_start: 0.8299 (mm-40) cc_final: 0.7729 (tp40) REVERT: o 56 THR cc_start: 0.8940 (m) cc_final: 0.8622 (t) REVERT: p 55 ASP cc_start: 0.8914 (OUTLIER) cc_final: 0.8612 (m-30) REVERT: q 71 ASP cc_start: 0.8527 (t0) cc_final: 0.7985 (p0) REVERT: q 123 THR cc_start: 0.9307 (m) cc_final: 0.8878 (p) REVERT: r 31 ARG cc_start: 0.7893 (mtp-110) cc_final: 0.7323 (mtm110) REVERT: r 49 ARG cc_start: 0.8072 (OUTLIER) cc_final: 0.7722 (ttt90) REVERT: r 55 THR cc_start: 0.8341 (p) cc_final: 0.8066 (p) REVERT: s 13 ASN cc_start: 0.8369 (m-40) cc_final: 0.8105 (t0) REVERT: s 44 MET cc_start: 0.8386 (tmm) cc_final: 0.8072 (tmm) REVERT: s 47 HIS cc_start: 0.8280 (m-70) cc_final: 0.7748 (m90) REVERT: t 92 ARG cc_start: 0.8525 (mtm-85) cc_final: 0.8040 (ttm-80) REVERT: t 101 LYS cc_start: 0.8678 (ttmt) cc_final: 0.8451 (ttmt) REVERT: t 105 ARG cc_start: 0.8609 (mmt180) cc_final: 0.8319 (mtt-85) REVERT: t 164 LYS cc_start: 0.8468 (mmpt) cc_final: 0.8056 (mmmt) REVERT: t 174 TYR cc_start: 0.7365 (m-10) cc_final: 0.6412 (m-10) REVERT: u 102 ARG cc_start: 0.7655 (tmm-80) cc_final: 0.7343 (ttp80) REVERT: d 50 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6676 (mm-30) REVERT: d 189 ASN cc_start: 0.8542 (t0) cc_final: 0.8223 (t0) REVERT: v 54 MET cc_start: -0.1139 (OUTLIER) cc_final: -0.1548 (ppp) REVERT: n 5 SER cc_start: 0.8031 (p) cc_final: 0.7637 (t) REVERT: n 26 SER cc_start: 0.9138 (t) cc_final: 0.8912 (p) REVERT: 8 352 MET cc_start: 0.1769 (mmm) cc_final: 0.0864 (ptt) REVERT: 8 366 MET cc_start: 0.4242 (tmm) cc_final: 0.3728 (tpt) outliers start: 147 outliers final: 77 residues processed: 930 average time/residue: 0.6066 time to fit residues: 911.6232 Evaluate side-chains 901 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 814 time to evaluate : 2.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 22 HIS Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 134 LEU Chi-restraints excluded: chain f residue 160 ASN Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 115 VAL Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain i residue 165 LEU Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 157 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 83 ASN Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 70 ILE Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 46 THR Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 48 SER Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 135 THR Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 61 THR Chi-restraints excluded: chain d residue 171 TYR Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 84 ASN Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 314 ILE Chi-restraints excluded: chain 8 residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 348 optimal weight: 8.9990 chunk 237 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 311 optimal weight: 7.9990 chunk 172 optimal weight: 1.9990 chunk 357 optimal weight: 6.9990 chunk 289 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 213 optimal weight: 5.9990 chunk 375 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 100 GLN c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 34 ASN h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** j 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 46 ASN m 138 ASN ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 75 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 ASN u 114 GLN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 HIS n 48 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 59585 Z= 0.335 Angle : 0.729 12.614 87738 Z= 0.369 Chirality : 0.040 0.471 10994 Planarity : 0.006 0.089 5617 Dihedral : 23.323 174.995 26481 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 19.61 Ramachandran Plot: Outliers : 0.48 % Allowed : 11.38 % Favored : 88.14 % Rotamer: Outliers : 7.29 % Allowed : 21.69 % Favored : 71.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.32 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.15), residues: 2917 helix: -0.10 (0.15), residues: 1117 sheet: -1.21 (0.24), residues: 457 loop : -2.74 (0.16), residues: 1343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP q 111 HIS 0.017 0.002 HIS q 84 PHE 0.031 0.002 PHE c 23 TYR 0.030 0.002 TYR h 132 ARG 0.016 0.001 ARG r 53 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1033 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 848 time to evaluate : 2.954 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: b 30 ARG cc_start: 0.7233 (OUTLIER) cc_final: 0.6386 (tpp80) REVERT: b 209 ASP cc_start: 0.6054 (OUTLIER) cc_final: 0.5802 (t0) REVERT: b 225 ILE cc_start: 0.8700 (mm) cc_final: 0.8409 (mt) REVERT: c 78 MET cc_start: 0.7959 (ptp) cc_final: 0.7757 (ptm) REVERT: e 171 HIS cc_start: 0.7834 (OUTLIER) cc_final: 0.6648 (p-80) REVERT: e 186 GLN cc_start: 0.8670 (tp40) cc_final: 0.8365 (tp40) REVERT: e 211 ASN cc_start: 0.8333 (t0) cc_final: 0.7759 (t0) REVERT: e 292 PHE cc_start: 0.8420 (m-80) cc_final: 0.7532 (p90) REVERT: f 177 THR cc_start: 0.9011 (m) cc_final: 0.8515 (p) REVERT: g 129 LYS cc_start: 0.8611 (mmmt) cc_final: 0.8115 (tmtt) REVERT: h 1 MET cc_start: 0.7774 (OUTLIER) cc_final: 0.7162 (tmm) REVERT: h 12 CYS cc_start: 0.8847 (m) cc_final: 0.8291 (m) REVERT: h 17 ASP cc_start: 0.8309 (p0) cc_final: 0.7886 (p0) REVERT: h 37 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8852 (ptmt) REVERT: h 70 LYS cc_start: 0.5896 (tttp) cc_final: 0.5446 (pttp) REVERT: i 73 ILE cc_start: 0.4626 (OUTLIER) cc_final: 0.4247 (pp) REVERT: i 113 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7677 (tm-30) REVERT: i 121 THR cc_start: 0.8600 (p) cc_final: 0.8373 (p) REVERT: j 123 ARG cc_start: 0.8595 (tpm170) cc_final: 0.8172 (tpm170) REVERT: j 150 VAL cc_start: 0.9201 (p) cc_final: 0.8898 (p) REVERT: j 162 THR cc_start: 0.9143 (m) cc_final: 0.8698 (p) REVERT: l 33 THR cc_start: 0.9304 (p) cc_final: 0.9059 (p) REVERT: l 47 SER cc_start: 0.8650 (t) cc_final: 0.8298 (t) REVERT: l 76 GLU cc_start: 0.8189 (tp30) cc_final: 0.7273 (tp30) REVERT: l 103 ASP cc_start: 0.8431 (t0) cc_final: 0.8160 (t0) REVERT: o 56 THR cc_start: 0.8807 (m) cc_final: 0.8397 (t) REVERT: o 74 ARG cc_start: 0.7877 (mtm110) cc_final: 0.7573 (mtm110) REVERT: p 12 LYS cc_start: 0.8670 (OUTLIER) cc_final: 0.8306 (tttt) REVERT: q 71 ASP cc_start: 0.8558 (t0) cc_final: 0.8153 (p0) REVERT: q 123 THR cc_start: 0.9405 (m) cc_final: 0.8890 (p) REVERT: r 49 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.7777 (ttm-80) REVERT: s 13 ASN cc_start: 0.8383 (m-40) cc_final: 0.8081 (t0) REVERT: s 44 MET cc_start: 0.8504 (tmm) cc_final: 0.7809 (tmm) REVERT: s 45 ILE cc_start: 0.9174 (mm) cc_final: 0.8816 (mm) REVERT: s 47 HIS cc_start: 0.8345 (m-70) cc_final: 0.7738 (m90) REVERT: t 101 LYS cc_start: 0.8757 (ttmt) cc_final: 0.8314 (ttmt) REVERT: t 105 ARG cc_start: 0.8562 (mmt180) cc_final: 0.8250 (mtt-85) REVERT: t 152 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8581 (p) REVERT: t 164 LYS cc_start: 0.8550 (mmpt) cc_final: 0.8128 (mmmt) REVERT: t 174 TYR cc_start: 0.7529 (m-10) cc_final: 0.6288 (m-10) REVERT: u 105 ARG cc_start: 0.6803 (OUTLIER) cc_final: 0.6255 (ttm-80) REVERT: u 120 ARG cc_start: 0.6747 (ttp-170) cc_final: 0.6501 (ttt180) REVERT: d 23 ASN cc_start: 0.7464 (t0) cc_final: 0.7075 (t0) REVERT: d 50 GLU cc_start: 0.7431 (mm-30) cc_final: 0.6951 (mm-30) REVERT: d 188 ILE cc_start: 0.9532 (pt) cc_final: 0.9318 (pt) REVERT: v 54 MET cc_start: -0.1230 (OUTLIER) cc_final: -0.1610 (ppp) REVERT: v 74 GLU cc_start: 0.3912 (mm-30) cc_final: 0.3333 (mt-10) REVERT: 8 352 MET cc_start: 0.1959 (mmm) cc_final: 0.1024 (ptt) outliers start: 185 outliers final: 127 residues processed: 928 average time/residue: 0.6199 time to fit residues: 936.0664 Evaluate side-chains 950 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 813 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 103 LEU Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 157 THR Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain c residue 196 CYS Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 171 HIS Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 119 THR Chi-restraints excluded: chain f residue 125 THR Chi-restraints excluded: chain f residue 134 LEU Chi-restraints excluded: chain f residue 167 ASN Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 124 LEU Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 ILE Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 130 VAL Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 105 SER Chi-restraints excluded: chain j residue 112 GLU Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 157 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 130 CYS Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 139 ASN Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 53 ILE Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 48 SER Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 152 THR Chi-restraints excluded: chain t residue 167 VAL Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 135 THR Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain w residue 139 GLU Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain d residue 171 TYR Chi-restraints excluded: chain d residue 198 SER Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 84 ASN Chi-restraints excluded: chain v residue 137 LEU Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 341 ASN Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 140 optimal weight: 1.9990 chunk 376 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 245 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 chunk 418 optimal weight: 6.9990 chunk 347 optimal weight: 8.9990 chunk 193 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 138 optimal weight: 2.9990 chunk 219 optimal weight: 9.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN c 134 GLN e 155 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 86 GLN i 135 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** j 117 GLN ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 149 HIS ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 75 ASN r 52 ASN u 114 GLN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 165 GLN ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 77 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 59585 Z= 0.183 Angle : 0.645 14.394 87738 Z= 0.328 Chirality : 0.036 0.308 10994 Planarity : 0.005 0.085 5617 Dihedral : 23.297 175.686 26481 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.41 % Allowed : 9.98 % Favored : 89.61 % Rotamer: Outliers : 6.15 % Allowed : 23.82 % Favored : 70.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.25 % 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: -1.90 (0.15), residues: 2917 helix: 0.16 (0.15), residues: 1110 sheet: -1.00 (0.25), residues: 455 loop : -2.65 (0.16), residues: 1352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP q 111 HIS 0.010 0.001 HIS q 84 PHE 0.030 0.002 PHE i 94 TYR 0.027 0.002 TYR o 75 ARG 0.013 0.001 ARG n 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 998 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 842 time to evaluate : 3.004 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: b 30 ARG cc_start: 0.7046 (OUTLIER) cc_final: 0.6126 (tpp80) REVERT: b 209 ASP cc_start: 0.5732 (OUTLIER) cc_final: 0.5477 (t0) REVERT: b 225 ILE cc_start: 0.8662 (mm) cc_final: 0.8364 (mt) REVERT: c 78 MET cc_start: 0.7894 (ptp) cc_final: 0.7667 (ptm) REVERT: e 186 GLN cc_start: 0.8558 (tp40) cc_final: 0.8345 (tp40) REVERT: e 211 ASN cc_start: 0.8258 (t0) cc_final: 0.7761 (t0) REVERT: e 292 PHE cc_start: 0.8377 (m-80) cc_final: 0.7496 (p90) REVERT: f 177 THR cc_start: 0.8884 (m) cc_final: 0.8384 (p) REVERT: g 129 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8102 (tmtt) REVERT: g 139 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8607 (mm-30) REVERT: h 1 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.6937 (tmm) REVERT: h 12 CYS cc_start: 0.8776 (m) cc_final: 0.8314 (m) REVERT: h 37 LYS cc_start: 0.9151 (ttpt) cc_final: 0.8821 (ptmt) REVERT: h 70 LYS cc_start: 0.5824 (tttp) cc_final: 0.5391 (pttp) REVERT: h 103 MET cc_start: 0.8214 (mmp) cc_final: 0.7580 (mmp) REVERT: h 110 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8631 (t) REVERT: i 73 ILE cc_start: 0.4631 (OUTLIER) cc_final: 0.4257 (pp) REVERT: i 165 LEU cc_start: 0.9076 (mm) cc_final: 0.8835 (mm) REVERT: j 150 VAL cc_start: 0.9156 (OUTLIER) cc_final: 0.8849 (p) REVERT: j 162 THR cc_start: 0.9077 (m) cc_final: 0.8686 (p) REVERT: l 33 THR cc_start: 0.9315 (p) cc_final: 0.8992 (p) REVERT: l 47 SER cc_start: 0.8616 (t) cc_final: 0.8256 (t) REVERT: o 50 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7726 (tp40) REVERT: o 56 THR cc_start: 0.8757 (m) cc_final: 0.8376 (t) REVERT: p 59 LYS cc_start: 0.9214 (mmmt) cc_final: 0.8591 (mmmt) REVERT: q 71 ASP cc_start: 0.8519 (t0) cc_final: 0.7968 (p0) REVERT: q 97 TYR cc_start: 0.8900 (m-10) cc_final: 0.8691 (m-80) REVERT: q 123 THR cc_start: 0.9333 (m) cc_final: 0.8875 (p) REVERT: r 49 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7899 (ttt90) REVERT: r 55 THR cc_start: 0.8339 (p) cc_final: 0.8072 (p) REVERT: s 13 ASN cc_start: 0.8472 (m-40) cc_final: 0.8235 (t0) REVERT: s 44 MET cc_start: 0.8422 (tmm) cc_final: 0.7787 (tmm) REVERT: s 45 ILE cc_start: 0.9047 (mm) cc_final: 0.8745 (mm) REVERT: s 47 HIS cc_start: 0.8158 (m-70) cc_final: 0.7667 (m90) REVERT: t 101 LYS cc_start: 0.8691 (ttmt) cc_final: 0.8452 (ttmt) REVERT: t 105 ARG cc_start: 0.8604 (mmt180) cc_final: 0.8373 (mtt-85) REVERT: t 164 LYS cc_start: 0.8524 (mmpt) cc_final: 0.8077 (mmmt) REVERT: y 91 ARG cc_start: 0.8780 (ptm-80) cc_final: 0.7532 (ttp-110) REVERT: d 23 ASN cc_start: 0.7223 (t0) cc_final: 0.6790 (t0) REVERT: d 50 GLU cc_start: 0.7187 (mm-30) cc_final: 0.6672 (mm-30) REVERT: d 112 ASN cc_start: 0.7926 (t0) cc_final: 0.7643 (t0) REVERT: d 188 ILE cc_start: 0.9476 (pt) cc_final: 0.9240 (pt) REVERT: v 45 HIS cc_start: 0.4639 (OUTLIER) cc_final: 0.4269 (p-80) REVERT: v 54 MET cc_start: -0.1212 (OUTLIER) cc_final: -0.1556 (ppp) REVERT: v 74 GLU cc_start: 0.4099 (mm-30) cc_final: 0.3333 (mt-10) REVERT: n 26 SER cc_start: 0.9176 (t) cc_final: 0.8905 (p) REVERT: 8 352 MET cc_start: 0.2001 (mmm) cc_final: 0.0998 (ptt) outliers start: 156 outliers final: 109 residues processed: 912 average time/residue: 0.5942 time to fit residues: 879.0030 Evaluate side-chains 925 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 807 time to evaluate : 2.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 35 ILE Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 147 HIS Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 134 LEU Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 141 THR Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 19 ASN Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 112 GLU Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 150 VAL Chi-restraints excluded: chain j residue 157 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain p residue 70 ILE Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 48 SER Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain r residue 72 LEU Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 159 ARG Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 135 THR Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 171 TYR Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 50 ILE Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 82 LYS Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 18 GLN Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 314 ILE Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 341 ASN Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 403 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 238 optimal weight: 5.9990 chunk 305 optimal weight: 10.0000 chunk 237 optimal weight: 5.9990 chunk 352 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 417 optimal weight: 8.9990 chunk 261 optimal weight: 5.9990 chunk 254 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 22 HIS ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 277 ASN ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 163 HIS ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 52 ASN ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 114 GLN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 116 GLN ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 181 GLN n 44 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.114 59585 Z= 0.534 Angle : 0.898 13.170 87738 Z= 0.449 Chirality : 0.046 0.301 10994 Planarity : 0.007 0.095 5617 Dihedral : 23.431 173.970 26481 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 25.38 Ramachandran Plot: Outliers : 0.55 % Allowed : 12.96 % Favored : 86.49 % Rotamer: Outliers : 8.24 % Allowed : 23.07 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.39 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.43 (0.15), residues: 2917 helix: -0.38 (0.15), residues: 1121 sheet: -1.24 (0.24), residues: 470 loop : -2.89 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP b 27 HIS 0.015 0.003 HIS j 157 PHE 0.034 0.003 PHE c 23 TYR 0.036 0.003 TYR h 132 ARG 0.018 0.001 ARG r 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1039 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 830 time to evaluate : 3.080 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: b 30 ARG cc_start: 0.7137 (OUTLIER) cc_final: 0.6681 (mmm-85) REVERT: b 209 ASP cc_start: 0.5644 (OUTLIER) cc_final: 0.5411 (t0) REVERT: b 225 ILE cc_start: 0.8869 (mm) cc_final: 0.8623 (mt) REVERT: c 68 ARG cc_start: 0.8502 (ttp80) cc_final: 0.8086 (ttp80) REVERT: c 78 MET cc_start: 0.7855 (ptp) cc_final: 0.7581 (ptm) REVERT: c 107 ASN cc_start: 0.7145 (m-40) cc_final: 0.6904 (m-40) REVERT: e 154 GLU cc_start: 0.7262 (mp0) cc_final: 0.7024 (mp0) REVERT: e 171 HIS cc_start: 0.8033 (OUTLIER) cc_final: 0.6831 (p-80) REVERT: e 186 GLN cc_start: 0.8704 (tp40) cc_final: 0.8431 (tp40) REVERT: e 211 ASN cc_start: 0.8351 (t0) cc_final: 0.7679 (t0) REVERT: e 292 PHE cc_start: 0.8606 (m-80) cc_final: 0.7621 (p90) REVERT: f 128 GLN cc_start: 0.8878 (mp10) cc_final: 0.8528 (mp10) REVERT: f 129 LYS cc_start: 0.8100 (OUTLIER) cc_final: 0.7632 (ptmm) REVERT: f 177 THR cc_start: 0.9011 (m) cc_final: 0.8524 (p) REVERT: g 110 LYS cc_start: 0.8424 (mmmt) cc_final: 0.7999 (mtmm) REVERT: g 126 ASP cc_start: 0.9174 (OUTLIER) cc_final: 0.8770 (t70) REVERT: g 129 LYS cc_start: 0.8626 (mmmt) cc_final: 0.8184 (tmtt) REVERT: h 1 MET cc_start: 0.7641 (OUTLIER) cc_final: 0.7068 (tmm) REVERT: h 12 CYS cc_start: 0.8828 (m) cc_final: 0.8316 (m) REVERT: h 17 ASP cc_start: 0.8524 (p0) cc_final: 0.8089 (p0) REVERT: h 37 LYS cc_start: 0.9106 (ttpt) cc_final: 0.8802 (ptmt) REVERT: h 70 LYS cc_start: 0.5729 (tttp) cc_final: 0.5359 (pttp) REVERT: i 73 ILE cc_start: 0.4635 (OUTLIER) cc_final: 0.4211 (pp) REVERT: i 113 GLN cc_start: 0.8135 (tm-30) cc_final: 0.7790 (tm-30) REVERT: i 135 HIS cc_start: 0.8610 (p90) cc_final: 0.8395 (p90) REVERT: j 150 VAL cc_start: 0.9273 (OUTLIER) cc_final: 0.9025 (p) REVERT: j 162 THR cc_start: 0.9173 (m) cc_final: 0.8741 (p) REVERT: l 25 ARG cc_start: 0.8100 (ptt-90) cc_final: 0.7732 (ptt-90) REVERT: l 47 SER cc_start: 0.8627 (t) cc_final: 0.8294 (t) REVERT: l 103 ASP cc_start: 0.8430 (t0) cc_final: 0.8091 (t0) REVERT: m 120 TYR cc_start: 0.8292 (OUTLIER) cc_final: 0.7883 (t80) REVERT: o 50 GLN cc_start: 0.8228 (mm-40) cc_final: 0.7788 (mm-40) REVERT: o 56 THR cc_start: 0.8872 (m) cc_final: 0.8513 (t) REVERT: p 12 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8340 (ttmt) REVERT: p 59 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8835 (mmmt) REVERT: p 73 ARG cc_start: 0.8451 (tpp80) cc_final: 0.8006 (tpp80) REVERT: q 66 ILE cc_start: 0.9038 (mm) cc_final: 0.8707 (mt) REVERT: q 71 ASP cc_start: 0.8579 (t0) cc_final: 0.8281 (p0) REVERT: q 123 THR cc_start: 0.9504 (m) cc_final: 0.8965 (p) REVERT: r 49 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.7803 (ttm-80) REVERT: r 68 GLN cc_start: 0.8321 (mt0) cc_final: 0.8002 (mt0) REVERT: s 44 MET cc_start: 0.8559 (tmm) cc_final: 0.7937 (tmm) REVERT: s 45 ILE cc_start: 0.9156 (mm) cc_final: 0.8880 (mm) REVERT: s 47 HIS cc_start: 0.8507 (m-70) cc_final: 0.7747 (m90) REVERT: t 101 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8356 (ttmt) REVERT: t 105 ARG cc_start: 0.8355 (mmt180) cc_final: 0.7956 (mtt-85) REVERT: t 112 ASP cc_start: 0.9071 (m-30) cc_final: 0.8736 (m-30) REVERT: t 141 LYS cc_start: 0.8946 (mmmt) cc_final: 0.8162 (mmmt) REVERT: t 155 ARG cc_start: 0.7718 (mtt90) cc_final: 0.7419 (mtt90) REVERT: t 164 LYS cc_start: 0.8671 (mmpt) cc_final: 0.8196 (mmmt) REVERT: y 91 ARG cc_start: 0.8806 (ptm-80) cc_final: 0.7516 (ttp-110) REVERT: y 169 ARG cc_start: 0.7437 (ttp80) cc_final: 0.7128 (ttp80) REVERT: d 23 ASN cc_start: 0.7710 (t0) cc_final: 0.7271 (t0) REVERT: d 190 GLU cc_start: 0.9089 (pm20) cc_final: 0.8698 (pm20) REVERT: v 54 MET cc_start: -0.0887 (OUTLIER) cc_final: -0.1205 (ppp) REVERT: v 74 GLU cc_start: 0.4195 (mm-30) cc_final: 0.3065 (mt-10) REVERT: 8 72 MET cc_start: 0.5604 (tmm) cc_final: 0.4987 (pmm) REVERT: 8 352 MET cc_start: 0.2007 (mmm) cc_final: 0.1113 (ptm) outliers start: 209 outliers final: 158 residues processed: 935 average time/residue: 0.5981 time to fit residues: 907.1574 Evaluate side-chains 976 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 806 time to evaluate : 2.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 126 THR Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 12 LEU Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 110 LEU Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain c residue 196 CYS Chi-restraints excluded: chain e residue 156 VAL Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 171 HIS Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain e residue 306 LEU Chi-restraints excluded: chain f residue 129 LYS Chi-restraints excluded: chain f residue 134 LEU Chi-restraints excluded: chain f residue 167 ASN Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain f residue 172 ILE Chi-restraints excluded: chain g residue 30 ILE Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 38 LEU Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 69 VAL Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 9 ILE Chi-restraints excluded: chain h residue 11 THR Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain i residue 139 LEU Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 105 SER Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 150 VAL Chi-restraints excluded: chain j residue 157 HIS Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 39 THR Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 56 ASN Chi-restraints excluded: chain m residue 80 LEU Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain m residue 120 TYR Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 59 LYS Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 12 LYS Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain q residue 58 MET Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 75 ASN Chi-restraints excluded: chain r residue 31 ARG Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 48 SER Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain r residue 71 ILE Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain s residue 77 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 134 GLU Chi-restraints excluded: chain t residue 159 ARG Chi-restraints excluded: chain t residue 167 VAL Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain u residue 126 GLN Chi-restraints excluded: chain y residue 112 VAL Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 135 THR Chi-restraints excluded: chain y residue 152 SER Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 78 SER Chi-restraints excluded: chain d residue 95 LEU Chi-restraints excluded: chain d residue 125 ILE Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 151 SER Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain d residue 198 SER Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 82 LYS Chi-restraints excluded: chain v residue 84 ASN Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 26 SER Chi-restraints excluded: chain n residue 47 LEU Chi-restraints excluded: chain n residue 60 HIS Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 74 ARG Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 303 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 341 ASN Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 258 optimal weight: 3.9990 chunk 166 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 80 optimal weight: 0.0970 chunk 265 optimal weight: 7.9990 chunk 284 optimal weight: 4.9990 chunk 206 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 328 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 135 HIS ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 13 GLN l 111 GLN m 68 HIS ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 130 ASN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 93 ASN ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 119 ASN ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 116 GLN v 163 ASN v 181 GLN n 44 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.4234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 59585 Z= 0.196 Angle : 0.686 15.602 87738 Z= 0.347 Chirality : 0.038 0.312 10994 Planarity : 0.005 0.084 5617 Dihedral : 23.340 175.385 26481 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.32 % Favored : 89.20 % Rotamer: Outliers : 5.44 % Allowed : 27.01 % Favored : 67.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.28 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.15), residues: 2917 helix: -0.09 (0.15), residues: 1107 sheet: -1.05 (0.25), residues: 459 loop : -2.72 (0.16), residues: 1351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP q 111 HIS 0.008 0.001 HIS t 170 PHE 0.035 0.002 PHE c 141 TYR 0.031 0.002 TYR o 75 ARG 0.016 0.001 ARG r 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 981 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 843 time to evaluate : 2.902 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: b 27 TRP cc_start: 0.8327 (p-90) cc_final: 0.7629 (p-90) REVERT: b 30 ARG cc_start: 0.6748 (OUTLIER) cc_final: 0.6462 (mmt90) REVERT: b 209 ASP cc_start: 0.5539 (OUTLIER) cc_final: 0.5319 (t0) REVERT: b 225 ILE cc_start: 0.8668 (mm) cc_final: 0.8373 (mt) REVERT: c 63 ILE cc_start: 0.9271 (mt) cc_final: 0.9070 (mp) REVERT: c 78 MET cc_start: 0.7783 (ptp) cc_final: 0.7544 (ptm) REVERT: c 107 ASN cc_start: 0.7007 (m-40) cc_final: 0.6769 (m-40) REVERT: e 171 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.6517 (p-80) REVERT: e 186 GLN cc_start: 0.8536 (tp40) cc_final: 0.8321 (tp40) REVERT: e 211 ASN cc_start: 0.8273 (t0) cc_final: 0.7737 (t0) REVERT: e 292 PHE cc_start: 0.8517 (m-80) cc_final: 0.7593 (p90) REVERT: f 128 GLN cc_start: 0.8991 (mp10) cc_final: 0.8741 (mp10) REVERT: f 177 THR cc_start: 0.8835 (m) cc_final: 0.8298 (p) REVERT: f 204 PHE cc_start: 0.8425 (m-80) cc_final: 0.7982 (m-80) REVERT: g 126 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8551 (t0) REVERT: g 129 LYS cc_start: 0.8541 (mmmt) cc_final: 0.8098 (tmtt) REVERT: h 1 MET cc_start: 0.7394 (OUTLIER) cc_final: 0.5374 (ttm) REVERT: h 12 CYS cc_start: 0.8786 (m) cc_final: 0.8383 (m) REVERT: h 17 ASP cc_start: 0.8421 (p0) cc_final: 0.8028 (p0) REVERT: h 37 LYS cc_start: 0.9100 (ttpt) cc_final: 0.8781 (ptmt) REVERT: h 70 LYS cc_start: 0.5746 (tttp) cc_final: 0.5284 (pttp) REVERT: h 103 MET cc_start: 0.8111 (mmp) cc_final: 0.7384 (mmp) REVERT: i 73 ILE cc_start: 0.4695 (OUTLIER) cc_final: 0.4217 (pp) REVERT: i 121 THR cc_start: 0.8612 (p) cc_final: 0.8328 (p) REVERT: j 123 ARG cc_start: 0.8328 (mtm110) cc_final: 0.8061 (mtm110) REVERT: j 150 VAL cc_start: 0.9163 (OUTLIER) cc_final: 0.8844 (p) REVERT: j 162 THR cc_start: 0.9081 (m) cc_final: 0.8724 (p) REVERT: l 33 THR cc_start: 0.9360 (p) cc_final: 0.9044 (p) REVERT: l 47 SER cc_start: 0.8608 (t) cc_final: 0.8257 (t) REVERT: l 103 ASP cc_start: 0.8374 (t0) cc_final: 0.8117 (t0) REVERT: l 111 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.8114 (mp10) REVERT: m 68 HIS cc_start: 0.7729 (OUTLIER) cc_final: 0.7510 (m90) REVERT: o 50 GLN cc_start: 0.7986 (mm-40) cc_final: 0.7644 (mm-40) REVERT: o 56 THR cc_start: 0.8729 (m) cc_final: 0.8426 (t) REVERT: p 77 PHE cc_start: 0.6762 (m-10) cc_final: 0.6381 (m-10) REVERT: p 78 LYS cc_start: 0.6986 (mmtt) cc_final: 0.6400 (mtpp) REVERT: q 71 ASP cc_start: 0.8485 (t0) cc_final: 0.8116 (p0) REVERT: r 49 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.8266 (ttt90) REVERT: r 55 THR cc_start: 0.8418 (p) cc_final: 0.8156 (p) REVERT: r 68 GLN cc_start: 0.8168 (mt0) cc_final: 0.7820 (mt0) REVERT: s 13 ASN cc_start: 0.8518 (m-40) cc_final: 0.8166 (t0) REVERT: s 44 MET cc_start: 0.8471 (tmm) cc_final: 0.7896 (tmm) REVERT: s 45 ILE cc_start: 0.9032 (mm) cc_final: 0.8737 (mm) REVERT: s 47 HIS cc_start: 0.8269 (m-70) cc_final: 0.7729 (m90) REVERT: t 92 ARG cc_start: 0.8515 (mtm-85) cc_final: 0.8292 (ttm-80) REVERT: t 101 LYS cc_start: 0.8684 (ttmt) cc_final: 0.8290 (ttmt) REVERT: t 105 ARG cc_start: 0.8529 (mmt180) cc_final: 0.8261 (mtt-85) REVERT: t 164 LYS cc_start: 0.8509 (mmpt) cc_final: 0.8069 (mmmt) REVERT: y 91 ARG cc_start: 0.8821 (ptm-80) cc_final: 0.7452 (ttp-110) REVERT: y 159 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8666 (mm) REVERT: d 23 ASN cc_start: 0.7012 (t0) cc_final: 0.6689 (t0) REVERT: d 50 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6574 (mm-30) REVERT: d 112 ASN cc_start: 0.7925 (t0) cc_final: 0.7657 (t0) REVERT: d 190 GLU cc_start: 0.9059 (pm20) cc_final: 0.8670 (pm20) REVERT: v 54 MET cc_start: -0.1132 (OUTLIER) cc_final: -0.1499 (ppp) REVERT: v 74 GLU cc_start: 0.3909 (mm-30) cc_final: 0.3236 (mt-10) REVERT: 8 72 MET cc_start: 0.5597 (tmm) cc_final: 0.5259 (pmm) REVERT: 8 352 MET cc_start: 0.1924 (mmm) cc_final: 0.0997 (ptt) outliers start: 138 outliers final: 107 residues processed: 902 average time/residue: 0.5868 time to fit residues: 854.2431 Evaluate side-chains 929 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 810 time to evaluate : 2.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 30 ARG Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 147 HIS Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 171 HIS Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 105 LEU Chi-restraints excluded: chain f residue 167 ASN Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 80 VAL Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 120 ASP Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 137 THR Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 150 VAL Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 95 ILE Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 68 HIS Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 64 LEU Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 159 ARG Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain y residue 129 LEU Chi-restraints excluded: chain y residue 159 LEU Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 50 ILE Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 82 LYS Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain v residue 163 ASN Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 303 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 379 optimal weight: 0.9990 chunk 399 optimal weight: 20.0000 chunk 364 optimal weight: 7.9990 chunk 388 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 169 optimal weight: 8.9990 chunk 305 optimal weight: 10.0000 chunk 119 optimal weight: 0.0270 chunk 351 optimal weight: 10.0000 chunk 367 optimal weight: 10.0000 chunk 387 optimal weight: 6.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN m 68 HIS ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** t 130 ASN u 114 GLN ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 116 GLN n 44 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.084 59585 Z= 0.428 Angle : 0.812 15.804 87738 Z= 0.409 Chirality : 0.043 0.285 10994 Planarity : 0.007 0.109 5617 Dihedral : 23.341 175.295 26481 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 23.09 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.86 % Favored : 86.73 % Rotamer: Outliers : 6.31 % Allowed : 26.34 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.15), residues: 2917 helix: -0.24 (0.15), residues: 1106 sheet: -1.03 (0.25), residues: 466 loop : -2.83 (0.16), residues: 1345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP q 111 HIS 0.014 0.002 HIS m 68 PHE 0.036 0.003 PHE i 94 TYR 0.037 0.003 TYR h 132 ARG 0.014 0.001 ARG t 103 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 809 time to evaluate : 2.936 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: b 209 ASP cc_start: 0.5622 (OUTLIER) cc_final: 0.5338 (t0) REVERT: b 225 ILE cc_start: 0.8813 (mm) cc_final: 0.8559 (mt) REVERT: c 68 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8054 (ttp80) REVERT: c 78 MET cc_start: 0.7789 (ptp) cc_final: 0.7528 (ptm) REVERT: c 143 LYS cc_start: 0.8125 (mmtt) cc_final: 0.7363 (mtmm) REVERT: c 171 LYS cc_start: 0.7917 (mptt) cc_final: 0.7695 (mppt) REVERT: e 171 HIS cc_start: 0.7911 (OUTLIER) cc_final: 0.6689 (p-80) REVERT: e 186 GLN cc_start: 0.8691 (tp40) cc_final: 0.8407 (tp40) REVERT: e 211 ASN cc_start: 0.8363 (t0) cc_final: 0.7803 (t0) REVERT: e 212 ILE cc_start: 0.9013 (mm) cc_final: 0.8805 (mm) REVERT: e 237 MET cc_start: 0.7610 (tmm) cc_final: 0.7276 (tmm) REVERT: e 292 PHE cc_start: 0.8633 (m-80) cc_final: 0.7641 (p90) REVERT: f 129 LYS cc_start: 0.8063 (OUTLIER) cc_final: 0.7639 (ptmm) REVERT: f 177 THR cc_start: 0.8980 (m) cc_final: 0.8501 (p) REVERT: g 41 GLN cc_start: 0.8322 (tm-30) cc_final: 0.7958 (tm-30) REVERT: g 110 LYS cc_start: 0.8418 (mmmt) cc_final: 0.7938 (mtmm) REVERT: g 126 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8581 (t0) REVERT: g 129 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8167 (tmtt) REVERT: h 1 MET cc_start: 0.7525 (OUTLIER) cc_final: 0.5547 (ttm) REVERT: h 12 CYS cc_start: 0.8804 (m) cc_final: 0.8350 (m) REVERT: h 17 ASP cc_start: 0.8566 (p0) cc_final: 0.8194 (p0) REVERT: h 37 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8768 (ptmt) REVERT: h 70 LYS cc_start: 0.5753 (tttp) cc_final: 0.5366 (pttp) REVERT: i 73 ILE cc_start: 0.4633 (OUTLIER) cc_final: 0.4182 (pp) REVERT: i 106 GLN cc_start: 0.8174 (tt0) cc_final: 0.7804 (tt0) REVERT: i 121 THR cc_start: 0.8696 (p) cc_final: 0.8417 (p) REVERT: j 123 ARG cc_start: 0.8341 (mtm110) cc_final: 0.8049 (mtm110) REVERT: j 150 VAL cc_start: 0.9246 (OUTLIER) cc_final: 0.9009 (p) REVERT: j 162 THR cc_start: 0.9138 (m) cc_final: 0.8724 (p) REVERT: l 33 THR cc_start: 0.9350 (p) cc_final: 0.9136 (p) REVERT: l 47 SER cc_start: 0.8581 (t) cc_final: 0.8242 (t) REVERT: l 103 ASP cc_start: 0.8409 (t0) cc_final: 0.8138 (t0) REVERT: l 111 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8126 (mp10) REVERT: m 68 HIS cc_start: 0.7983 (OUTLIER) cc_final: 0.7738 (m90) REVERT: o 56 THR cc_start: 0.8834 (m) cc_final: 0.8490 (t) REVERT: q 71 ASP cc_start: 0.8531 (t0) cc_final: 0.8240 (p0) REVERT: q 123 THR cc_start: 0.9461 (m) cc_final: 0.8923 (p) REVERT: r 49 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.7932 (ttm-80) REVERT: r 55 THR cc_start: 0.8646 (p) cc_final: 0.8131 (p) REVERT: r 68 GLN cc_start: 0.8295 (mt0) cc_final: 0.8060 (mt0) REVERT: s 44 MET cc_start: 0.8574 (tmm) cc_final: 0.7933 (tmm) REVERT: s 45 ILE cc_start: 0.9118 (mm) cc_final: 0.8815 (mm) REVERT: s 47 HIS cc_start: 0.8416 (m-70) cc_final: 0.7656 (m90) REVERT: t 101 LYS cc_start: 0.8728 (ttmt) cc_final: 0.8398 (ttmt) REVERT: t 105 ARG cc_start: 0.8484 (mmt180) cc_final: 0.8204 (mtt-85) REVERT: t 141 LYS cc_start: 0.8909 (mmmt) cc_final: 0.8127 (mmmt) REVERT: t 164 LYS cc_start: 0.8621 (mmpt) cc_final: 0.8095 (mmmt) REVERT: y 159 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8726 (mm) REVERT: d 23 ASN cc_start: 0.7555 (t0) cc_final: 0.7099 (t0) REVERT: d 50 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6852 (mm-30) REVERT: d 190 GLU cc_start: 0.9189 (pm20) cc_final: 0.8809 (pm20) REVERT: v 54 MET cc_start: -0.1090 (OUTLIER) cc_final: -0.1431 (ppp) REVERT: v 74 GLU cc_start: 0.3811 (mm-30) cc_final: 0.3065 (mt-10) REVERT: n 28 LYS cc_start: 0.9332 (ttmm) cc_final: 0.9116 (mtpt) REVERT: 8 352 MET cc_start: 0.2024 (mmm) cc_final: 0.1089 (ptt) outliers start: 160 outliers final: 127 residues processed: 887 average time/residue: 0.5945 time to fit residues: 855.6680 Evaluate side-chains 936 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 797 time to evaluate : 2.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 110 THR Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 187 THR Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 156 VAL Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 171 HIS Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 129 LYS Chi-restraints excluded: chain f residue 167 ASN Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 105 LEU Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain j residue 105 SER Chi-restraints excluded: chain j residue 120 ASP Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 150 VAL Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 80 ILE Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 114 ILE Chi-restraints excluded: chain k residue 119 VAL Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 68 HIS Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain o residue 33 ILE Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain q residue 75 ASN Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 35 LEU Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 159 ARG Chi-restraints excluded: chain t residue 167 VAL Chi-restraints excluded: chain t residue 174 TYR Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 114 VAL Chi-restraints excluded: chain y residue 135 THR Chi-restraints excluded: chain y residue 159 LEU Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain d residue 21 LEU Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 50 ILE Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 82 LYS Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 303 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 341 ASN Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 255 optimal weight: 8.9990 chunk 411 optimal weight: 8.9990 chunk 251 optimal weight: 7.9990 chunk 195 optimal weight: 0.4980 chunk 285 optimal weight: 6.9990 chunk 431 optimal weight: 6.9990 chunk 397 optimal weight: 20.0000 chunk 343 optimal weight: 5.9990 chunk 35 optimal weight: 0.6980 chunk 265 optimal weight: 8.9990 chunk 210 optimal weight: 0.9980 overall best weight: 3.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 68 HIS ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 105 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 153 GLN ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 200 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 HIS ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 59585 Z= 0.329 Angle : 0.751 15.866 87738 Z= 0.380 Chirality : 0.040 0.305 10994 Planarity : 0.006 0.095 5617 Dihedral : 23.349 175.532 26481 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.03 % Favored : 87.56 % Rotamer: Outliers : 6.15 % Allowed : 26.74 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.15), residues: 2917 helix: -0.20 (0.15), residues: 1107 sheet: -1.09 (0.25), residues: 454 loop : -2.76 (0.16), residues: 1356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP q 111 HIS 0.009 0.002 HIS m 68 PHE 0.039 0.002 PHE i 94 TYR 0.043 0.002 TYR h 132 ARG 0.011 0.001 ARG t 103 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5834 Ramachandran restraints generated. 2917 Oldfield, 0 Emsley, 2917 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 960 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 804 time to evaluate : 3.080 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: b 60 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7204 (tp) REVERT: b 209 ASP cc_start: 0.5525 (OUTLIER) cc_final: 0.5242 (t0) REVERT: b 225 ILE cc_start: 0.8790 (mm) cc_final: 0.8529 (mt) REVERT: c 68 ARG cc_start: 0.8424 (ttp80) cc_final: 0.8027 (ttp80) REVERT: c 78 MET cc_start: 0.7773 (ptp) cc_final: 0.7514 (ptm) REVERT: c 143 LYS cc_start: 0.8074 (mmtt) cc_final: 0.7324 (mtpp) REVERT: c 171 LYS cc_start: 0.7920 (mptt) cc_final: 0.7693 (mppt) REVERT: e 171 HIS cc_start: 0.7879 (OUTLIER) cc_final: 0.6596 (p-80) REVERT: e 186 GLN cc_start: 0.8649 (tp40) cc_final: 0.8355 (tp40) REVERT: e 211 ASN cc_start: 0.8316 (t0) cc_final: 0.7789 (t0) REVERT: e 212 ILE cc_start: 0.8980 (mm) cc_final: 0.8776 (mm) REVERT: e 237 MET cc_start: 0.7426 (tmm) cc_final: 0.6944 (tmm) REVERT: e 269 GLN cc_start: 0.8218 (mt0) cc_final: 0.7541 (mm110) REVERT: e 292 PHE cc_start: 0.8594 (m-80) cc_final: 0.7619 (p90) REVERT: f 128 GLN cc_start: 0.8903 (mp10) cc_final: 0.8542 (mp10) REVERT: f 129 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7694 (ptmm) REVERT: f 177 THR cc_start: 0.8926 (m) cc_final: 0.8449 (p) REVERT: g 33 HIS cc_start: 0.9053 (OUTLIER) cc_final: 0.8476 (p-80) REVERT: g 41 GLN cc_start: 0.8297 (tm-30) cc_final: 0.7943 (tm-30) REVERT: g 126 ASP cc_start: 0.9044 (OUTLIER) cc_final: 0.8508 (t0) REVERT: g 129 LYS cc_start: 0.8600 (mmmt) cc_final: 0.8216 (tmtt) REVERT: h 1 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.5549 (ttm) REVERT: h 12 CYS cc_start: 0.8791 (m) cc_final: 0.8353 (m) REVERT: h 17 ASP cc_start: 0.8578 (p0) cc_final: 0.8221 (p0) REVERT: h 37 LYS cc_start: 0.9119 (ttpt) cc_final: 0.8781 (ptmt) REVERT: h 70 LYS cc_start: 0.5668 (tttp) cc_final: 0.5199 (pttp) REVERT: h 103 MET cc_start: 0.8179 (mmp) cc_final: 0.7423 (mmp) REVERT: h 115 MET cc_start: 0.8105 (ptt) cc_final: 0.7880 (ptt) REVERT: i 73 ILE cc_start: 0.4599 (OUTLIER) cc_final: 0.4140 (pp) REVERT: j 123 ARG cc_start: 0.8335 (mtm110) cc_final: 0.8053 (mtm110) REVERT: j 150 VAL cc_start: 0.9215 (OUTLIER) cc_final: 0.8900 (p) REVERT: j 162 THR cc_start: 0.9122 (m) cc_final: 0.8711 (p) REVERT: l 33 THR cc_start: 0.9357 (p) cc_final: 0.9078 (p) REVERT: l 47 SER cc_start: 0.8525 (t) cc_final: 0.8176 (t) REVERT: l 103 ASP cc_start: 0.8381 (t0) cc_final: 0.8092 (t0) REVERT: m 68 HIS cc_start: 0.7892 (OUTLIER) cc_final: 0.7621 (m90) REVERT: o 56 THR cc_start: 0.8808 (m) cc_final: 0.8465 (t) REVERT: q 71 ASP cc_start: 0.8450 (t0) cc_final: 0.8128 (p0) REVERT: q 123 THR cc_start: 0.9418 (m) cc_final: 0.8872 (p) REVERT: r 49 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: r 55 THR cc_start: 0.8622 (p) cc_final: 0.8149 (p) REVERT: r 68 GLN cc_start: 0.8255 (mt0) cc_final: 0.8048 (mt0) REVERT: s 44 MET cc_start: 0.8531 (tmm) cc_final: 0.7898 (tmm) REVERT: s 45 ILE cc_start: 0.9080 (mm) cc_final: 0.8758 (mm) REVERT: s 47 HIS cc_start: 0.8411 (m-70) cc_final: 0.7702 (m90) REVERT: t 101 LYS cc_start: 0.8700 (ttmt) cc_final: 0.8394 (ttmt) REVERT: t 105 ARG cc_start: 0.8474 (mmt180) cc_final: 0.8192 (mtt-85) REVERT: t 141 LYS cc_start: 0.8897 (mmmt) cc_final: 0.8115 (mmmt) REVERT: t 164 LYS cc_start: 0.8591 (mmpt) cc_final: 0.8091 (mmmt) REVERT: y 159 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8684 (mm) REVERT: d 23 ASN cc_start: 0.7151 (t0) cc_final: 0.6892 (t0) REVERT: d 50 GLU cc_start: 0.7307 (mm-30) cc_final: 0.6765 (mm-30) REVERT: d 190 GLU cc_start: 0.9144 (pm20) cc_final: 0.8784 (pm20) REVERT: v 54 MET cc_start: -0.1137 (OUTLIER) cc_final: -0.2287 (ppp) REVERT: v 74 GLU cc_start: 0.3822 (mm-30) cc_final: 0.3286 (mt-10) REVERT: n 28 LYS cc_start: 0.9290 (ttmm) cc_final: 0.9061 (mtpt) REVERT: 8 352 MET cc_start: 0.1841 (mmm) cc_final: 0.0899 (ptt) outliers start: 156 outliers final: 130 residues processed: 876 average time/residue: 0.5909 time to fit residues: 841.6774 Evaluate side-chains 934 residues out of total 2540 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 791 time to evaluate : 2.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 48 THR Chi-restraints excluded: chain b residue 60 LEU Chi-restraints excluded: chain b residue 94 HIS Chi-restraints excluded: chain b residue 121 LEU Chi-restraints excluded: chain b residue 164 ILE Chi-restraints excluded: chain b residue 175 THR Chi-restraints excluded: chain b residue 190 LEU Chi-restraints excluded: chain b residue 202 ILE Chi-restraints excluded: chain b residue 209 ASP Chi-restraints excluded: chain c residue 23 PHE Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 36 ASP Chi-restraints excluded: chain c residue 60 ILE Chi-restraints excluded: chain c residue 135 LEU Chi-restraints excluded: chain c residue 151 LEU Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain c residue 195 TYR Chi-restraints excluded: chain e residue 156 VAL Chi-restraints excluded: chain e residue 163 THR Chi-restraints excluded: chain e residue 165 VAL Chi-restraints excluded: chain e residue 171 HIS Chi-restraints excluded: chain e residue 189 VAL Chi-restraints excluded: chain e residue 197 VAL Chi-restraints excluded: chain e residue 214 THR Chi-restraints excluded: chain e residue 220 TYR Chi-restraints excluded: chain e residue 222 THR Chi-restraints excluded: chain e residue 256 VAL Chi-restraints excluded: chain e residue 272 SER Chi-restraints excluded: chain e residue 286 VAL Chi-restraints excluded: chain f residue 129 LYS Chi-restraints excluded: chain f residue 134 LEU Chi-restraints excluded: chain f residue 167 ASN Chi-restraints excluded: chain f residue 169 LEU Chi-restraints excluded: chain g residue 33 HIS Chi-restraints excluded: chain g residue 37 SER Chi-restraints excluded: chain g residue 40 TYR Chi-restraints excluded: chain g residue 50 ILE Chi-restraints excluded: chain g residue 66 ILE Chi-restraints excluded: chain g residue 120 LEU Chi-restraints excluded: chain g residue 122 SER Chi-restraints excluded: chain g residue 126 ASP Chi-restraints excluded: chain g residue 142 HIS Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 19 ASN Chi-restraints excluded: chain h residue 24 VAL Chi-restraints excluded: chain h residue 40 LEU Chi-restraints excluded: chain h residue 79 LEU Chi-restraints excluded: chain h residue 91 SER Chi-restraints excluded: chain h residue 107 ILE Chi-restraints excluded: chain h residue 110 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 95 ILE Chi-restraints excluded: chain i residue 97 ASN Chi-restraints excluded: chain i residue 129 ASP Chi-restraints excluded: chain i residue 131 PHE Chi-restraints excluded: chain i residue 148 LEU Chi-restraints excluded: chain j residue 105 SER Chi-restraints excluded: chain j residue 120 ASP Chi-restraints excluded: chain j residue 133 VAL Chi-restraints excluded: chain j residue 145 LEU Chi-restraints excluded: chain j residue 150 VAL Chi-restraints excluded: chain j residue 157 HIS Chi-restraints excluded: chain j residue 168 ASP Chi-restraints excluded: chain j residue 173 THR Chi-restraints excluded: chain k residue 43 VAL Chi-restraints excluded: chain k residue 46 VAL Chi-restraints excluded: chain k residue 51 VAL Chi-restraints excluded: chain k residue 80 ILE Chi-restraints excluded: chain k residue 83 VAL Chi-restraints excluded: chain k residue 138 VAL Chi-restraints excluded: chain l residue 12 ARG Chi-restraints excluded: chain l residue 24 LEU Chi-restraints excluded: chain l residue 27 CYS Chi-restraints excluded: chain l residue 40 ILE Chi-restraints excluded: chain l residue 51 LYS Chi-restraints excluded: chain l residue 82 VAL Chi-restraints excluded: chain l residue 97 ILE Chi-restraints excluded: chain l residue 111 GLN Chi-restraints excluded: chain m residue 46 CYS Chi-restraints excluded: chain m residue 52 VAL Chi-restraints excluded: chain m residue 54 ILE Chi-restraints excluded: chain m residue 68 HIS Chi-restraints excluded: chain m residue 84 PHE Chi-restraints excluded: chain m residue 92 LEU Chi-restraints excluded: chain o residue 36 LEU Chi-restraints excluded: chain o residue 43 HIS Chi-restraints excluded: chain o residue 66 TYR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain p residue 1 MET Chi-restraints excluded: chain p residue 50 VAL Chi-restraints excluded: chain p residue 54 LEU Chi-restraints excluded: chain p residue 55 ASP Chi-restraints excluded: chain p residue 67 VAL Chi-restraints excluded: chain q residue 67 CYS Chi-restraints excluded: chain q residue 69 THR Chi-restraints excluded: chain r residue 34 SER Chi-restraints excluded: chain r residue 35 LEU Chi-restraints excluded: chain r residue 49 ARG Chi-restraints excluded: chain r residue 51 VAL Chi-restraints excluded: chain s residue 14 HIS Chi-restraints excluded: chain s residue 57 HIS Chi-restraints excluded: chain s residue 63 THR Chi-restraints excluded: chain t residue 81 LYS Chi-restraints excluded: chain t residue 102 THR Chi-restraints excluded: chain t residue 126 VAL Chi-restraints excluded: chain t residue 132 ILE Chi-restraints excluded: chain t residue 159 ARG Chi-restraints excluded: chain t residue 167 VAL Chi-restraints excluded: chain t residue 174 TYR Chi-restraints excluded: chain u residue 105 ARG Chi-restraints excluded: chain y residue 98 VAL Chi-restraints excluded: chain y residue 108 LEU Chi-restraints excluded: chain y residue 159 LEU Chi-restraints excluded: chain y residue 164 ILE Chi-restraints excluded: chain y residue 168 LEU Chi-restraints excluded: chain d residue 36 SER Chi-restraints excluded: chain d residue 42 SER Chi-restraints excluded: chain d residue 124 ASP Chi-restraints excluded: chain d residue 135 THR Chi-restraints excluded: chain d residue 172 LYS Chi-restraints excluded: chain d residue 192 LEU Chi-restraints excluded: chain v residue 45 HIS Chi-restraints excluded: chain v residue 50 ILE Chi-restraints excluded: chain v residue 54 MET Chi-restraints excluded: chain v residue 68 VAL Chi-restraints excluded: chain v residue 82 LYS Chi-restraints excluded: chain v residue 124 VAL Chi-restraints excluded: chain n residue 4 LYS Chi-restraints excluded: chain n residue 7 ILE Chi-restraints excluded: chain n residue 8 GLN Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 79 SER Chi-restraints excluded: chain n residue 86 MET Chi-restraints excluded: chain n residue 89 THR Chi-restraints excluded: chain x residue 77 LYS Chi-restraints excluded: chain 8 residue 251 MET Chi-restraints excluded: chain 8 residue 268 VAL Chi-restraints excluded: chain 8 residue 303 VAL Chi-restraints excluded: chain 8 residue 310 LEU Chi-restraints excluded: chain 8 residue 326 LEU Chi-restraints excluded: chain 8 residue 341 ASN Chi-restraints excluded: chain 8 residue 360 ILE Chi-restraints excluded: chain 8 residue 370 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 433 random chunks: chunk 272 optimal weight: 7.9990 chunk 365 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 316 optimal weight: 6.9990 chunk 50 optimal weight: 0.4980 chunk 95 optimal weight: 4.9990 chunk 344 optimal weight: 7.9990 chunk 143 optimal weight: 4.9990 chunk 353 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 125 ASN ** e 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 65 HIS ** i 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 111 GLN m 68 HIS ** o 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 172 GLN ** d 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 115 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 GLN ** v 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 44 HIS ** 8 317 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.107817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.086100 restraints weight = 158690.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.088495 restraints weight = 54538.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.089898 restraints weight = 30799.675| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.4530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 59585 Z= 0.284 Angle : 0.728 16.077 87738 Z= 0.368 Chirality : 0.039 0.289 10994 Planarity : 0.006 0.110 5617 Dihedral : 23.316 175.983 26481 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 19.97 Ramachandran Plot: Outliers : 0.38 % Allowed : 12.07 % Favored : 87.56 % Rotamer: Outliers : 5.99 % Allowed : 27.29 % Favored : 66.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.33 % Twisted General : 0.21 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.15), residues: 2917 helix: -0.13 (0.15), residues: 1118 sheet: -1.10 (0.25), residues: 452 loop : -2.78 (0.16), residues: 1347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP q 111 HIS 0.016 0.002 HIS m 68 PHE 0.036 0.002 PHE i 94 TYR 0.032 0.002 TYR h 132 ARG 0.010 0.001 ARG t 103 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13839.93 seconds wall clock time: 243 minutes 47.34 seconds (14627.34 seconds total)